PaperBLAST

PaperBLAST Hits for tr|Q9I0L5|Q9I0L5_PSEAE Isocitrate dehydrogenase [NADP] OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=icd PE=3 SV=1 (418 a.a., MGYQKIQVPA...)

Show query sequence

>tr|Q9I0L5|Q9I0L5_PSEAE Isocitrate dehydrogenase [NADP] OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=icd PE=3 SV=1
MGYQKIQVPATGDKITVNADMSLSVPKNPIIPFIEGDGIGVDISPVMIKVVDAAVEKAYK
GERKIAWMEVYAGEKATQVYDQDTWLPQETLDAVRDYVVSIKGPLTTPVGGGIRSLNVAL
RQQLDLYVCQRPVRWFEGVPSPVKKPGDVDMVIFRENSEDIYAGVEWKAGSPEAEKVIKF
LTEEMGVKKIRFTENCGIGIKPVSQEGTKRLVRKALQYAVDNDRSSVTLVHKGNIMKFTE
GAFKDWGYEVARDEFGAELLDGGPWMQFKNPKTGKNVVVKDVIADAMLQQILLRPAEYDV
IATLNLNGDYLSDALAAEVGGIGIAPGANLSDSVAMFEATHGTAPKYAGQDKVNPGSLIL
SAEMMLRHMGWTEAADLIIKGTNGAIAAKTVTYDFERLMDGATLLSCSEFGDAMIAKM

Running BLASTp...

Found 250 similar proteins in the literature:

IDH_PSEAB / Q02NB5 Isocitrate dehydrogenase [NADP]; IDH; IDP; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 from Pseudomonas aeruginosa (strain UCBPP-PA14) (see paper)
PA2623 isocitrate dehydrogenase from Pseudomonas aeruginosa PAO1
NP_251313 isocitrate dehydrogenase from Pseudomonas aeruginosa PAO1
Q9I0L5 Isocitrate dehydrogenase [NADP] from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA14_30190 isocitrate dehydrogenase from Pseudomonas aeruginosa UCBPP-PA14
100% identity, 100% coverage

• function: Catalyzes the oxidative decarboxylation of isocitrate to 2- oxoglutarate and carbon dioxide with the concomitant reduction of NADP(+).
  catalytic activity: D-threo-isocitrate + NADP(+) = 2-oxoglutarate + CO2 + NADPH (RHEA:19629)
  cofactor: Mg(2+) Mn(2+) (Binds 1 Mg(2+) or Mn(2+) ion per subunit.)
  subunit: Homodimer.
• Identification of complex III, NQR, and SDH as primary bioenergetic enzymes during the stationary phase of Pseudomonas aeruginosa cultured in urine-like conditions
  Hu, Frontiers in microbiology 2024
  • “...lpd 2-oxoglutarate dehydrogenase complex dihydrolipoyl dehydrogenase PA1787 NP_250478 2,610 acnB Aconitate synthase Aconitate hydratase B PA2623 NP_251313 1,257 icd Isocitrate dehydrogenase Isocitrate dehydrogenase PA2624 NP_251314 2,226 idh Isocitrate dehydrogenase PA1585 NP_250276 2,832 sucA 2-Ketoglutarate dehydrogenase 2-oxoglutarate dehydrogenase subunit E1 PA1586 NP_250277 1,230 sucB 2-oxoglutarate dehydrogenase complex...”
• <i>Pseudomonas aeruginosa</i> transcriptome analysis of metal restriction in <i>ex vivo</i> cystic fibrosis sputum
  Neff, Microbiology spectrum 2024
  • “...Y N PA4470 fumC2 Fumarate hydratase Y Y PA1596 htpG Heat shock protein N Y PA2623 icd Isocitrate dehydrogenase N Y PA1803 lon Lon protease N Y PA2853 oprI Major outer membrane lipoprotein N Y PA5568 yidC Membrane protein insertase Y N PA0524 norB Nitric oxide...”
• From genotype to phenotype: adaptations of Pseudomonas aeruginosa to the cystic fibrosis environment
  Camus, Microbial genomics 2021
  • “...Phosphate ABC transporter, periplasmic phosphate-binding protein 25 26 NA NA TonB-dependent receptor 24 25 Icd PA2623 Isocitrate dehydrogenase 21 30 RpsB PA3656 30S ribosomal protein S2 20 28 RplS PA3742 50S ribosomal protein L19 23 26 Convergent phenotypes are selected by P. aeruginosa adaptation As a...”
• The Breadth and Molecular Basis of Hcp-Driven Type VI Secretion System Effector Delivery
  Howard, mBio 2021
  • “...4.5 2.42 Probable acyl-CoA thiolase 41.4 PA4854 PurH 4.4 2.02 Bifunctional purine biosynthesis protein 57.7 PA2623 Icd 4.2 3.12 Isocitrate dehydrogenase (NADP) 45.6 PA4464 PtsN 4 1.30 Nitrogen regulatory protein 16.7 PA2015 LiuA 4 2.25 Putative isovaleryl-CoA dehydrogenase 42.2 PA4483 GatA 3.9 1.39 Glutamyl-tRNA(Gln) amidotransferase subunit...”
• Ciprofloxacin binding to GyrA causes global changes in the proteome of Pseudomonas aeruginosa
  Jedrey, FEMS microbiology letters 2018
  • “...the superoxide-insensitive isozyme of fumarate hydratase (FumC1), two differentially modulated isozymes of iso citrate dehydrogenase (PA2623 ( icd , down-regulated) and PA2624 ( idh , up-regulated)) and malic enzyme. Consistent with the up-regulation of FumC1 (indicating oxidative stress), we also observed that the house-keeping catalase (KatA)...”
• Gluconeogenic precursor availability regulates flux through the glyoxylate shunt in Pseudomonas aeruginosa
  Crousilles, The Journal of biological chemistry 2018
  • “...ORFs encoding the ICL (PA2634), IDH (PA2624), and ICD (PA2623) enzymes were PCR-amplified from the genomic DNA of P. aeruginosa strain PAO1 and cloned into a...”
• Proteomic Response of Pseudomonas aeruginosa PAO1 Adhering to Solid Surfaces
  Guilbaud, Frontiers in microbiology 2017
  • “...0.0 4.6 3.0E-04 1.5E-07 quinone oxidoreductase PA0023 qor 1.6 0.6 5.2 3.2E-03 1.7E-05 isocitrate dehydrogenase PA2623 icd 22.2 28.8 32.0 5.6E-03 Fatty acid and phospholipid metabolism acetyl-CoA acetyltransferase PA2001 atoB 4.0 5.0 10.6 2.2E-04 3.0E-03 DNA replication, recombination, modification and repair DNA-binding protein HU PA1804 hupB...”
• Pseudomonas aeruginosa MifS-MifR Two-Component System Is Specific for α-Ketoglutarate Utilization
  Tatke, PloS one 2015
  • “...genes encoding aconitate hydratase 1 ( acnA ( PA1562 )) isocitrate dehydrogenase ( idh ( PA2623 )) isocitrate dehydrogenase, -KG dehydrogenase complex ( icd ( PA2623 )), sucA ( PA1585) and lpd3 ( PA4829 ), and 54 ( rpoN ( PA4462 )) were analyzed in mifSR...”
  • “...expression levels of genes encoding sigma-54 rpoN ( PA4462 ), iso-citrate dehydrogenase ( idh ( PA2623 ) and icd ( PA2624 )), -KG dehydrogenase complex ( sucA ( PA1585) and lpd3 ( PA4829 )) were done essentially as described above. The cycling conditions used were 95C/2...”
• More
• Identification of complex III, NQR, and SDH as primary bioenergetic enzymes during the stationary phase of Pseudomonas aeruginosa cultured in urine-like conditions
  Hu, Frontiers in microbiology 2024
  • “...2-oxoglutarate dehydrogenase complex dihydrolipoyl dehydrogenase PA1787 NP_250478 2,610 acnB Aconitate synthase Aconitate hydratase B PA2623 NP_251313 1,257 icd Isocitrate dehydrogenase Isocitrate dehydrogenase PA2624 NP_251314 2,226 idh Isocitrate dehydrogenase PA1585 NP_250276 2,832 sucA 2-Ketoglutarate dehydrogenase 2-oxoglutarate dehydrogenase subunit E1 PA1586 NP_250277 1,230 sucB 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue...”
• Proteome-wide identification of druggable targets and inhibitors for multidrug-resistant <i>Pseudomonas aeruginosa</i> using an integrative subtractive proteomics and virtual screening approach
  Vemula, Heliyon 2025
• Acetylomics reveals an extensive acetylation diversity within Pseudomonas aeruginosa
  Broeckaert, microLife 2024
  • “...K86) DNA-binding protein HU-beta hupB Venkat et al. ( 2018 ) E. coli P08200 (K55) Q9I0L5 (K57) Isocitrate dehydrogenase (NADP) icd Sun et al. ( 2016 ) E. coli A0A140N627 (K266, K284, and K373) Q9I5Z0 (K267, K285, and K386) S -adenosylmethionine synthase metK Carabetta et al....”
• Over-Expression of Hypochlorite Inducible Major Facilitator Superfamily (MFS) Pumps Reduces Antimicrobial Drug Susceptibility by Increasing the Production of MexXY Mediated by ArmZ in Pseudomonas aeruginosa
  Dulyayangkul, Frontiers in microbiology 2020
  • “...0.006 0.12 0.014 Q9I0L1 High frequency lysogenization protein HflD homolog HflD 10.30 0.001 5.39 0.008 Q9I0L5 Isocitrate dehydrogenase [NADP] Icd <0.05 0.000 0.16 0.007 Q9I2W9 Phosphoenolpyruvate synthase PpsA <0.05 0.002 <0.05 0.002 Q9I314 Type III export protein PscJ PscJ 11.57 0.002 6.07 0.010 Q9I3F5 Aconitate hydratase...”
• Gene Expression Profiling of <i>Pseudomonas aeruginosa</i> Upon Exposure to Colistin and Tobramycin
  Cianciulli, Frontiers in microbiology 2021
  • “...dehydrogenase I subunit F 13.36 8.16 nuoE PA14_29980 NADH dehydrogenase subunit E 13.55 5.35 icd PA14_30190 Iisocitrate dehydrogenase 3.09 ND sucD PA14_43940 Succinyl-CoA synthetase subunit alpha 9.39 3.27 sucC PA14_43950 Succinyl-CoA synthetase subunit beta 3.73 ND lpdG PA14_43970 Dihydrolipoamide dehydrogenase 16.47 5.26 sucB PA14_44000 Dihydrolipoamide succinyltransferase...”
• The Pseudomonas aeruginosa Transcriptional Landscape Is Shaped by Environmental Heterogeneity and Genetic Variation
  Dötsch, mBio 2015
  • “...from the sequences of nine consistently expressed genes: spuD (PA14_03920), nirS (PA14_06750), rpoB (PA14_08760), icd (PA14_30190), clpX (PA14_41230), tig (PA14_41250), hpd (PA14_53070), ftsZ (PA14_57275), and atpD (PA14_73240). The resulting tree showed high similarity with the k-mer-based tree but offered much less resolution in the segregation of...”

PPUBIRD1_1803 NADP-dependent isocitrate dehydrogenase from Pseudomonas putida BIRD-1
90% identity, 100% coverage

• Understanding butanol tolerance and assimilation in Pseudomonas putida BIRD-1: an integrated omics approach
  Cuenca, Microbial biotechnology 2016
  • “...found upregulated genes for energy production, including: quinones and cytochromes (cytochrome c oxidase); isocitrate dehydrogenase (PPUBIRD1_1803) and other TCArelated proteins, such as fumarate reductase (PPUBIRD1_3075). In addition, genes related with cellular division were primarily downregulated (i.e. FtsL, PPUBIRD1_4233). When comparing cells grown in glucose plus butanol...”

PP4011 isocitrate dehydrogenase, NADP-dependent, prokaryotic-type from Pseudomonas putida KT2440
PP_4011 NADP-dependent isocitrate dehydrogenase from Pseudomonas putida KT2440
90% identity, 100% coverage

• Hierarchical routing in carbon metabolism favors iron-scavenging strategy in iron-deficient soil Pseudomonas species
  Mendonca, Proceedings of the National Academy of Sciences of the United States of America 2020
  • “...5 A ). Within the TCA cycle, the abundances of 6 metabolic enzymes (mqo3, acnA-1, PP4011, fumC, lpd, and lpdV) were elevated in the Fe-limited cells ( Fig. 5 A ). Most significant was a threefold increase in fumC, which converts fumarate to malate ( Fig....”
• Pseudomonas putida KT2440 Strain Metabolizes Glucose through a Cycle Formed by Enzymes of the Entner-Doudoroff, Embden-Meyerhof-Parnas, and Pentose Phosphate Pathways
  Nikel, The Journal of biological chemistry 2015
  • “...(PP1022) Zwf-2 (PP4042) Zwf-3 (PP5351) Gnd (PP4043) Icd (PP4011) PP4012 Mdh (PP0654) PP5391 KguD (PP3376) Gap-1 (PP1009) Gap-2 (PP2149) PP0665 PP3443 MaeB...”
• Production of medium chain length polyhydroxyalkanoate in metabolic flux optimized Pseudomonas putida
  Borrero-de, Microbial cell factories 2014
  • “...0.7 0.7 acnA PP2112 Aconitate hydratase 0.4 -0.4 acnB PP2339 Aconitate hydratase 0.7 0.3 icd PP4011 Isocitrate dehydrogenase 0.3 -0.5 sucA PP4189 2-Oxoglutarate dehydrogenase -0.7 -0.2 sucD PP4185 Succinyl-CoA synthetase sub alpha -0.1 -0.3 sucC PP4186 Succinyl-CoA synthetase sub beta 0.2 0.3 sdhA PP4191 Succinate dehydrogenase...”
  • “...-0.2 0.7 acnA PP2112 Aconitate hydratase 0.8 -0.5 acnB PP2339 Aconitate hydratase -0.2 0.3 icd PP4011 Isocitrate dehydrogenase -0.3 -0.3 sucA PP4189 2-Oxoglutarate dehydrogenase -0.6 0.2 sucD PP4185 Succinyl-CoA synthetase sub alpha -0.2 0.5 sucC PP4186 Succinyl-CoA synthetase sub beta -0.1 0.1 sdhA PP4191 Succinate dehydrogenase...”
• The metabolic response of P. putida KT2442 producing high levels of polyhydroxyalkanoate under single- and multiple-nutrient-limited growth: highlights from a multi-level omics approach
  Poblete-Castro, Microbial cell factories 2012
  • “...PP4055 GlgX 4.5 20 1.9 0.05 Acetolactate synthase PP3365 3.5 15 -1.0 n.s. Isocitrate dehydrogenase PP4011 ICD -5.0 28 -1.4 n.s. Acetoin dehydrogenase -sub PP0555 AcoA -4.0 7 -8.3 0 Acetoin dehydrogenase -sub PP0554 AcoB -5.6 23 -4.2 0 Acetoin dehydrogenase PP0553 AcoC -3.7 10 -4.0...”
  • “...TrxB -5.6 11 1.3 n.s. Isocitrate lyase PP4116 AceA -4.2 19 1.3 n.s. Isocitrate dehydrogenase PP4011 ICD -2.1 14 1.1 n.s. Fatty acid metabolism 3-hydroxyacyl-CoA dehydrogenase PP2047 only in N 18 20.9 0 Acetyl-CoA acetyltransferase PP2051 AtoB only in N 20 27.9 0 acetyl-CoA carboxylase PP0558...”
• Transcriptome analysis of a phenol-producing Pseudomonas putida S12 construct: genetic and physiological basis for improved production
  Wierckx, Journal of bacteriology 2008
  • “...dehydrogenase, NADP dependent, prokaryotic type Malic enzyme PP0897 PP2835 PP4011 PP5085 0.5 111.5 1.9 2.2 a b Fold change in expression level in P. putida...”
• Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology
  Puchałka, PLoS computational biology 2008
  • “...dehydrogenase (membrane) PP1444 d -Glucose 7.05 28.51 0.83 4.17 6-Phosphoglucono lactonase PP1023 3 Isocitrate dehydrogenase PP4011 or PP4012 l -Serine 22.41 23.01 6.66 10.67 Formate dehydrogenase PP0490 or PP0491 PP2183 or PP2184 or PP2185 or PP2186 4 Citrate synthase PP4194 l -Valine 21.85 0.83 1.00 2-Methylcitrate...”
• Development of a CRISPR/Cas9n-based tool for metabolic engineering of Pseudomonas putida for ferulic acid-to-polyhydroxyalkanoate bioconversion
  Zhou, Communications biology 2020
  • “...for the following genome editing (Fig. 2 and Supplementary Fig. 2a ). The icd gene (PP_4011), encoding isocitrate dehydrogenase in the TCA cycle, was chosen as a target gene to test the CRP approach. The pBBR1-3 plasmid, which contains the P trc ::sgRNA for icd ,...”
• Multi-omics analysis unravels a segregated metabolic flux network that tunes co-utilization of sugar and aromatic carbons in Pseudomonas putida
  Kukurugya, The Journal of biological chemistry 2019 (secret)
• Comparison of mcl-Poly(3-hydroxyalkanoates) synthesis by different Pseudomonas putida strains from crude glycerol: citrate accumulates at high titer under PHA-producing conditions
  Poblete-Castro, BMC biotechnology 2014
  • “...One of the most affected proteins under high NADH levels is isocitrate dehydrogenase (PP_4012 and PP_4011), which catalyzes the conversion of isocitrate into oxalosuccinate. This effect limits the proper functioning of the Krebs cycle to further oxidize citrate. We have previously reported that intracellular concentrations of...”
• Differential proteomics and physiology of Pseudomonas putida KT2440 under filament-inducing conditions
  Crabbé, BMC microbiology 2012
  • “...of urea (PP_0999, 0.23-fold; PP_1000, 0.28-fold; PP_1001, 0.24-fold) and glyoxylate (PP_4116, 0.27-fold; PP_2112, 0.42-fold and PP_4011, 0.25-fold), (iii) down-regulation of proteins involved in the production of ATP (PP_1478, 0.23-fold; PP_0126, 0.37-fold and PP_1478, 0.23-fold), (iv) differential expression of proteins involved in the metabolism of amino acids...”
  • “...PP_3765 gi|26990470 0.24* Transcriptional regulator MvaT, P16 subunit, putative PP_3839 AdhA gi|26990544 0.30* Alcohol dehydrogenase PP_4011 Icd gi|26990716 0.25* Isocitrate dehydrogenase, NADP-dependent PP_4034 gi|26990737 0.38* Allantoate amidohydrolase PP_4037 gi|26990739 0.32* Putative oxidoreductase PP_4038 gi|26990740 0.26* Dihydropyrimidine dehydrogenase PP_4116 AceA gi|26990810 0.27* Isocitrate lyase PP_4486 gi|26991172 0.51...”
• Random and cyclical deletion of large DNA segments in the genome of Pseudomonas putida
  Leprince, Environmental microbiology 2012
  • “...efflux transporter 91 (3) PP_3529 Ssud-like monooxygenase 113 (9) PP_0971 Conserved hypothetical protein 253 (3) PP_4011 (icd) Isocitrate dehydrogenase, NADP-dependent 407 (7) PP_3733 ABC transporter lipoprotein, putative 475 (10) IR_52755276 IR, intergenic region. The mini-transposon insertions in the SMT and TMT mutants highlighted the non-essentiality of...”
• Regulatory tasks of the phosphoenolpyruvate-phosphotransferase system of Pseudomonas putida in central carbon metabolism
  Chavarría, mBio 2012
  • “...synthase (PP_4194); AcnA, aconitate hydratase 1 (PP_2112); AcnB, aconitate hydratase 2 (PP_2339); Icd, isocitrate dehydrogenase (PP_4011); Kgd, alpha-ketoglutarate decarboxylase (PP_4189); KgdB, dihydrolipoamide acetyltransferase (PP_4188); SucA, 2-oxoglutarate dehydrogenase E1 component (PP_4189); SucC, succinyl-CoA synthetase beta subunit (PP_4186); SucD, succinyl-CoA synthetase (PP_4185); SdhA, succinate dehydrogenase flavoprotein subunit (PP_4191);...”
• Transcriptome dynamics of Pseudomonas putida KT2440 under water stress
  Gülez, Applied and environmental microbiology 2012
  • “...polysaccharides and lipopolysaccharides) PP_3613 PP_3621 PP_3970 PP_4011 PP_4034 PP_0103 PP_0104 PP_0105 PP_0106 PP_0490 PP_0552 PP_0553 PP_0554 PP_0555 PP_0556...”
• The metabolic response of P. putida KT2442 producing high levels of polyhydroxyalkanoate under single- and multiple-nutrient-limited growth: highlights from a multi-level omics approach
  Poblete-Castro, Microbial cell factories 2012
  • “...(Table 2 ). At the protein level only one enzyme, isocitrate dehydrogenase ICD (encoded by PP_4011), showed a fold change less than 2 (Table 3 ). The deficiency in the TCA cycle was confirmed by the metabolome analysis, where the increase in the pool size of...”
  • “...a particular modulation of another important enzyme in the cycle, isocitrate dehydrogenase ICD (encoded by PP_4011), which can be repressed by various mechanisms together with the low expression of ICD, two enzymes of the glyoxylate shunt, isocitrate lyase (encoded by PP_4116) and malate synthase (encoded by...”

T1E_0537 NADP-dependent isocitrate dehydrogenase from Pseudomonas putida DOT-T1E
90% identity, 100% coverage

• Insights into the susceptibility of Pseudomonas putida to industrially relevant aromatic hydrocarbons that it can synthesize from sugars
  García-Franco, Microbial cell factories 2023
  • “...genes were organized in clusters such as suc (T1E_0425 to T1E_0429), sdh and icd/idh genes (T1E_0537 and T1E_0538). Two citrate synthase genes ( glt A and prp C) (T1E_0434 and T1E_5347) were also induced, leading to an increased ability to channel acetyl-CoA quickly and efficiently into...”

PPUTLS46_011960 NADP-dependent isocitrate dehydrogenase from Pseudomonas putida LS46
90% identity, 100% coverage

• Quantitative 'Omics Analyses of Medium Chain Length Polyhydroxyalkanaote Metabolism in Pseudomonas putida LS46 Cultured with Waste Glycerol and Waste Fatty Acids
  Fu, PloS one 2015
  • “...LS46 up-regulated enzymatic reactions putatively to replenish the cellular NADPH pool via NADP-dependent isocitrate dehydrogenase (PPUTLS46_011960) [ 49 ] and 6-phosphogluconate dehydrogenase (PPUTLS46_012100), whereas expression of numerous tricarboxylic acid (TCA) cycle enzymes that supply bulk of NADH, such as putative NAD + -dependent isocitrate dehydrogenase and...”

PFLU3808 isocitrate dehydrogenase from Pseudomonas fluorescens SBW25
89% identity, 100% coverage

• Characterization of the CrbS/R Two-Component System in Pseudomonas fluorescens Reveals a New Set of Genes under Its Control and a DNA Motif Required for CrbR-Mediated Transcriptional Activation
  Sepulveda, Frontiers in microbiology 2017
  • “...CrbR. Therefore, experimental verification should be obtained for the most interesting predictions, for example, genes pflu3808 and pflu4952 , which code for Isocitrate dehydrogenase and Fumarase, respectively. Both enzymes are part of the TCA cycle, and particularly the Isocitrate dehydrogenase is located at the branching point...”
  • “...rplJ Ribosomal protein R50 0.345 TAAGACTTACGTCGCCT PFLU4006 Ribose ABC transporter ATP binding protein 0.373 CTTGACCAAGGTCGATT PFLU3808 NADP(+) Isocitrate dehydrogenase 0.517 TACGCCTAAAGTCGCAC PFLU1460 Putative phage regulatory protein 0.517 TAAGACCTTGGTCTATC dsbA Thiol:disulfide interchange protein 0.552 TAAAACCTACGTTGAAT PFLU4471 CrbS 0.6 GTCGACCAAGGTCGTGT PFLUt81 tRNA-Met 0.633 TAATCCCTTGGTCGTAG PFLU0110 Acyl-CoA Hydrolase 0.633...”

y1802 isocitrate dehydrogenase, specific for NADP+ from Yersinia pestis KIM
79% identity, 95% coverage

• Deletion of Yersinia pestis ail Causes Temperature-Sensitive Pleiotropic Effects, Including Cell Lysis, That Are Suppressed by Carbon Source, Cations, or Loss of Phospholipase A Activity
  Kolodziejek, Journal of bacteriology 2021
  • “...TCA cycle 1 1.5 y1953 Hypothetical protein Unknown; belongs to glutaredoxin (GRX) family 1 10.7 y1802 icdA Isocitrate dehydrogenase Energy metabolism, carbon: TCA cycle 1 3.5 y1507 Putative aminotransferase Amino acid biosynthesis: alanine 1 3.9 y1485 crr Glucose specific PTS system component Transport of small molecules;...”
• Proteomic analysis of iron acquisition, metabolic and regulatory responses of Yersinia pestis to iron starvation
  Pieper, BMC microbiology 2010
  • “...pepT putative peptidase T CY 310 51106 5.89 - 0.18 < 0.05 N.D. N.D. 26 y1802 icdA isocitrate dehydrogenase, specific for NADP+ CY 459 53760 5.46 0.92 1.80 0.511 0.002 1.238 27 y1934 sufA iron-sulfur cluster assembly scaffold protein SufA U Fur 156 13330 4.48 0.13...”

YPTB2427 isocitrate dehydrogenase [NADP] from Yersinia pseudotuberculosis IP 32953
YPO1641 isocitrate dehydrogenase [NADP] from Yersinia pestis CO92
79% identity, 99% coverage

• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...YPTB2248 (ldhA) YPO2329 D-lactate dehydrogenase 0.615 (0.006) YPTB2253 (nifJ) YPO2334 putative pyruvate-flavodoxin oxidoreductase 1.697 (0.014) YPTB2427 (icdA) YPO1641 isocitrate dehydrogenase [NADP] 0.632 (0.013) YPTB2529 YPO2492 putative dioxygenase beta subunit 0.535 (0.02) YPTB2578 (nuoK) or3622 NADH dehydrogenase i chain k 0.642 (0.001) YPTB2581 (nuoH) YPO2549 NADH dehydrogenase...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...YPO2329 D-lactate dehydrogenase 0.615 (0.006) YPTB2253 (nifJ) YPO2334 putative pyruvate-flavodoxin oxidoreductase 1.697 (0.014) YPTB2427 (icdA) YPO1641 isocitrate dehydrogenase [NADP] 0.632 (0.013) YPTB2529 YPO2492 putative dioxygenase beta subunit 0.535 (0.02) YPTB2578 (nuoK) or3622 NADH dehydrogenase i chain k 0.642 (0.001) YPTB2581 (nuoH) YPO2549 NADH dehydrogenase I chain...”

PMI0891 isocitrate dehydrogenase [NADP] from Proteus mirabilis HI4320
79% identity, 99% coverage

• Identification of emergent bla CMY-2 -carrying Proteus mirabilis lineages by whole-genome sequencing
  Mac, New microbes and new infections 2016
  • “...of seven conserved genes present in all strains ( adk ; PMI0375 , fumC ; PMI0891 , gyrB ; PMI1296 , icd ; PMI2184 , mdh ; PMI1732 , purA ; PMI3370 and recA ; PMI3400 ). Sequences from 24 P.mirabilis isolates from this study and...”

SPC_2506 isocitrate dehydrogenase from Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
80% identity, 99% coverage

• Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
  Liu, Plants (Basel, Switzerland) 2023
  • “...SPC_0733 0.107 2-oxoglutarate dehydrogenase E1 component SPC_0729 0.111 Succinate dehydrogenase cytochrome b556 large membrane subunit SPC_2506 0.119 Isocitrate dehydrogenase SPC_0735 0.217 Succinyl-CoA synthetase subunit beta SPC_0734 0.227 Dihydrolipoamide acetyltransferase SPC_0736 0.25 Succinyl-CoA synthetase alpha subunit SPC_3569 0.296 Phosphoenolpyruvate carboxykinase SPC_0727 0.5 Citrate synthase SPC_0164 3.325 Dihydrolipoamide...”

STY1278 isocitrate dehydrogenase from Salmonella enterica subsp. enterica serovar Typhi str. CT18
80% identity, 99% coverage

• Inversions over the terminus region in Salmonella and Escherichia coli: IS200s as the sites of homologous recombination inverting the chromosome of Salmonella enterica serovar typhi
  Alokam, Journal of bacteriology 2002
  • “...and its orthologue in S. enterica serovar Typhi CT18 (STY1278) are to the left of the inverted region. In serovar Typhimurium, icdA is adjacent to STM1239 (an...”

ABO_1282 isocitrate dehydrogenase (NADP-dependent) from Alcanivorax borkumensis SK2
79% identity, 100% coverage

• An impaired metabolic response to hydrostatic pressure explains Alcanivorax borkumensis recorded distribution in the deep marine water column
  Scoma, Scientific reports 2016
  • “...= 0.48 182.4 253.9 1044 ABO_0622 pyruvate dehydrogenase subunit E1 = 0.5 110.3 156.3 1267 ABO_1282 isocitrate dehydrogenase 0.56 346.8 512.4 1237 ABO_1500 succinate dehydrogenase, cytochrome b556 subunit 0.76 162.4 275.5 128 ABO_0623 pyruvate dehydrogenase, E2 component 1.27 321.6 778.2 872 ABO_0694 aconitate hydratase ATP synthase...”

Q1XIQ8 isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) from Colwellia psychrerythraea (see paper)
79% identity, 99% coverage

STM1238 isocitrate dehydrogenase in e14 prophage, specific for NADP+ from Salmonella typhimurium LT2
80% identity, 99% coverage

• Transcriptomic Responses of Salmonella enterica Serovars Enteritidis in Sodium Hypochlorite
  Wang, Frontiers in cellular and infection microbiology 2022
  • “...dehydrogenase E1 component STM0737 sucB -1.4 2-oxoglutarate dehydrogenase STM0730 gltA -2.5 type II citrate synthase STM1238 icdA -1.9 NADP-dependent isocitrate dehydrogenase STM1468 fumA -1.8 fumarate hydratase STM0738 sucC -1.4 ADP-forming succinateCoA ligase subunit beta STM0739 sucD -1.2 succinateCoA ligase subunit alpha STM3290 argG -1.5 argininosuccinate synthetase...”
• Global transcriptional analysis of dehydrated Salmonella enterica serovar Typhimurium
  Gruzdev, Applied and environmental microbiology 2012
  • “...1.84 1.82 Energy production and conversion icdA (STM1238) fumA (STM1468) glpC (STM2286) nifU (STM2542) glpK (STM4086) aceB (STM4183) aceA (STM4184) Isocitrate...”
• Repression of Salmonella enterica phoP expression by small molecules from physiological bile
  Antunes, Journal of bacteriology 2012
  • “...PSLT052 STM1231 STM4159 STM3557 STM0734 STM0662 ORF01131 STM1238 STM1712 STM0549 STM2141 STM0735 STM0738 STM1744 PSLT046 STM2190 STM2799 STM1292 STM0730 STM3321...”
• Host gene expression changes and DNA amplification during temperate phage induction
  Frye, Journal of bacteriology 2005
  • “...to STM1600) (Fig. 3B). It was centered at icdA (STM1238), an isocitrate dehydrogenase gene homologous to a gene found in the Escherichia coli e14 prophage....”
  • “...Gifsy-1 (STM2584-STM2636) Amplification I (STM0891)b Amplification III (STM1238) Amplification IV (STM2003) 2-hr DNA 1489 1490 FRYE ET AL. J. BACTERIOL. FIG....”
• Inversions over the terminus region in Salmonella and Escherichia coli: IS200s as the sites of homologous recombination inverting the chromosome of Salmonella enterica serovar typhi
  Alokam, Journal of bacteriology 2002
  • “...Fig. 2D and E, the icdA gene of serovar Typhimurium (STM1238) and its orthologue in S. enterica serovar Typhi CT18 (STY1278) are to the left of the inverted...”

IcdE / b1136 isocitrate dehydrogenase (EC 1.1.1.42) from Escherichia coli K-12 substr. MG1655 (see 8 papers)
icd / P08200 isocitrate dehydrogenase (EC 1.1.1.42) from Escherichia coli (strain K12) (see 3 papers)
IDH_ECOLI / P08200 Isocitrate dehydrogenase [NADP]; IDH; IDP; NADP(+)-dependent isocitric dehydrogenase; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 from Escherichia coli (strain K12) (see 9 papers)
P08200 [Isocitrate dehydrogenase (NADP+)] kinase (EC 2.7.11.5) from Escherichia coli (see paper)
4aj3A / P08200 3d structure of e. Coli isocitrate dehydrogenase in complex with isocitrate, calcium(ii) and NADP - the pseudo-michaelis complex (see paper)
NP_415654 isocitrate dehydrogenase from Escherichia coli str. K-12 substr. MG1655
b1136 isocitrate dehydrogenase from Escherichia coli str. K-12 substr. MG1655
Y75_p1106 NADP-dependent isocitrate dehydrogenase from Escherichia coli str. K-12 substr. W3110
79% identity, 99% coverage

• function: Catalyzes the oxidative decarboxylation of isocitrate to 2- oxoglutarate and carbon dioxide with the concomitant reduction of NADP(+).
  catalytic activity: D-threo-isocitrate + NADP(+) = 2-oxoglutarate + CO2 + NADPH (RHEA:19629)
  cofactor: Mg(2+) Mn(2+) (Binds 1 Mg(2+) or Mn(2+) ion per subunit (PubMed:10623532, PubMed:11284679, PubMed:7761851). Both Mn(2+) and Mg(2+) can be used, but Mn(2+) is 10-fold more effective than Mg(2+) in vitro at the same concentration (PubMed:4400493).)
  subunit: Homodimer.
• Ligands: nadp nicotinamide-adenine-dinucleotide phosphate; calcium ion (4aj3A)
• From a dimer to a monomer: Construction of a chimeric monomeric isocitrate dehydrogenase.
  Tian, Protein science : a publication of the Protein Society 2021
  • GeneRIF: From a dimer to a monomer: Construction of a chimeric monomeric isocitrate dehydrogenase.
• Interaction of enzymes of the tricarboxylic acid cycle in Bacillus subtilis and Escherichia coli: a comparative study.
  Jung, FEMS microbiology letters 2018 (PubMed)
  • GeneRIF: GltA, icd and mdh do not form a transcription unit, are scattered around the chromosome and are expressed from different promoters.
• Point mutation (R153H or R153C) in Escherichia coli isocitrate dehydrogenase: Biochemical characterization and functional implication.
  Song, Journal of basic microbiology 2017 (PubMed)
  • GeneRIF: introduced single point mutations (Arg153His, Arg153Cys); both the R153H and R153C mutants nearly lost wild-type IDH activity yet acquired the neomorphic ability to catalyze the conversion of alpha-ketoglutarate to 2-hydroxyglutarate
• Dimerization and bifunctionality confer robustness to the isocitrate dehydrogenase regulatory system in Escherichia coli.
  Dexter, The Journal of biological chemistry 2013
  • GeneRIF: Dimerization and bifunctionality confer robustness to the isocitrate dehydrogenase regulatory system in Escherichia coli
• Control of isocitrate dehydrogenase catalytic activity by protein phosphorylation in Escherichia coli.
  Cozzone, Journal of molecular microbiology and biotechnology 2005 (PubMed)
  • GeneRIF: control of catalytic activity by phosphorylation [review]
• Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12.
  Link, Electrophoresis 1997 (PubMed)
  • GeneRIF: N-terminus verified by Edman degradation on complete protein
• Metalloproteomics Reveals Multi-Level Stress Response in Escherichia coli When Exposed to Arsenite
  Larson, International journal of molecular sciences 2024
  • “...were part of the TCA cycle. These proteins were acetyl-coenzyme A synthetase (P27550), isocitrate dehydrogenase (P08200), fumarase A (P0AC33) and fumarase B (P14407). These results suggest that E. coli responds to As III by increasing metallocofactor biosynthesis proteins and that TCA cycle proteins appear to be...”
• CRP and IHF act as host regulators in Royal Jelly's antibacterial activity
  Xia, Scientific reports 2024
  • “...P0ADU5 BOF family protein YgiW ygiw 0.12 2.48E07 P0AC62 Reduced glutaredoxin 3 grxC 0.15 5.02E05 P08200 Isocitrate dehydrogenase icd 0.19 3.37E04 P0A862 Lipid hydroperoxide peroxidase tpx 0.20 4.67E06 P0AGD3 Superoxide dismutase (Fe) sodB 0.22 2.62E05 P0AA25 Reduced thioredoxin 1 trxA 0.36 2.05E04 P0A9P0 Lipoamide dehydrogenase lpd...”
• Acetylomics reveals an extensive acetylation diversity within Pseudomonas aeruginosa
  Broeckaert, microLife 2024
  • “...K80, and K86) DNA-binding protein HU-beta hupB Venkat et al. ( 2018 ) E. coli P08200 (K55) Q9I0L5 (K57) Isocitrate dehydrogenase (NADP) icd Sun et al. ( 2016 ) E. coli A0A140N627 (K266, K284, and K373) Q9I5Z0 (K267, K285, and K386) S -adenosylmethionine synthase metK Carabetta...”
• Simulation-based Reconstructed Diffusion unveils the effect of aging on protein diffusion in Escherichia coli
  Mantovanelli, PLoS computational biology 2023
  • “...1.9 7.8 1.8 LeuS P07813 122.9 3.9 0.8 2.4 0.5 4.2 0.9 2.7 0.7 Icd P08200 142.8 5.0 0.9 3.8 0.7 5.5 1.1 4.5 0.9 TrxA2_hvo A0A558GCJ2 37.8 8.2 1.3 6.0 1.0 9.3 1.7 7.4 1.3 TrxA_lla A0A089XQE8 37.4 6.4 1.1 4.6 1.1 7.2 1.5 5.6...”
• Protein diffusion in Escherichia coli cytoplasm scales with the mass of the complexes and is location dependent
  Śmigiel, Science advances 2022
  • “...37.5 8.7 1.8 16 P07813 LeuS 20 1,505 0.005 97.2 1 122.9 4.1 0.8 19 P08200 Icd 23 24,591 1.020 45.7 2 142.8 5.0 0.9 15_hvo A0A558GCJ2 TrxA2_hvo 23 12.1 1 37.8 8.1 1.2 15_lla A0A089XQE8 TrxA_lla 24 11.7 1 37.4 6.6 1.3 Correlation between diffusion...”
• Chaperonin Abundance Enhances Bacterial Fitness
  Kumar, Frontiers in molecular biosciences 2021
  • “...51.36 Four Homodimer F c.27.1.1; d.41.3.1; a.46.2.1 20.63 (Stable) Cytoplasm deoA (b4382) 0 15.8 IDH_ECOLI (P08200) Isocitrate dehydrogenase [NADP] (EC:1.1.1.42) (Oxalosuccinate decarboxylase) 45.7 5.15 19 65.28 Homodimer C c.77.1.1 34.73 (Stable) Cytoplasm icd (b1136) 0 5.8 ACEA_ECOLI (P0A9G6) Isocitrate lyase (EC:4.1.3.1) 47.4 5.16 11 40.32 Homo-tetramer...”
• Investigation of the Importance of Protein 3D Structure for Assessing Conservation of Lysine Acetylation Sites in Protein Homologs
  Jew, Frontiers in microbiology 2021
  • “...substrate proteins we analyzed in this work include Adk (UniProt ID P69441), Icd (UniProt ID P08200), KatE (UniProt ID P21179), Fmt (UniProt ID P23882), and YaaA (UniProt ID P0A8I3). A prior study identified K136 of Adk as a site of acetylation for both YfiQ and YiaC,...”
• Identification of Functional Interactome of Colistin Resistance Protein MCR-1 in Escherichia coli
  Li, Frontiers in microbiology 2020
  • “...51 P0A912 Peptidoglycan-associated lipoprotein 18,869 pa1 52 P0A905 Outer membrane lipoprotein SlyB 15,649 slyB 53 P08200 Isocitrate dehydrogenase (NADP) 46,070 icd 54 A0A0R6L508 MCR-1 60,428 mcr-1 To elucidate the functional relationships between the MCR-1 interacting proteins, we extracted a PPI network over these proteins from the...”
• More
• Automated characterization and analysis of expression compatibility between regulatory sequences and metabolic genes in Escherichia coli
  Wen, Synthetic and systems biotechnology 2024
  • “...dehydrogenase E1 component b0420 dxs 1-Deoxy-d-xylulose-5-phosphate synthase b0720 gltA Citrate synthase b0754 aroG 3-Deoxy-7-phosphoheptulonate synthase b1136 icd Isocitrate dehydrogenase b1207 prs Ribose-phosphate diphosphokinase b1603 pntA Proton-translocating NAD(P)+transhydrogenase subunit alpha b1676 pykF Pyruvate kinase b1702 ppsA Phosphoenolpyruvate synthase b1761 gdhA Glutamate dehydrogenase b1852 zwf Glucose-6-phosphate 1-dehydrogenase b1854...”
• Chaperonin Abundance Enhances Bacterial Fitness
  Kumar, Frontiers in molecular biosciences 2021
  • “...[NADP] (EC:1.1.1.42) (Oxalosuccinate decarboxylase) 45.7 5.15 19 65.28 Homodimer C c.77.1.1 34.73 (Stable) Cytoplasm icd (b1136) 0 5.8 ACEA_ECOLI (P0A9G6) Isocitrate lyase (EC:4.1.3.1) 47.4 5.16 11 40.32 Homo-tetramer C c.1.12.7 36.53 (Stable) Cytoplasm aceA (b4015) 0 11.5 DPO3B_ECOLI (P0A988) DNA polymerase III beta subunit protein (EC:2.7.7.7)...”
• Essential Genome of the Metabolically Versatile Alphaproteobacterium Rhodopseudomonas palustris
  Pechter, Journal of bacteriology 2015
  • “...ilvC idh thrB serC b3735 b2818 b3957 b2019 b3774 b1136 b0003 b0907 atpH argA argE hisG ilvC icd thrB serC ATP synthase F0F1 subunit N-Acetylglutamate synthase...”
• Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models
  Hamilton, Biophysical journal 2013
  • “...Lethal Lethal Lethal Nonlethal Nonlethal Worse in RTMFA b1136 icd Lethal Lethal Lethal Lethal Nonlethal Lethal b2780 pyrG Lethal Lethal Lethal Lethal Nonlethal...”
• Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions
  Orth, BMC systems biology 2012
  • “...aspC (b0928) tyrB (b4054) 4.00E-94 fabH (b1091) none identified pabC (b1096) ilvE (b3770) 7.00E-8 icd (b1136) dmlA (b1800) 3.00E-19 aldA (b1415) gabD (b2661) 1.00E-90 prr (b1444) 3.00E-80 feaB (b1385) 1.00E-69 aldB (b3588) 2.00E-66 betB (b0312) 4.00E-65 ubiX (b2311) none identified luxS (b2687) none identified thyA (b2827)...”
  • “...IV global orphan R00695 (R) I global orphan R00709 (F) IV dmlA (b1800) 6.00E-26 icd (b1136) 1.00E-26 leuB (b0073) 2.00E-15 R00732 (R) III aroA (b0908) 5.00E-32 murA (b3189) 7.00E-8 R00733 (R) III tyrA (b2600) 2.80E-2 R01393 (R) I global orphan R01618 (R) IV glgP (b3428) 2.10...”
• Accurate estimation of nucleic acids by amplification efficiency dependent PCR
  Chatterjee, PloS one 2012
  • “...acnA 1.90 1.80 4.66 1.06 1.25 b0118 aconitate hydratase, acnB 1.95 1.96 1.26 1.32 2.17 b1136 isocitrate dehydrogenase 1.80 1.87 0.60 0.93 1.32 b4016 isocitrate dehydrogenase kinase 1.91 1.82 37.32 8.20 2.41 b4015 isocitrate lyase 1.84 1.92 10.55 15.67 3.39 b2976 malate synthase G 1.94 1.95...”
• Reconstitution of the Mycobacterium tuberculosis pupylation pathway in Escherichia coli
  Cerda-Maira, EMBO reports 2011 (secret)
• Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach
  Xu, BMC bioinformatics 2009
  • “...b4245 SS NSP CAC GSM TTPM TIM genes b0639 b0720 b0907 b0908, b1260 b0914 b1098 b1136 b1261, b1262 s0001 b2827 b1263, b1264 b3648 b1693, b2329 s0001 b2599, b2600 b3389 SS AAM FM ACM HM CM genes b0928 b1415 b1415 b2019, b2020 b2750, b2751 b3941 b3608 b2021,...”
• More
• An evolutionary optimization of a rhodopsin-based phototrophic metabolism in Escherichia coli
  Kim, Microbial cell factories 2017
  • “...zero-coverage region after mapping analysis. It might have been caused by a crossover between icd (Y75_p1106, 1251bp) and icdC (pseudo; Y75_p1130, 153bp). Sequence alignment showed that icdC is the C-term part of icd (93% nucleotide identities). The image was captured from the output screen of the...”

Q8X722 Isocitrate dehydrogenase [NADP] from Escherichia coli O157:H7
79% identity, 99% coverage

• Yeast Mannan-Rich Fraction Modulates Endogenous Reactive Oxygen Species Generation and Antibiotic Sensitivity in Resistant E. coli
  Smith, International journal of molecular sciences 2022
  • “...P0A9Q3 ARCA 4 3 41 27 +0.52 0.19 0.01 0.92 +0.78 0.03 MRF + AMP Q8X722 ICD 8 8 62 23 0.20 0.30 0.13 0.40 +0.72 0.03 MRF + AMP A0A0H3JCM9 GLTA 2 2 17 6 +0.37 0.22 +0.46 0.17 +1.65 0.05 MRF + AMP Q8X957...”

S1238 isocitrate dehydrogenase from Shigella flexneri 2a str. 2457T
UTI89_C1266 NADP Isocitrate dehydrogenase from Escherichia coli UTI89
SF1155 isocitrate dehydrogenase from Shigella flexneri 2a str. 301
79% identity, 99% coverage

• The proteome of Shigella flexneri 2a 2457T grown at 30 and 37 degrees C
  Zhu, Molecular & cellular proteomics : MCP 2010
  • “...30043222 ahpC tsf ompA icdA eno tufB atpA S0529 S0163 S1023 S1238 S2988 S3682 S3954 465 549 30039968 30042978 rpsB hupA S0162 S3663 % a Score greater than 49 is...”
• Genome-wide analysis of fitness-factors in uropathogenic Escherichia coli during growth in laboratory media and during urinary tract infections
  García, Microbial genomics 2021
  • “...Protein transport/cell cycle, cell division (U) 2.03 UTI89_C2053 eda KHG/KDPG aldolase Carbohydrate metabolism (G) 2.01 UTI89_C1266 icdA Isocitrate dehydrogenase Tricarboxylic acid cycle (C) 2.01 UTI89_C1265 UTI89_C1265 Hypothetical protein (NI) 2.01 UTI89_C0016 dnaK Chaperone protein DnaK DNA replication/stress response (O) 2.00 Genes found as fitness-genes during infection...”
• Efficacy of beta-glucuronidase assay for identification of Escherichia coli by the defined-substrate technology
  Rice, Applied and environmental microbiology 1990
  • “...457d/460 (99.3) 441a/460 (95.9) 99b/105 (94.3) 1051/105 (100) 52c155 (94.5) Sf1155 (100) 459/460 (99.8) 80% 4+, 11% 3+, 6% 2+, 3% 1+. 85% 4+, 5% 3+, 5% 2+, 5%...”

A6T7K6 Isocitrate dehydrogenase [NADP] from Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
79% identity, 99% coverage

• Profiling of the Klebsiella pneumoniae Phosphoproteome under Iron-Limited and Iron-Replete Conditions
  Reitzel, Microbiology resource announcements 2023
  • “...aldo/keto-reductase A6T671 KPN_00642 1 S 144 Biotin sulfoxide reductase A6T6D3 pgm 1 S 146 Phosphoglucomutase A6T7K6 icdA 1 S 113 Isocitrate dehydrogenase A6T818 KPN_01306 2 T 331, 335 Putative transport protein A6TAE1 lpp 1 S 53 Major outer membrane lipoprotein A6TAG7 ppsA 1 T 419 Phosphoenolpyruvate...”
• Phosphoproteome Profiling of Klebsiella pneumoniae under Zinc-Limited and Zinc-Replete Conditions
  Reitzel, Microbiology resource announcements 2023
  • “...T, H 497, 498 Bacterial extracellular solute-binding protein A6T789 KPN_01025 1 Y 30 Short-chain dehydrogenase/reductase A6T7K6 icdA 1, 2 D, S 50, 113 Isocitrate dehydrogenase (NADP) A6T818 KPN_01306 2, 2 T, T 331, 335 Transport protein A6T870 KPN_01359 1 Y 44 Bacterial regulatory protein A6T8U7 ydfI...”

KPK_3407 isocitrate dehydrogenase, NADP-dependent from Klebsiella pneumoniae 342
79% identity, 99% coverage

• Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice
  Fouts, PLoS genetics 2008
  • “...36346 bp in size, with a G+C% of 47.4%, and appears to have inserted into KPK_3407 (isocitrate dehydrogenase) at nucleotide positions 3425830-3389485 ( Table S2 ). PHAGE02 is slightly larger (48557 bp) with a slightly higher G+C content of 52.8%. It is inserted into a tRNA-Arg...”

Entcl_2658 NADP-dependent isocitrate dehydrogenase from [Enterobacter] lignolyticus SCF1
79% identity, 99% coverage

• Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1
  Deangelis, Frontiers in microbiology 2013
  • “...(complement(4764359..4765249)) ABC transporters 2.020 1.704 Entcl_1207 ABC transporter, substrate-binding protein (complement(1260320..1261303)) ABC transporters 2.380 1.564 Entcl_2658 Isocitrate dehydrogenase, NADP-dependent (complement(2808830..2810080)) Glutathione metabolism 2.010 1.091 Entcl_0176 D-xylose ABC transporter, periplasmic substrate-binding protein (complement(183475..184470)) ABC transporters 2.410 1.035 Entcl_3614 2-oxo-acid dehydrogenase E1 subunit, homodimeric type (complement(3877006..3879669)) Glycolysis/Gluconeogenesis 2.500...”

lpg0816 isocitrate dehydrogenase, NADP-dependent from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Q5ZXB6 Isocitrate dehydrogenase [NADP] from Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)
78% identity, 99% coverage

• The Passage of Chaperonins to Extracellular Locations in <i>Legionella pneumophila</i> Requires a Functional Dot/Icm System
  Robertson, Biomolecules 2025
  • “...100 amino acids, were ligated in frame to the 5 end of: (i) icd ( lpg0816 ) lacking its stop codon, to create plasmids pICD-Cterm-50 and pICD-Cterm-100, and (ii) a G-block mini gene encoding the E. coli periplasmic phosphatase, PhoA, lacking a secretion signal peptide and...”
• The Temporal Expression of Global Regulator Protein CsrA Is Dually Regulated by ClpP During the Biphasic Life Cycle of Legionella pneumophila
  Ge, Frontiers in microbiology 2019
  • “...TP of WT and clpP are shown in Supplementary Table S3 ; ICDH (Protein Accession: Q5ZXB6 ) was calculated as a loading control. Proteomics analysis of the peptide data of CsrA and IHFB purified by the ClpP trapping system is shown in Supplementary Table S4 ;...”

6c0eA / Q5ZXB6 Crystal structure of isocitrate dehydrogenase from legionella pneumophila with bound NADPH with an alpha-ketoglutarate adduct
78% identity, 100% coverage

• Ligands: (3~{s})-3-[(4~{s})-3-aminocarbonyl-1-[(2~{r},3~{r},4~{s},5~{r})-5-[[[[(2~{r},3~{r},4~{r},5~{r})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]-4~{h}-pyridin-4-yl]-2-oxidanylidene-pentanedioic acid; glycine (6c0eA)

lpp0878 isocitrate dehydrogenase from Legionella pneumophila str. Paris
78% identity, 100% coverage

• The Legionella pneumophila genome evolved to accommodate multiple regulatory mechanisms controlled by the CsrA-system
  Sahr, PLoS genetics 2017
  • “...carboxyltransferase, Ppc (Lpp1572) Phosphoenolpyruvate carboxylase, SfcA (Lpp3043), NAD-specific malic enzyme, AcnA (LPP1659), Aconitate hydratase, Icd (Lpp0878), Isocitrate dehydrogenase, Sdh (Lpp0595), Succinate dehydrogenase, Suc (Lpp0597), 2-Oxoglutarate dehydrogenase, Ald (Lpp0986), Alanine dehydrogenase, SdaA (Lpp0854), Serine dehydratase, PhbB (Lpp0621), acetoacetyl-CoA reductase, PhbC (Lpp2038), Polyhydroxyalkanoate synthase, Adc (Lpp0728) Acetoacetate decarboxylase,...”

JHW33_RS08805 NADP-dependent isocitrate dehydrogenase from Rahnella aceris
77% identity, 99% coverage

• Comparative Genomics Assisted Functional Characterization of Rahnella aceris ZF458 as a Novel Plant Growth Promoting Rhizobacterium
  Xu, Frontiers in microbiology 2022
  • “...hydratase JHW33_RS04170 WP_037034468.1 WP_013575910.1 100 WP_015690067.1 99 WP_013575910.1 99 WP_015697115.1 98 icd NADP-dependent Isocitrate dehydrogenase JHW33_RS08805 WP_013576210.1 WP_013576210.1 100 WP_013576210.1 100 WP_013576210.1 100 WP_015697904.1 99 aceK bifunctional isocitrate dehydrogenase JHW33_RS14895 WP_200223135.1 WP_112197688.1 99 WP_015690563.1 99 WP_013577389.1 98 WP_015699020.1 95 icl isocitrate lyase/phosphoenolpyruvate mutase family protein JHW33_RS17355...”

ACIAD1190 isocitrate dehydrogenase from Acinetobacter sp. ADP1
78% identity, 96% coverage

• Rapid and assured genetic engineering methods applied to Acinetobacter baylyi ADP1 genome streamlining
  Suárez, Nucleic acids research 2020
  • “...the knockout strain collection. ADP1 encodes two isocitrate dehydrogenase isozymes encoded by the ACIAD1187 and ACIAD1190 genes ( 30 ). Both of these genes were simultaneously deleted in this strain. We suspect that this leads to synthetic lethality in this minimal medium that has succinate as...”
• iTRAQ-Based Comparative Proteomic Analysis of Acinetobacter baylyi ADP1 Under DNA Damage in Relation to Different Carbon Sources
  Jiang, Frontiers in microbiology 2019
  • “...2.78 5.3 3.44 2.44 Diacetyl reductase budC ACIAD1022 1.82 6.79 2.99 1.8 Isocitrate dehydrogenase icd ACIAD1190 2.68 3.91 2.56 3.05 Aryl-alcohol dehydrogenase areB ACIAD1429 2.81 8.24 2.47 3.31 Linalool 8-monooxygenase linC ACIAD1575 1.25 1.27 1.31 1.36 Methylmalonate-semialdehyde dehydrogenase mmsA ACIAD1604 2.33 5.7 3.19 3.44 3-hydroxyisobutyrate dehydrogenase...”
• Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium
  Barbe, Nucleic acids research 2004
  • “...ADP1 possesses two isocitrate dehydrogenases (ACIAD1187 and ACIAD1190), 743 and 436 residues long, respectively, which present no significant similarities. This...”

LT988_17130 NADP-dependent isocitrate dehydrogenase from Thiocapsa bogorovii
77% identity, 100% coverage

• The Complete Genome of a Novel Typical Species Thiocapsa bogorovii and Analysis of Its Central Metabolic Pathways
  Petushkova, Microorganisms 2024
  • “...aconitate hydratase [EC:4.2.1.3] LT988_17115 acnA ; aconitate hydratase AcnA 4, 5 K00031 isocitrate dehydrogenase [EC:1.1.1.42] LT988_17130 icd ; NADP-dependent isocitrate dehydrogenase 6, 7 K00164 2-oxoglutarate dehydrogenase E1 component [EC:1.2.4.2] LT988_19210 2-oxoglutarate dehydrogenase E1 component 8 K00658 2-oxoglutarate dehydrogenase E2 component (dihydrolipoamide succinyltransferase) [EC:2.3.1.61] LT988_19205 odhB ;...”

VAS14_05433 NADP-dependent isocitrate dehydrogenase from Photobacterium angustum S14
78% identity, 99% coverage

• Shotgun redox proteomics: identification and quantitation of carbonylated proteins in the UVB-resistant marine bacterium, Photobacterium angustum S14
  Matallana-Surget, PloS one 2013
  • “...VGVQNGSTHQSYLTDQMPGV T AVPYTSYQDAFIDMK VAS14_04998 elongation factor EF-2 J 2 AGPQLLE P IMHVDVFTPEDHVGDVIGDLNR GMQLVLDAVVDYLPSPTEVDPQPLTDPETGEPTGEVA T VSADEPLK VAS14_05433 isocitrate dehydrogenase C 1 FTEGAF K DWGYEVALQEFGAELLDGGPWMTLK VAS14_05968 hypothetical protein / 3 SDVSNNTLTTE P ETCTVEFTQTSGAIDMSNSK VAS14_06363 glycosyl transferase / 1 KESR KK LFNDESSSPWVLFNTLSK VAS14_06513 formate acetyltransferase C 19 TPEYDELFSGD P...”

D0Z8Y6 isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) from Edwardsiella tarda (see paper)
ETAE_2050 isocitrate dehydrogenase, specific for NADP+ from Edwardsiella tarda EIB202
76% identity, 99% coverage

• Genome sequence of the versatile fish pathogen Edwardsiella tarda provides insights into its adaptation to broad host ranges and intracellular niches
  Wang, PloS one 2009
  • “...ETAE_1771 ldhA D-lactate dehydrogenase ETAE_1899 kduD 2-Deoxy-D-gluconate 3-dehydrogenase ETAE_1922 3-Hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases ETAE_2050 Isocitrate dehydrogenase, specific for NADP+ ETAE_2070 ndh NADH dehydrogenase, FAD-containing subunit ETAE_2118 D-beta-hydroxybutyrate dehydrogenase ETAE_2276 hisD Histidinol dehydrogenase ETAE_2380 nuoG NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75 kD subunit (chain G) ETAE_2416 asd...”

Rmet_2895 NADP-dependent isocitrate dehydrogenase from Cupriavidus metallidurans CH34
Rmet_2895 isocitrate dehydrogenase, NADP-dependent from Ralstonia metallidurans CH34
78% identity, 100% coverage

• Importance of RpoD- and Non-RpoD-Dependent Expression of Horizontally Acquired Genes in Cupriavidus metallidurans
  Große, Microbiology spectrum 2022
  • “...mdh 13.8 165 38 TATTGGTGCG 13 GCTAAAATCA Rmet_2486 sdhC 4.4 2,042 33 TGGCGTGCCC 13 TGCATAATAT Rmet_2895 icd 7.1 2,941 38 TTGCACCTCC 14 GGCAAAATTC Rmet_3729 icdA 7.4 1,295 36 TTGCATCGAT 15 TCTAGTATAT Rmet_4268 citA 10.8 723 35 TTGATCTGGC 14 TCTACAATCA Rmet_5296 acnB 12.6 a The 3,000 transcriptional...”
• The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments
  Janssen, PloS one 2010
  • “...that D-isocitrate, as for full TCA cycles, is transfigured into 2-ketoglutarate by isocitrate dehydrogenase ICDH (Rmet_2895, Rmet_3729). The carbon skeleton of 2-ketoglutarate then is used, depending on cellular ammonia levels and energy status, by either one of the two enzymes glutamate dehydrogenase GDH (Rmet_1181) or glutamate...”

H16_A3056 isocitrate dehydrogenase [NADP] from Ralstonia eutropha H16
H16_A3056 NADP-dependent isocitrate dehydrogenase from Cupriavidus necator H16
78% identity, 100% coverage

• Detection of phase-dependent transcriptomic changes and Rubisco-mediated CO2 fixation into poly (3-hydroxybutyrate) under heterotrophic condition in Ralstonia eutropha H16 based on RNA-seq and gene deletion analyses
  Shimizu, BMC microbiology 2013
  • “...throughout cultivation. gltA (H16_A2627), acnA and acnB (H16_A2638 and H16_B0568, respectively), and icd1 and icd2 (H16_A3056 and H16_B1931, respectively), which encode enzymes for the conversion of C 6 -acids in TCA cycle, were highly expressed in the growth phase, but had slightly lower expression levels in...”

IDH1_PSYS3 / A0A5A4WIX0 Isocitrate dehydrogenase [NADP] 1; IDH 1; EC 1.1.1.42 from Psychrobacter sp. (strain 13A) (see paper)
77% identity, 100% coverage

• function: Catalyzes the oxidative decarboxylation of isocitrate to 2- oxoglutarate and carbon dioxide with the concomitant reduction of NADP(+) (PubMed:34101864). Cannot use NAD(+) (PubMed:34101864).
  catalytic activity: D-threo-isocitrate + NADP(+) = 2-oxoglutarate + CO2 + NADPH (RHEA:19629)
  cofactor: Mg(2+) Mn(2+) (Binds 1 Mg(2+) or Mn(2+) ion per subunit (By similarity). Mn(2+) is the most effective divalent cation in vitro, but the enzyme can also use Mg(2+), Co(2+), Zn(2+) and Ni(2+), with lower efficiency (PubMed:34101864).)
  subunit: Homodimer.

E2566_10015 NADP-dependent isocitrate dehydrogenase from Pectobacterium punjabense
76% identity, 99% coverage

• Identification and characterization of opportunistic pathogen Pectobacterium polonicum causing potato blackleg in China
  Han, Frontiers in plant science 2023
  • “...E2566_16880 100% 97.65% Sarfraz etal., 2018 proA E2566_16520 100% 91.56% gapA E2566_10485 99% 98.10% icdA E2566_10015 100% 94.41% acnA E2566_12300 98% 93.02% mdh E2566_03350 100% 91.46% P. polonicum DPMP315 T groundwater in vegetable field Poland 2016 rpoS EDI29_13735 100% 99.87% Waleron etal., 2019 proA EDI29_17855 100%...”

BURPS1710b_1108 isocitrate dehydrogenase, NADP-dependent from Burkholderia pseudomallei 1710b
Q3JV82 Isocitrate dehydrogenase [NADP] from Burkholderia pseudomallei (strain 1710b)
BPSL0896 isocitrate dehydrogenase from Burkholderia pseudomallei K96243
77% identity, 100% coverage

• Combining functional and structural genomics to sample the essential Burkholderia structome
  Baugh, PloS one 2013
  • “...39.8, 96.1 Yes BURPS1710b_1080 Adenylate kinase (adk) 3GMT B. pseudomallei BTH_I0739 P54819 48.5, 98.1 Yes BURPS1710b_1108 Isocitrate dehydrogenase (icd) 3DMS B. pseudomallei BTH_I0759 P50213 31.4, 94.0 Yes BTH_I0848 Pantothenate synthetase (panC) 3UK2 B. thailandensis BTH_I0848 Yes BTH_I0860 Deoxycytidine triphosphate deaminase (dcd) 4DHK B. thailandensis BTH_I0860 No...”
• Induced fit and the catalytic mechanism of isocitrate dehydrogenase
  Gonçalves, Biochemistry 2012
  • “...1.30 Citrate, NAD + 2d4v:D 0.76 1.38 Citrate, NAD + Burkholderia pseudomallei Strain 1710b (UNIPROT Q3JV82), 74.2% identity 3dms 71 1.65 2011 0.92 0.62 - Aeropyrum pernix ATCC 700893(UNIPROT Q9YE81), 45.2% identity 1kd:A 20 2.3 2005 2.24 1.94 Ca 2+ , ICT, NADP + 1kd:B 0.99...”
• Host-Adaptation of Burkholderia pseudomallei Alters Metabolism and Virulence: a Global Proteome Analysis
  Mariappan, Scientific reports 2017
  • “...Pyrophosphatase (ppa) 52* 0.026 BPSL1021 2.5 23 19149/19030 5.37/5.37 cytoplamic Isocitrate dehydrogenase (idhI) 77 0.043 BPSL0896 2.0 24 46116/46015 5.76/5.63 unknown F0F1 ATP synthase subunit beta (atpD) 83 0.013 BPSL3396 2.0 21 50417/50492 5.24/5.26 cytoplamic F0F1 ATP synthase subunit beta (atpD) 84 0.018 BPSL3396 2.0 20...”
• Burkholderia pseudomallei isocitrate lyase is a persistence factor in pulmonary melioidosis: implications for the development of isocitrate lyase inhibitors as novel antimicrobials
  van, Infection and immunity 2009
  • “...3, isocitrate dehydrogenase (ICD) (BPSS0011, homologue to BPSL0896); 4, fumarate hydratase (FUM) (BPSL2469); 5, MCL (BPSS0206). These genes where selected using...”

EDI29_02475 NADP-dependent isocitrate dehydrogenase from Pectobacterium polonicum
76% identity, 99% coverage

• Identification and characterization of opportunistic pathogen Pectobacterium polonicum causing potato blackleg in China
  Han, Frontiers in plant science 2023
  • “...EDI29_13735 100% 99.87% Waleron etal., 2019 proA EDI29_17855 100% 98.98% gapA EDI29_02940 99% 99.97% icdA EDI29_02475 100% 99.44% acnA EDI29_04400 100% 99.72% mdh EDI29_11450 100% 100% a The superscript T indicates type strain. Genome sequence and in silico analyses Illumina NovaSeq generated 22,938,662 paired-end short reads,...”

IDH1_COLMA / P41560 Isocitrate dehydrogenase [NADP] 1; IDH-I; IDP-1; NADP(+)-specific ICDH 1; Oxalosuccinate decarboxylase 1; EC 1.1.1.42 from Colwellia maris (see 2 papers)
icd / BAA03135.1 isocitrate dehydrogenase isozyme IDH-I from Colwellia maris (see paper)
77% identity, 99% coverage

• function: Catalyzes the oxidative decarboxylation of isocitrate to 2- oxoglutarate and carbon dioxide with the concomitant reduction of NADP(+).
  catalytic activity: D-threo-isocitrate + NADP(+) = 2-oxoglutarate + CO2 + NADPH (RHEA:19629)
  cofactor: Mg(2+) Mn(2+) (Binds 1 Mg(2+) or Mn(2+) ion per subunit.)
  subunit: Homodimer.
• Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi.
  Islam, Microbial biotechnology 2016
  • “...P99167 ), B .subtilis ( P39126 ), E .coli ( P08200 ), C .maris ( P41560 ), B .taurus ( P41563 ) and H .sapiens ( P50213 ). 2015 Society for Applied Microbiology and John Wiley & Sons Ltd MSA of Dm PMI sequence with its...”

IDH_COXBU / Q9ZH99 Isocitrate dehydrogenase [NADP]; IDH; IDP; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 from Coxiella burnetii (strain RSA 493 / Nine Mile phase I) (see 2 papers)
77% identity, 97% coverage

• function: Catalyzes the oxidative decarboxylation of isocitrate to 2- oxoglutarate and carbon dioxide with the concomitant reduction of NADP(+).
  catalytic activity: D-threo-isocitrate + NADP(+) = 2-oxoglutarate + CO2 + NADPH (RHEA:19629)
  cofactor: Mg(2+) Mn(2+) (Binds 1 Mg(2+) or Mn(2+) ion per subunit.)
  subunit: Homodimer.
• Evaluation of a Human T Cell-Targeted Multi-Epitope Vaccine for Q Fever in Animal Models of Coxiella burnetii Immunity
  Sluder, Frontiers in immunology 2022
  • “...methionine-binding protein 7 13 p48 SPAVLSAAKKIFGDGA CBU_0109 Q83F42 methionine-binding protein 23 30 p50 LRPVRYFTGVPSPVKTPE CBU_1200 Q9ZH99 icd 20 22 Epitope IDs are those reported by Scholzen etal. ( 23 ). Recall responses to epitopes were previously assessed by cultured IFN ELISpot in individuals with demonstrated responses...”
• Promiscuous Coxiella burnetii CD4 Epitope Clusters Associated With Human Recall Responses Are Candidates for a Novel T-Cell Targeted Multi-Epitope Q Fever Vaccine
  Scholzen, Frontiers in immunology 2019
  • “...DQRITQLKNLNSNNSDSSNDN CBU_0092 Q83F57 ybgF DRB1*0101, DRB1*0301, DRB1*0401, DRB1*0701, DRB1*0801, DRB1*1101, DRB1*1301, DRB1*1501 p50 LRPVRYFTGVPSPVKTPE CBU_1200 Q9ZH99 icd DRB1*0101, DRB1*0401, DRB1*0701, DRB1*1101, DRB1*1301, DRB1*1501 Table 3 HLA class I epitopes selected for immune reactivity screening. ID Sequence Source antigen Set a Primary HLA I Predicted HLA I...”

CBU_1200 isocitrate dehydrogenase from Coxiella burnetii RSA 493
77% identity, 97% coverage

• Evaluation of a Human T Cell-Targeted Multi-Epitope Vaccine for Q Fever in Animal Models of Coxiella burnetii Immunity
  Sluder, Frontiers in immunology 2022
  • “...Q83F42 methionine-binding protein 7 13 p48 SPAVLSAAKKIFGDGA CBU_0109 Q83F42 methionine-binding protein 23 30 p50 LRPVRYFTGVPSPVKTPE CBU_1200 Q9ZH99 icd 20 22 Epitope IDs are those reported by Scholzen etal. ( 23 ). Recall responses to epitopes were previously assessed by cultured IFN ELISpot in individuals with demonstrated...”
• Promiscuous Coxiella burnetii CD4 Epitope Clusters Associated With Human Recall Responses Are Candidates for a Novel T-Cell Targeted Multi-Epitope Q Fever Vaccine
  Scholzen, Frontiers in immunology 2019
  • “...p49 DQRITQLKNLNSNNSDSSNDN CBU_0092 Q83F57 ybgF DRB1*0101, DRB1*0301, DRB1*0401, DRB1*0701, DRB1*0801, DRB1*1101, DRB1*1301, DRB1*1501 p50 LRPVRYFTGVPSPVKTPE CBU_1200 Q9ZH99 icd DRB1*0101, DRB1*0401, DRB1*0701, DRB1*1101, DRB1*1301, DRB1*1501 Table 3 HLA class I epitopes selected for immune reactivity screening. ID Sequence Source antigen Set a Primary HLA I Predicted HLA...”
• Proteomics paves the way for Q fever diagnostics
  Kowalczewska, Genome medicine 2011
  • “...in SCV and LCV forms. SP: CBU_1718, CBU_0236, CBU_0229, CBU_1943, CBU_1416, CBU_0952, CBU_0963, CBU_0737, CBU_0497, CBU_1200 [ 31 ] SP for serodiagnosis of Q fever endocarditis IP (2-DE/MALDI-TOF) TPE Cb NM II (CC, Vero) HS (acute Q fever or IE Q fever) Markers of chronic Q...”

RSc2490 PROBABLE ISOCITRATE DEHYDROGENASE [NADP] OXIDOREDUCTASE PROTEIN from Ralstonia solanacearum GMI1000
77% identity, 100% coverage

• Changes in DNA methylation contribute to rapid adaptation in bacterial plant pathogen evolution
  Gopalan-Nair, PLoS biology 2024
  • “...6mA 6mA 6mA 6mA 6mA 6mA 6mA 6mA 6mA 6mA 6mA 6mA 6mA 6mA 6mA RSc2490 / RSc2492 GTTAAC upstream icd/ Isocitrate dehydrogenase / Acid phosphatase 2697793 6mA 6mA 6mA 6mA 6mA 6mA 6mA 6mA 6mA 6mA 6mA 6mA 6mA 6mA 6mA 6A 6mA 6mA 6mA...”
  • “...-2.31 -1.78 -0.53 -2.10 -1.49 -0.58 -0.08 -1.23 -1.00 -1.18 -0.88 -0.91 -1.00 -1.18 -1.13 RSc2490 -0.60 -0.30 -0.05 -0.10 -0.19 0.12 0.13 0.28 0.57 0.01 0.46 0.56 -0.31 1.00 0.80 0.26 -0.03 0.85 -0.13 -0.63 -0.02 -0.03 -0.01 -0.49 -0.61 -0.32 -0.03 -0.07 -0.24 -0.22...”

Q2T0I4 Isocitrate dehydrogenase [NADP] from Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264)
BTH_I0759 isocitrate dehydrogenase, NADP-dependent from Burkholderia thailandensis E264
76% identity, 100% coverage

• Using a multi-omic approach to investigate the mechanism of 12-bis-THA activity against Burkholderia thailandensis
  Pattinson, Frontiers in microbiology 2022
  • “...Q2T4T8 Mdh2 BTH_II1671 0.13 0.79 Q2T7I5 GltA BTH_II0665 0.06 0.47 Q2T7J6 AcnA BTH_II0654 0.04 0.04 Q2T0I4 Icd BTH_I0759 0.07 0.14 Q2SVH6 SucA BTH_I2556 0.03 0.89 Q2SVH7 SucB BTH_I2555 0.08 0.89 Q2T0U7 SucC BTH_I0646 0.02 0.46 Q2T0U6 SucD BTH_I0647 0.08 0.47 Q2T7J0 Succinate dehydrogenase cytochrome b556 subunit...”
• Using a multi-omic approach to investigate the mechanism of 12-bis-THA activity against Burkholderia thailandensis
  Pattinson, Frontiers in microbiology 2022
  • “...BTH_II1671 0.13 0.79 Q2T7I5 GltA BTH_II0665 0.06 0.47 Q2T7J6 AcnA BTH_II0654 0.04 0.04 Q2T0I4 Icd BTH_I0759 0.07 0.14 Q2SVH6 SucA BTH_I2556 0.03 0.89 Q2SVH7 SucB BTH_I2555 0.08 0.89 Q2T0U7 SucC BTH_I0646 0.02 0.46 Q2T0U6 SucD BTH_I0647 0.08 0.47 Q2T7J0 Succinate dehydrogenase cytochrome b556 subunit BTH_II0660 0.05...”
• Combining functional and structural genomics to sample the essential Burkholderia structome
  Baugh, PloS one 2013
  • “...3GMT B. pseudomallei BTH_I0739 P54819 48.5, 98.1 Yes BURPS1710b_1108 Isocitrate dehydrogenase (icd) 3DMS B. pseudomallei BTH_I0759 P50213 31.4, 94.0 Yes BTH_I0848 Pantothenate synthetase (panC) 3UK2 B. thailandensis BTH_I0848 Yes BTH_I0860 Deoxycytidine triphosphate deaminase (dcd) 4DHK B. thailandensis BTH_I0860 No BURPS1710b_1237 Inorganic pyrophosphatase 6 structures B. pseudomallei...”

RSUY_RS12515 NADP-dependent isocitrate dehydrogenase from Ralstonia solanacearum
77% identity, 100% coverage

• Gene expression changes throughout the life cycle allow a bacterial plant pathogen to persist in diverse environmental habitats
  de, PLoS pathogens 2023
  • “...RSUY_RS09555; Thiolase : RSUY_RS09565; Citrate synthase : RSUY_RS11275; Aconitate hydratase : RSUY_RS17195; Isocitrate dehydrogenase : RSUY_RS12515; 2-ketoglutarate dehydrogenase : RSUY_RS08325, RSUY_RS08325; succinate thiokinase : RSUY_RS13215, RSUY_RS13220; succinate dehydrogenase : RSUY_RS11285, RSUY_RS11290, RSUY_RS11295, RSUY_RS11300; Fumarase : RSUY_RS11110; Malate dehydrogenase : RSUY_RS11310; Isocitrate lyase : RSUY_RS08780; Malate synthase...”

BP2488 isocitrate dehydrogenase [NADP] from Bordetella pertussis Tohama I
76% identity, 100% coverage

• A Functional Tricarboxylic Acid Cycle Operates during Growth of Bordetella pertussis on Amino Acid Mixtures as Sole Carbon Substrates
  Izac, PloS one 2015
  • “...acnA-F TGTCAGTTCTATTCGCTGCC acnA (BP2014) acnA-R CAGCTTCATGTTCAGGTCGA acnB (BP2021) acnB-F CCAAGCAAGGCAAGAAGAAC acnB (BP2021) acnB-R CTCGTCTTCATAGCCGTTGG icd (BP2488) icd-F TCATGAAGTTCACGGAAGGC icd (BP2488) icd-R GAGATGTAGTCGCCGTTCAG Enzymatic assays All the following steps were achieved at 4C. B . pertussis Tohama I was grown in the chemically defined medium previously described....”
  • “...hydratase citrate isocitrate (intermediary: cis -aconitate) acnB BP2021 bifunctional aconitate hydratase 2 isocitrate -ketoglutarate icd BP2488 isocitrate dehydrogenase -ketoglutarate succinyl-CoA odhB BP1125 dihydrolipoamide succinyltransferase -ketoglutarate succinyl-CoA sucA BP1124 2-oxoglutarate dehydrogenase -ketoglutarate succinyl-CoA odhL BP1126 2-oxoglutarate dehydrogenase complex subunit dihydrolipoamide dehydrogenase -ketoglutarate succinyl-CoA lpdA BP0995lpd dihydrolipoamide dehydrogenase...”

BCAL2736 isocitrate dehydrogenase from Burkholderia cenocepacia J2315
76% identity, 100% coverage

• Characterization of the Burkholderia cenocepacia J2315 Surface-Exposed Immunoproteome
  Sousa, Vaccines 2020
  • “...3) Lactate/malate dehydrogenase, NAD binding domain (PF00056) Lactate/malate dehydrogenase, alpha/beta C-terminal domain (PF02866) 0.430 (6) BCAL2736 Isocitrate dehydrogenase 17 (25) U (Class 3) Isocitrate/isopropylmalate dehydrogenase (PF00180) 0.460 (8) BCAL3203 (TolB) Translocation protein TolB 17 (22) U (Class 3) TolB amino-terminal domain (PF04052) WD40-like Beta Propeller Repeat...”
• Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species
  Van, PloS one 2013
  • “...Aconitate hydratase CGGTGATCCAGGCGCAGGAT CAGGCGCATCCACGATGCAC BCAM1833 Aconitate hydratase/methylisocitrate dehydratase GCATGCTGACGGTCGCCAAG GGTCGGGCAGGCCTTCGATT BCAL2735 Isocitrate dehydrogenase CGCTGAAGCCGGAAGCGAAC ACCGCGCTGCCCTTGATCTT BCAL2736 Isocitrate dehydrogenase ATCAAGGGGCCGCTCACGAC GGCGCAGGCACACGTAGAGA BCAL1517 Dihydrolipoamide dehydrogenase GAAGTGAGCGGCGAGGGTGA TCGGCACCGAGTCGAACGTC BCAL0957 Succinyl-CoA synthethase subunit alpha ACGCAGGGCATTACCGGCAA CGCGGCCGTTTGCGTATTCA BCAM0970 Succinate dehydrogenase iron-sulfur subunit CCTCCAGTCGCCGGAAGAGC CACCAGAAGCTCGGGCACGA BCAM0965 Malate dehydrogenase CCGGTCGCGTCGATCGAGAA GCGAAGCGGAAGTCCGGGTA Other genes...”
  • “...Aconitate hydratase 1.3* 1.3 BCAM1833 Aconitate hydratase/methylisocitrate dehydratase 1.5* 1.1 BCAL2735 Isocitrate dehydrogenase 1.3* 2.5* BCAL2736 Isocitrate dehydrogenase 1.4 1.5 BCAL1515 -ketoglutarate dehydrogenase E1 2.0* BCAL1516 Dihydrolipoamide succinyltransferase 3.3* BCAL1517 Dihydrolipoamide dehydrogenase 2.5* BCAL2207 Putative dihydrolipoamide dehydrogenase 1.3* BCAL1215 Dihydrolipoamide dehydrogenase 1.4* BCAL0956 Succinyl-CoA synthetase beta...”

CtesDRAFT_PD1824 NADP-dependent isocitrate dehydrogenase from Comamonas testosteroni KF-1
73% identity, 99% coverage

• Complex regulation in a Comamonas platform for diverse aromatic carbon metabolism
  Wilkes, Nature chemical biology 2023
  • “...18 . Protein production and purification Mdh (CtesDRAFT_PD1281), ME (CtesDRAFT_PD0934 and CtesDRAFT_PD5092), IDH (CtesDRAFT_PD1820 and CtesDRAFT_PD1824), 4HB 3-monooxygenase (CtesDRAFT_PD2627) and PEP synthase (CtesDRAFT_PD3828) from C. testosteroni KF-1 were recombinantly produced in E. coli BL21 (DE3) and subsequently purified (Supplementary Fig. 9 ). The gene fragments encoding...”
  • “...Cofactor specificity The cofactor specificity of Mdh (CtesDRAFT_PD1281), ME (CtesDRAFT_PD0934 and CtesDRAFT_PD5092), IDH (CtesDRAFT_PD1820 and CtesDRAFT_PD1824) and 4HB 3-monooxygenase (CtesDRAFT_PD2627) was determined by comparing the activity of the enzymes with both cofactors. For Mdh, the reaction mixture contained 50mM HEPES (pH 7.5), 10mM sodium OAA (preparing...”

V6E02_11500 NADP-dependent isocitrate dehydrogenase from Thiobacter aerophilum
75% identity, 99% coverage

• <i>Thiobacter aerophilum</i> sp. nov., a Thermophilic, Obligately Chemolithoautotrophic, Sulfur-Oxidizing Bacterium from a Hot Spring and Proposal of <i>Thiobacteraceae</i> fam. nov
  Dukat, Microorganisms 2024
  • “...encodes for the tricarboxylic acid cycle including citrate synthase (V6E02_06885), aconitate hydratase (V6E02_07900), isocitrate dehydrogenase (V6E02_11500), 2-oxoacid/ferredoxin oxidoreductases (V6E02_02945-V6E02_02960), succinyl-CoA synthetase (V6E02_03145 and V6E02_06280), succinate dehydrogenase (V6E02_00295-V6E02_00310), and class II fumarate hydratase (V6E02_07515). The gene encoding NAD-dependent malate dehydrogenase was absent, while the gene encoding NADP-dependent...”

MS2370 NADP-dependent isocitrate dehydrogenase from [Mannheimia] succiniciproducens MBEL55E
MS2370 Icd protein from Mannheimia succiniciproducens MBEL55E
70% identity, 99% coverage

• A genomic perspective on the potential of Actinobacillus succinogenes for industrial succinate production
  McKinlay, BMC genomics 2010
  • “...A. succinogenes , it has genes encoding a citrate synthase (MS2371) and an isocitrate dehydrogenase (MS2370). Although the two succinogens have an incomplete assimilatory sulfate reduction pathway, they, along with various A. pleuropneumoniae strains and Actinobacillus minor NM305, have the most complete assimilatory sulfate reduction pathway...”

A1S_2475 isocitrate dehydrogenase from Acinetobacter baumannii ATCC 17978
78% identity, 89% coverage

• Mucin acts as a nutrient source and a signal for the differential expression of genes coding for cellular processes and virulence factors in Acinetobacter baumannii
  Ohneck, PloS one 2018
  • “...CydB A1S_2166 2.026413775 0.018869709 Cytochrome bo(3) ubiquinol oxidase, CyoA A1S_2338 2.321699725 0.000396794 Malate dehydrogenase, MaeB A1S_2475 2.285469911 0.002414222 Isocitrate dehydrogenase (Icd) sucA (A1S_2715) 2.048840719 0.007128676 2-oxoglutarate dehydrogenase A1S_2716 2.19742636 0.003297483 2-oxoglutarate dehydrogenase, SucB A1S_2717 2.23412058 0.002492584 Dihydrolipoamide dehydrogenase A1S_2718 2.207779293 0.002958372 Succinyl-CoA synthetase subunit beta, SucC...”

Q1GZD1 isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) from Methylobacillus flagellatus (see paper)
70% identity, 99% coverage

HPG27_RS00150 isocitrate dehydrogenase (NADP(+)) from Helicobacter pylori G27
68% identity, 97% coverage

• Acid-regulated gene expression of Helicobacter pylori: Insight into acid protection and gastric colonization
  Marcus, Helicobacter 2018
  • “...HP0779 2.15 0.03 0.00 1.36 0.03 0.00 1.16 0.09 0.20 aconitase B ( acnB ) HPG27_RS00150 HP0027 1.64 0.12 0.03 1.98 0.09 0.00 2.82 0.20 0.00 isocitrate dehydrogenase ( icd ) HPG27_RS02860 HP0588 1.63 0.15 0.05 1.14 0.10 0.26 1.19 0.03 0.02 OorD subunit of the...”

icd / B2ZP83 isocitrate dehydrogenase subunit (EC 1.1.1.42) from Helicobacter pylori (see 4 papers)
68% identity, 97% coverage

P56063 Isocitrate dehydrogenase [NADP] from Helicobacter pylori (strain ATCC 700392 / 26695)
HP0027 isocitrate dehydrogenase (icd) from Helicobacter pylori 26695
68% identity, 97% coverage

• Outer Membrane Vesicles Secreted by Helicobacter pylori Transmitting Gastric Pathogenic Virulence Factors
  Wei, ACS omega 2022
  • “...O25905 HP_1350 10 P55994 dnaK 11 P55987 atpA 12 P56418 acnB 13 O25242 dnaN 14 P56063 icd 15 P56112 HP_0175 16 P56185 rnj 17 P55975 tsf 18 P94845 glnA 19 P55988 atpD 20 P55969 hpaA 21 O25806 rpoBC 22 O25743 Ggt 23 O25294 pepA 24 O25017...”
  • “...O24870 Omp2 9 P55987 atpA 10 O25743 HP_1118 11 P56418 acnB 12 P55975 tsf 13 P56063 icd 14 O25011 msrAB 15 P0A0V0 lpp20 16 P71404 clpB 17 P55969 hpaA 18 P55994 dnaK 19 O25905 HP_1350 20 O25286 HP_0561 21 O25751 tolB 22 P94845 glnA 23 O25242...”
• Targeted identification of glycosylated proteins in the gastric pathogen Helicobacter pylori (Hp)
  Champasa, Molecular & cellular proteomics : MCP 2013
  • “...P56002 fusA 80.9 Translation elongation factor Duodenal ulcer-related antigen Cytoplasm, surface 36 8 21.0 HP0027 P56063 icd 50.1 Isocitrate dehydrogenase Immunogen, induces humoral immune system Cytoplasm 21 4 15.6 HP0192 O06913 frdA 84.0 Fumarate reductase Immunogen, crucial for survival in gastric mucosa Inner membrane 28 5...”
• Acid-regulated gene expression of Helicobacter pylori: Insight into acid protection and gastric colonization
  Marcus, Helicobacter 2018
  • “...2.15 0.03 0.00 1.36 0.03 0.00 1.16 0.09 0.20 aconitase B ( acnB ) HPG27_RS00150 HP0027 1.64 0.12 0.03 1.98 0.09 0.00 2.82 0.20 0.00 isocitrate dehydrogenase ( icd ) HPG27_RS02860 HP0588 1.63 0.15 0.05 1.14 0.10 0.26 1.19 0.03 0.02 OorD subunit of the 2-oxoglutarate...”
• Aconitase Functions as a Pleiotropic Posttranscriptional Regulator in Helicobacter pylori
  Austin, Journal of bacteriology 2015
  • “...and locus tag Unregulated soluble proteins HP0109 HP1037 HP0027 HP1199 HP0500 HP0902 HP1103 HP0865 HP1108 HP1301 HP0827 HP1388 hemE porA cheA ileS secA rpsM...”
• Targeted identification of glycosylated proteins in the gastric pathogen Helicobacter pylori (Hp)
  Champasa, Molecular & cellular proteomics : MCP 2013
  • “...HP1195 P56002 fusA 80.9 Translation elongation factor Duodenal ulcer-related antigen Cytoplasm, surface 36 8 21.0 HP0027 P56063 icd 50.1 Isocitrate dehydrogenase Immunogen, induces humoral immune system Cytoplasm 21 4 15.6 HP0192 O06913 frdA 84.0 Fumarate reductase Immunogen, crucial for survival in gastric mucosa Inner membrane 28...”
• Analysis of Helicobacter pylori cagA promoter elements required for salt-induced upregulation of CagA expression
  Loh, Infection and immunity 2012
  • “...Hypothetical GuaB RdxA FtsZ HopQ RocF Hypothetical HP0014 HP0027 HP0109 HP0162 HP0310 HP0547 HP0606 HP0688 HP0829 HP0954 HP0979 HP1177 HP1399 HP1588 Unknown...”
• A comparison of murine and human immunoproteomes of Helicobacter pylori validates the preclinical murine infection model for antigen screening
  Bumann, Infection and immunity 2002
  • “...2017 by University of California, Berkeley HP0010 HP0011 HP0027 HP0072 HP0073 HP0109 HP0115 HP0153 HP0154 HP0175 HP0177 HP0192 HP0210 HP0231 HP0243 HP0264...”
• Multiparameter selection of Helicobacter pylori antigens identifies two novel antigens with high protective efficacy
  Sabarth, Infection and immunity 2002
  • “...epitopesc,g Homology to other organismsh Protection HP0010 HP0011 HP0027 HP0072 HP0073 HP0109 HP0115 HP0153 HP0154 HP0175 groEL groES icd ureB ureA dnaK flaB...”
• Identification of immunodominant antigens from Helicobacter pylori and evaluation of their reactivities with sera from patients with different gastroduodenal pathologies
  Kimmel, Infection and immunity 2000
  • “...HP no. MW (103) pI HP0243 HP0011 HP1563 HP1293 HP0027 HP0318 HP0177 HP0153 HP1555 HP1110 HP0649 HP0601 HP0109 HP0795 HP0752 HP0072 HP1125 HP1205 HP0010 HP1199...”
• Metabolism and genetics of Helicobacter pylori: the genome era
  Marais, Microbiology and molecular biology reviews : MMBR 1999
  • “...HP0026), aconitase (acnB, HP0779), isocitrate dehydrogenase (icd, HP0027), fumarase (fumC, HP1325), and fumarate reductase (frdABC, HP0191 to HP0193) and the...”
• More

Q9ZN36 Isocitrate dehydrogenase [NADP] from Helicobacter pylori (strain J99 / ATCC 700824)
jhp0023 ISOCITRATE DEHYDROGENASE from Helicobacter pylori J99
68% identity, 97% coverage

• Protein signature characterizing Helicobacter pylori strains of patients with autoimmune atrophic gastritis, duodenal ulcer and gastric cancer
  De, Infectious agents and cancer 2017
  • “...22335/5.9 P21762 Probable peroxiredoxin, tsaA H. pylori 48 56% 0.02 MALDI-TOF DU 1.75 271 47660/6.7 Q9ZN36 Isocitrate dehydrogenase, icd H. pylori J99 70 30% 1.76E-03 MALDI-TOF DU 1.75 270 47660/6.7 Q9ZN36 Isocitrate dehydrogenase, icd H. pylori J99 49 8% 1.76E-05 MALDI-TOF DU 1.69 253 12018/5.16 THIO...”
• Complexomics study of two Helicobacter pylori strains of two pathological origins: potential targets for vaccine development and new insight in bacteria metabolism
  Bernarde, Molecular & cellular proteomics : MCP 2010
  • “...20.3 % Cov. LC-MS/MS information JHP0341 JHP0251 JHP0023 JHP1290 JHP0068 JHP0181 JHP0216 JHP0573 JHP0791 JHP1030 JHP1004 JHP0180 JHP0161 JHP0161 JHP0551 JHP0992...”
  • “...JHP0631 DnaK HemE JHP0632 JHP0633 JHP0631 JHP0295 JHP1290 JHP0023 JHP0508 RfaD FabG SodB, SodF JHP1035 PorG JHP0101 JHP0551 JHP1140 JHP1140 PurD PurD JHP0432...”

DR1540, DR_1540 isocitrate dehydrogenase from Deinococcus radiodurans R1
Q9RU54 Isocitrate dehydrogenase [NADP] from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)
66% identity, 97% coverage

• Proteometabolomic response of Deinococcus radiodurans exposed to UVC and vacuum conditions: Initial studies prior to the Tanpopo space mission
  Ott, PloS one 2017
  • “...all part of the TCA cycle, are citrate synthase (gltA), aconitate hydratase (acn), isocitrate dehydrogenase (DR_1540), 2-oxoglutarate dehydrogenase (sucA), dihydrolipoamide succinyltransferase (DR_0083), succinate-CoA ligase (sucC), succinyl-CoA synthetase (sdhB), fumarate hydratase (fumC) and malate dehydrogenase (mdh). 10.1371/journal.pone.0189381.g007 Fig 7 Main components of the TCA cycle in Deinococcus...”
• Characteristics of dr1790 disruptant and its functional analysis in Deinococcus radiodurans
  Cheng, Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] 2015
  • “...2-DE analysis. Protein spot Locus Length (aa) Functional category Expression ratio, mutant 1790/WT (fold) 1 DR1540 430 Isocitrate dehydrogenase (IDH) 0.05 2 DR2013 268 Fructose 1,6-bisphosphatase II (FBP2) 0.09 3 DR0325 330 Malate dehydrogenase (MDH) 0.03 4 DR1512 264 Elongation factor Ts 0.09 5 DR0350 571...”
• Genome-wide transcriptome and antioxidant analyses on gamma-irradiated phases of deinococcus radiodurans R1
  Luan, PloS one 2014
  • “...down-regulated genes was 72 and 77, respectively. As shown in Figure 5 , the genes DR_1540 ( icd ), DR_0757 ( gltA ), and DR_0953 ( shhC ) involved in the TCA pathway were significantly repressed during irradiation and recovery, consistent with the report of Liu,...”
• Oxidative stress resistance in Deinococcus radiodurans
  Slade, Microbiology and molecular biology reviews : MMBR 2011
  • “...Malate synthase (GlcB) Isocitrate lyase (AceA) DR0757 DR1720 DR1540 DR0287 DR0083 DR1247 DR1248 DR0700 DR0701 DR0698 DR0702 DR0697 DR0699 DR0695 DR0696 Sulfur...”
• Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation
  Liu, Proceedings of the National Academy of Sciences of the United States of America 2003
  • “...(DR0083)] are substantially down-regulated like icd (DR1540). Malate synthase (DRA0277) of the glyoxylate bypass is slightly down-regulated. Four...”
• Predicted highly expressed and putative alien genes of Deinococcus radiodurans and implications for resistance to ionizing radiation damage
  Karlin, Proceedings of the National Academy of Sciences of the United States of America 2001
  • “...421 304 489 303 1.66 1.47 1.36 1.29 1.05 DR1720 DR0828 DR1540 DR0325 DR1247 DR0287 DR2627 DR1248 DR1674 DR0757 DR0083 905 463 430 329 385 955 812 300 332 410...”
• iTRAQ-based proteomic analysis of Deinococcus radiodurans in response to ¹²C⁶⁺ heavy ion irradiation
  Gao, BMC microbiology 2022
  • “...(SsB), involved in DNA repair. Group 5 includes proteins Q9RTU7 (Oligopeptidase A), Q9RUP1 (Glyceraldehyde-3-phosphate dehydrogenase), Q9RU54 (Isocitrate dehydrogenase), Q9RTN7 (Aconitate hydratase A), and Q9RR60 (Enolase), which are enzymes involved in either peptide or energy metabolism. The last one protein is Q9RWM2, an uncharacterized protein. The consistent...”

Dgeo_1166 isocitrate/isopropylmalate dehydrogenase from Deinococcus geothermalis DSM 11300
66% identity, 99% coverage

• Physiology of resistant Deinococcus geothermalis bacterium aerobically cultivated in low-manganese medium
  Liedert, Journal of bacteriology 2012
  • “...metabolism via this pathway. Conversely, isocitrate dehydrogenase (Dgeo_1166, #64) was upregulated (Fig. 3). According to the bioinformatic portal UniprotKB...”

YP_092619 Icd from Bacillus licheniformis DSM 13
63% identity, 94% coverage

• Induction of osmoadaptive mechanisms and modulation of cellular physiology help Bacillus licheniformis strain SSA 61 adapt to salt stress
  Paul, Current microbiology 2015
  • “...520 35,863/5.11 39 YP_080753 6 Isocitrate dehydrogenase [ Bacillus licheniformis ATCC 14580] 324 48,027/5.05 23 YP_092619 6 Phosphopyruvate hydratase [ Bacillus licheniformis ATCC 14580] 1025 46,610/4.67 55 YP_080749 10 Chaperonin GroEL [ Bacillus licheniformis ATCC 14580] 1450 57,534/4.71 53 YP_077851 10 Molecular chaperone DnaK [ Bacillus...”

N007_05885 NADP-dependent isocitrate dehydrogenase from Alicyclobacillus acidoterrestris ATCC 49025
65% identity, 95% coverage

• Transcriptome-Based Selection and Validation of Reference Genes for Gene Expression Analysis of Alicyclobacillus acidoterrestris Under Acid Stress
  Zhao, Frontiers in microbiology 2021
  • “...F: GTCGGGTTCCCTTGTAGT 138 R: CAAATGCGGTGTATGGTT N007_09410 Lactate utilization protein lldF F: CCATGATTACCGGCCCAAAG 158 R: CGGGCAGACGTTTAGACAAG N007_05885 Isocitrate dehydrogenase icd F: TCACCTTGTCTAAATTCGCA 202 R: CAGCAAATTCTTACACGTCC N007_06870 4-Hydroxy-tetrahydrodipicolinate synthase dapA F: GGCTGACCAATCAACTCCA 286 R: TTACTCAAATCTCCCACATCG N007_09120 16S Ribosomal RNA 16s rRNA F: GCATGAAGCCGGAATTGCTA 126 R: AACGGTTACCTCACCGACTT N007_07600 Transcriptional...”

GYA98_RS12235 NADP-dependent isocitrate dehydrogenase from Bacillus velezensis
64% identity, 97% coverage

• Comparative transcriptome analysis reveals the biocontrol mechanism of Bacillus velezensis E68 against Fusarium graminearum DAOMC 180378, the causal agent of Fusarium head blight
  Liang, PloS one 2023
  • “...the enzymes of the TCA cycle: 2 citrate synthases (GYA98_RS03820, 12240), aconitase (GYA98_RS08030), isocitrate dehydrogenase (GYA98_RS12235), 2-oxoglutarate dehydrogenase (GYA98_RS08685, 08690), succinate dehydrogenase (GYA98_RS11900, 11905), succinyl-CoA ligase (GYA98_RS07090, 07095) and fumarate dehydrogenase (GYA98_RS14210), as well as a citrate/malate transporter (GYA98_RS17095) ( S2 Table ). Malate dehydrogenase (GYA98_RS12230),...”

IDH_BACSU / P39126 Isocitrate dehydrogenase [NADP]; IDH; IDP; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 from Bacillus subtilis (strain 168) (see 2 papers)
icd / GB|CAB14873.1 isocitrate dehydrogenase; EC 1.1.1.42 from Bacillus subtilis (see 2 papers)
NP_390791 isocitrate dehydrogenase from Bacillus subtilis subsp. subtilis str. 168
63% identity, 97% coverage

• function: Catalyzes the oxidative decarboxylation of isocitrate to 2- oxoglutarate and carbon dioxide with the concomitant reduction of NADP(+).
  catalytic activity: D-threo-isocitrate + NADP(+) = 2-oxoglutarate + CO2 + NADPH (RHEA:19629)
  cofactor: Mg(2+) Mn(2+) (Binds 1 Mg(2+) or Mn(2+) ion per subunit.)
  subunit: Homodimer.
• Interaction of enzymes of the tricarboxylic acid cycle in Bacillus subtilis and Escherichia coli: a comparative study.
  Jung, FEMS microbiology letters 2018 (PubMed)
  • GeneRIF: In B. subtilis, the genes encoding citrate synthase, isocitrate dehydrogenase and malate dehydrogenase form an operon (citZ-icd-mdh) and predominantly are co-transcribed from a single promoter.
• Prediction of prkC-mediated protein serine/threonine phosphorylation sites for bacteria
  Zhang, PloS one 2018
  • “...Bacillus subtilis 20389117 P12425 207 glnA Bacillus subtilis 20389117 P12425 286 glnA Bacillus subtilis 20389117 P39126 138 icd Bacillus subtilis 20389117 P39126 147 icd Bacillus subtilis 20389117 P39126 396 icd Bacillus subtilis 20389117 Q04777 88 alsD Bacillus subtilis 20389117 P08877 12 ptsH Bacillus subtilis 20389117 O34530...”
• Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi.
  Islam, Microbial biotechnology 2016
  • “...O29610 ), C .noboribetus ( P96318 ), S .aureus ( P99167 ), B .subtilis ( P39126 ), E .coli ( P08200 ), C .maris ( P41560 ), B .taurus ( P41563 ) and H .sapiens ( P50213 ). 2015 Society for Applied Microbiology and John Wiley...”
• Correction: Comprehensive Analysis of Temporal Alterations in Cellular Proteome of Bacillus subtilis under Curcumin Treatment
  Reddy, PloS one 2015
  • “...3.869 6.546 P09339 Aconitate hydratase CitB 33.22 25 1.14 3.94 4.56 12 1.449 4.064 3.887 P39126 Isocitrate dehydrogenase [NADP] Icd 44.21 20 1.10 3.06 3.53 9 1.003 3.302 2.885 P23129 2-oxoglutarate dehydrogenase E1 component OdhA 35.28 27 1.37 2.90 1.96 14 1.113 1.911 1.634 P16263 Dihydrolipoyllysine-residue...”
• Proteomics analyses of Bacillus subtilis after treatment with plumbagin, a plant-derived naphthoquinone
  Reddy, Omics : a journal of integrative biology 2015
  • “...subunit alpha P08066 Succinate dehydrogenase iron-sulfur subunit P39126 Isocitrate dehydrogenase [NADP] OS P09339 Aconitate hydratase OS P39120 Citrate synthase...”
• Comprehensive analysis of temporal alterations in cellular proteome of Bacillus subtilis under curcumin treatment
  Reddy, PloS one 2015
  • “...3.706 8.131 P09339 Aconitate hydratase CitB 33.22 25 1.14 3.94 4.56 12 2.032 4.297 4.724 P39126 Isocitrate dehydrogenase [NADP] Icd 44.21 20 1.10 3.06 3.53 9 2.008 2.694 3.139 P23129 2-oxoglutarate dehydrogenase E1 component OdhA 35.28 27 1.37 2.90 1.96 14 1.286 2.223 1.744 P16263 Dihydrolipoyllysine-residue...”
• Induced fit and the catalytic mechanism of isocitrate dehydrogenase
  Gonçalves, Biochemistry 2012
  • “..., ICT, NADP + 1kd:B 0.99 1.33 ICT, NADP + Bacillus subtilis Strain 168 (UNIPROT P39126), 65.0% identity 1hqs:A 72 1.55 2001 1.08 0.95 ICT 1hqs:B 1.22 0.70 ICT Rmsd-1 is calculated between C -atoms of matched residues at best 3D superposition of the query 4aj3...”
• A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: an application study
  Albaum, Proteome science 2011
  • “...regarded significant by the Kruskal-Wallis test, but not by the ANOVA after p -value adjustment. P39126, a NADP-dependent dehydrogenase, is not showing any clearly distinguishable and significant pattern of expression. A reason therefore might be a high biological variance but, of course, also technical errors in...”

Pcar_1038 isocitrate dehydrogenase, NADP-dependent from Pelobacter carbinolicus str. DSM 2380
59% identity, 90% coverage

• Evolution from a respiratory ancestor to fill syntrophic and fermentative niches: comparative fenomics of six Geobacteraceae species
  Butler, BMC genomics 2009
  • “...cell [ 25 ]. Instead, the Pelobacter species contained non-orthologous isocitrate dehydrogenase genes (Ppro_0452 and Pcar_1038 in cluster 3107) of the more common, homodimeric type [ 25 ]. In addition, both Pelobacter species lacked the dehydrogenase (GSU0509GSU0510) believed to transfer the electrons from NADPH into the...”

BAS4487 isocitrate dehydrogenase, NADP-dependent from Bacillus anthracis str. Sterne
64% identity, 94% coverage

• Unveiling the novel dual specificity protein kinases in Bacillus anthracis: identification of the first prokaryotic dual specificity tyrosine phosphorylation-regulated kinase (DYRK)-like kinase
  Arora, The Journal of biological chemistry 2012
  • “...PrkG among multiple probable substrates (Ef-Tu, Ef-G, SsbA, Bas4487, and Bas1176) using the same strategy. PknG of Corynebacterium glutamicum is known to...”

W8Y9G2 Isocitrate dehydrogenase [NADP] from Bacillus thuringiensis DB27
BC4593 Isocitrate dehydrogenase [NADP] from Bacillus cereus ATCC 14579
64% identity, 95% coverage

• Role of hsp20 in the Production of Spores and Insecticidal Crystal Proteins in Bacillus thuringiensis
  Xie, Frontiers in microbiology 2019
  • “...0.47 mdh Malate dehydrogenase W8Y6I8 0.46 citB Aconitate hydratase A W8Y5Y6 0.46 thiM Hydroxyethylthiazole kinase W8Y9G2 0.46 icd Isocitrate dehydrogenase [NADP] W8Y7A6 0.46 sucD Succinate CoA ligase [ADP-forming] subunit alpha W8YK96 0.45 metG Methionine tRNA ligase W8Y8A7 0.45 ndk Nucleoside diphosphate kinase W8Z497 0.44 pdhC Dihydrolipoyllysine-residue...”
• Assessment of CcpA-mediated catabolite control of gene expression in Bacillus cereus ATCC 14579
  van, BMC microbiology 2008
  • “...cycle citZ 1 Citrate synthase BC4594 RZC01265 3.76 2.23 1 citC 2 Isocitrate dehydrogenase [NADP] BC4593 RZC01263 5.56 4.38 1 mdh 3 Malate dehydrogenase BC4592 RZC01264 5.81 4.32 + citB Aconitate hydratase BC3616 RZC04993 1.62 1.26 1 odhA 1 Oxoglutarate dehydrogenase BC1252 RZC06639 2.07 3.80 4...”

UH47_10560 NADP-dependent isocitrate dehydrogenase from Staphylococcus pseudintermedius
62% identity, 97% coverage

• Carprofen-induced depletion of proton motive force reverses TetK-mediated doxycycline resistance in methicillin-resistant Staphylococcus pseudintermedius
  Magnowska, Scientific reports 2019
  • “...2-oxoglutarate dehydrogenase sucA 1.3 1.9 TCA cycle UH47_10555 citrate synthase gltA 2 3.1 TCA cycle UH47_10560 isocitrate dehydrogenase icd 2 3.4 TCA cycle UH47_11305 fumarate hydratase fum 1.1 1.9 TCA cycle UH47_05755 succinate dehydrogenase sdhC 1 2.1 TCA cycle/electron transport Respiration UH47_10780 ATP synthase F0F1 subunit...”

SAPIG1748 NADP-dependent isocitrate dehydrogenase from Staphylococcus aureus subsp. aureus ST398
62% identity, 97% coverage

• Methicillin-resistant Staphylococcus aureus from infections in horses in Germany are frequent colonizers of veterinarians but rare among MRSA from infections in humans
  Cuny, One health (Amsterdam, Netherlands) 2016
  • “...by Price et al. [39] , we identified a further canSNP in position 1837869 in SAPIG1748 (AM990992.1, [40] ), which can be easily identified by ordinary PCR and use of degenerated forward primers (SNP at the very 3end, degenerated nucleotide in the second last position in...”
  • “...n=1). All of these 158 isolates were subjected to PCR for the can SNP in SAPIG1748; 143 isolates were attributed to non-equine LA-MRSA CC398, and 15 isolates were attributed to the equine clinic subpopulation. Of the latter ones 4 originated from blood cultutres. The characteristics of...”
• Genome-wide high-throughput screening to investigate essential genes involved in methicillin-resistant Staphylococcus aureus Sequence Type 398 survival
  Christiansen, PloS one 2014
  • “...SAPIG0142 726.16 1.10 9.3631 0.0024 SAPIG1650 492.68 1.10 8.8088 0.0128 SAPIG1041 799.62 2.20 8.5048 0.0025 SAPIG1748 352.17 1.10 8.3244 0.0249 SAPIG1921 306.01 1.10 8.1163 0.0430 SAPIG0315 605.24 2.21 8.1003 0.0090 SAPIG2670 256.41 1.10 7.8613 0.0406 SAPIG2057 469.89 2.21 7.7351 0.0203 SAPIG1726 853.28 4.40 7.5998 0.0038 SAPIG1977...”
  • “...2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylic acid synthase/2-oxoglutarate decarboxylase Menaquinone biosynthetic pathway Respiration. Involved in protection against haem toxicity SAPIG1748 (icd) Isocitrate dehydrogenase (IDH), NADP-dependent (icd gene) Regulation of tricarboxylic acid (TCA) cycle Icd up-regulation under acidic conditions. Regulation of the TCA cycle. SAPIG1921 RNA methyltransferase, TrmH family, group 2...”

SAUSA300_1640 isocitrate dehydrogenase, NADP-dependent from Staphylococcus aureus subsp. aureus USA300_FPR3757
P99167 Isocitrate dehydrogenase [NADP] from Staphylococcus aureus (strain N315)
Q2FXN4 Isocitrate dehydrogenase [NADP] from Staphylococcus aureus (strain NCTC 8325 / PS 47)
SA1517 isocitrate dehydrogenase from Staphylococcus aureus subsp. aureus N315
SAV1694 isocitrate dehydrogenase from Staphylococcus aureus subsp. aureus Mu50
SAOUHSC_01801 isocitrate dehydrogenase, NADP-dependent from Staphylococcus aureus subsp. aureus NCTC 8325
SACOL1741 isocitrate dehydrogenase, NADP-dependent from Staphylococcus aureus subsp. aureus COL
62% identity, 97% coverage

• Human Urine Alters Methicillin-Resistant Staphylococcus aureus Virulence and Transcriptome
  Paudel, Applied and environmental microbiology 2021 (secret)
• Growth and Stress Tolerance Comprise Independent Metabolic Strategies Critical for Staphylococcus aureus Infection
  Kim, mBio 2021
  • “...994 + + + + SAUSA300_1015 ctaA 40580 **** 19354 1011 + + + + SAUSA300_1640 icd 10691 6940 8423 + + + + SAUSA300_1641 gltA 183127 16451 983 + + + + SAUSA300_2067 glyA 137106 9756 987 + + + + 3,250 1,309 ** 267,500...”
  • “...105.8414.60 45.6122.26 10.38 **** SAUSA300_1138 sucC TCA 9.34 0.910.03 3.29 96.7519.34 106.6639.93 22.220.98 * 0.530.10 SAUSA300_1640 icd 5.75 1.060.03 **** 3.25 109.2535.93 105.3740.85 40.678.63 0.840.29 ** SAUSA300_1641 gltA 7.5 1.090.03 ** 3.23 108.524.61 119.6325.29 35.076.38 0.60.21 SAUSA300_1246 acnA 4.8 1.020.04 2.51 77.0834.94 * 85.6320.98 29.829.97 0.760.31...”
• Novel Regulation of Alpha-Toxin and the Phenol-Soluble Modulins by Peptidyl-Prolyl cis/trans Isomerase Enzymes in Staphylococcus aureus
  Keogh, Toxins 2019
  • “...SAUSA300_0492 FolP 0.47 Biosynthesis of cofactors, prosthetic groups, and carriers SAUSA300_2076 0.46 Central intermediary metabolism SAUSA300_1640 Icd 0.46 Energy metabolism SAUSA300_0841 0.46 Conserved hypothetical protein SAUSA300_2197 RplP 0.45 Protein synthesis SAUSA300_1443 RluB 0.45 Protein synthesis SAUSA300_1159 NusA 0.45 Transcription SAUSA300_1530 YbeY 0.44 Conserved hypothetical protein SAUSA300_0820...”
• Enzymes Catalyzing the TCA- and Urea Cycle Influence the Matrix Composition of Biofilms Formed by Methicillin-Resistant Staphylococcus aureus USA300
  De, Microorganisms 2018
  • “...NE491 (NR-47034) JE2 Tn mutant (insertion position: 1799416) in isocitrate dehydrogenase, NADP-dependent ( icd , SAUSA300_1640; 1798291-1799559). NARSA repository NE569 JE2 Tn mutant (insertion position: 1247122) in succinyl-CoA synthetase, beta subunit ( sucC , SAUSA300_1138; 1246832-1247998). NARSA repository NE594 (NR-47137) JE2 Tn mutant (insertion position: 1800430)...”
• Heparin Mimics Extracellular DNA in Binding to Cell Surface-Localized Proteins and Promoting Staphylococcus aureus Biofilm Formation
  Mishra, mSphere 2017
  • “...SAUSA300_0532 Elongation factor G 15 16 32 IKKNKG|SRRGRVGRIHKI SAUSA300_1201 Glutamine synthetase 10 9 16 ARKHNLHA SAUSA300_1640 Isocitrate dehydrogenase 5 7 18 None SAUSA300_2362 2,3-Bisphosphoglycerate-dependent phosphoglycerate mutase 8 20 52 None SAUSA300_0536 Molecular chaperone Hsp31 10 13 31 None SAUSA300_1138 Succinyl-CoA synthetase, beta subunit 11 7 18...”
• Reversible antibiotic tolerance induced in Staphylococcus aureus by concurrent drug exposure
  Haaber, mBio 2015
  • “...tetR Intercellular adhesion operon transcription regulator (IcaR) 1.67 Metabolism SAUSA300_0684 fruB Fructose 1-phosphate kinase 3.01 SAUSA300_1640 icd ( citC ) Isocitrate dehydrogenase 2.97 SAUSA300_1641 gltA Citrate synthetase 3.75 SAUSA300_2319 Pyridine nucelotide-disulfide oxidoreductase 6.26 SAUSA300_2377 Glycerate kinase 3.64 Transport SAUSA300_1790 prsA Foldase protein PrsA 2.52 SAUSA300_2630 nixA...”
• Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi.
  Islam, Microbial biotechnology 2016
  • “...rot) are: A .fulgidus ( O29610 ), C .noboribetus ( P96318 ), S .aureus ( P99167 ), B .subtilis ( P39126 ), E .coli ( P08200 ), C .maris ( P41560 ), B .taurus ( P41563 ) and H .sapiens ( P50213 ). 2015 Society for...”
• Integrated Multi-omics, Virtual Screening and Molecular Docking Analysis of Methicillin-Resistant Staphylococcus aureus USA300 for the Identification of Potential Therapeutic Targets: An In-Silico Approach
  Rahman, International journal of peptide research and therapeutics 2021
  • “...reductase subunit alpha (nrdA) 46 Q2FY51 Dihydrolipoyl dehydrogenase 20 Q2G077 Ribonucleoside-diphosphate reductase subunit (nrdF) 47 Q2FXN4 NADP-dependent isocitrate dehydrogenase 21 A8Z002 Ribonucleotide-diphosphate reductase subunit gamma (nrdI) 48 Q2FE05 UTPglucose-1-phosphate uridylyltransferase (gtaB) 22 Q2G0W2 NADH dehydrogenase subunit 5 49 P64126 Ferrochelatase (cpfC) 23 Q2FYS4 DNA topoisomerase IV...”
• Borosilicate bioactive glass synergizing low-dose antibiotic loaded implants to combat bacteria through ATP disruption and oxidative stress to sequentially achieve osseointegration
  Fan, Bioactive materials 2025
  • “...was synchronously downregulated in the B/PMMA group. Additionally, NAD binding-related genes, for example, MMP0706 , SA1517 , MW1630 , in S. aureus were also inhibited in the B/G/PMMA group, indicating a synergistic inhibition of ATP synthesis between 30wt% BSG and 1wt% GS. In the ATP testing,...”
• Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism
  Bohn, Nucleic acids research 2010
  • “...Hypothetical Mn 2+ and Fe 2+ transporter SA1434 0.43 AcetylCoA carboxylase SA1435 0.45 AcetylCoA carboxylase SA1517 ( citC ) 0.40 Isocitrate dehydrogenase SA1518 ( citZ ) 0.37 0.48 14.80 Methylcitrate synthase SA1553 ( fhs ) 0.30 f 14.08 Formatetetrahydrofolate ligase SA1858 ( ilvD ) 3.45 1.90...”
• An RpoB mutation confers dual heteroresistance to daptomycin and vancomycin in Staphylococcus aureus
  Cui, Antimicrobial agents and chemotherapy 2010
  • “...SA1088 SA1089 SA1131 SA1132 SA1184 SA1244 SA1245 SA1349 SA1517 SA1518 SA1609 sdhC sdhA sdhB sucC sucD Cell envelope and cellular processes SA0111 SA0126 SA0127...”
• Transcriptome analysis of the responses of Staphylococcus aureus to antimicrobial peptides and characterization of the roles of vraDE and vraSR in antimicrobial resistance
  Pietiäinen, BMC genomics 2009
  • “...SA1254 3.1 3.5 VraSR, VCM Hypothetical protein SA1476 4.2 5.3 3.3 VraSR, VCM Hypothetical protein SA1517 citC 4.9 5.8 3.1 VCM Isocitrate dehydrogenase SA1545 serA 4.6 2.5 VCM Similar to soluble hydrogenase 42 kD subunit SA1549 htrA 2.9 3.0 2.0 VraSR, VCM Similar to serine proteinase...”
• Transcriptome and functional analysis of the eukaryotic-type serine/threonine kinase PknB in Staphylococcus aureus
  Donat, Journal of bacteriology 2009
  • “...Gene SA0995 SA0996 SA1088 SA1089 SA1141 SA1142 SA1184 SA1517 SA1553 SA1554 SA1609 SA1669 SA1679 SA1927 SA2155 SA2304 SAS020 sdhA sdhB sucC sucD glpK glpD...”
• Reporter metabolite analysis of transcriptional profiles of a Staphylococcus aureus strain with normal phenotype and its isogenic hemB mutant displaying the small-colony-variant phenotype
  Seggewiss, Journal of bacteriology 2006
  • “...group and ORF (N315) SA0654 SA1517 Description hypothetical hypothetical hypothetical hypothetical hypothetical hypothetical hypothetical protein protein...”
  • “...(citB, SA1184, 0.34-fold), isocitrate dehydrogenase (citC, SA1517, 0.39-fold), and citrate synthase (citZ, SA1518, 0.42-fold). In addition, intermediate...”
• Transcription profiling-based identification of Staphylococcus aureus genes regulated by the agr and/or sarA loci
  Dunman, Journal of bacteriology 2001
  • “...SA0537 SA2438 SA1138 SA0411 SA2341 SA2240 SA0253 SA0923 SA1517 SA1961 SA2424 SA0187 SA1140 SA2293 SA0186 SA0021 SA0212 SA0271 SA0363 SA0412 SA1618 SA1937 SA2378...”
• The SAV1322 gene from Staphylococcus aureus: genomic and proteomic approaches to identification and characterization of gene function
  Kim, BMC microbiology 2016
  • “...Down A277 gi|15924841 Fumarate hydratase 601 fumC SAV1851 Down A043 gi|15924684 Isocitrate dehydrogenase 845 citC SAV1694 Down A286 gi|15924412 Glucose-specific enzyme II, PTS system A component 297 crr SAV1422 Down A287 gi|15924701 Acetate kinase 750 ackA SAV1711 Up Energy metabolism A029 gi|15925597 Malate:quinone oxidoreductase 1353 mqo2...”
• Increased mutability of Staphylococci in biofilms as a consequence of oxidative stress
  Ryder, PloS one 2012
  • “...SAOUHSC_01685 hrcA Heat-inducible transcription repressor HrcA 2.84 up SAOUHSC_01720 Putative Holliday junction resolvase 2.00 up SAOUHSC_01801 icd Isocitrate dehydrogenase 2.26 up SAOUHSC_01880 Transposase domain protein 3.32 down SAOUHSC_02261 agrB Accessory gene regulator protein B 2.76 up SAOUHSC_02262 agrD Accessory gene regulator protein D 3.56 up SAOUHSC_02264...”
• Advantage of upregulation of succinate dehydrogenase in Staphylococcus aureus biofilms
  Gaupp, Journal of bacteriology 2010
  • “...(SAOUHSC_01347); CitC, isocitrate dehyrogenase (SAOUHSC_01801); OdhA/ Kgd, 2-oxoglutarate dehydrogenase E1 component/alpha-ketoglutarate decarboxylase...”
• Global analysis of the Staphylococcus aureus response to mupirocin
  Reiss, Antimicrobial agents and chemotherapy 2012
  • “...Fhs SACOL2737 SACOL1321 SACOL2105 SACOL1371 SACOL0005 SACOL0825 SACOL1271 SACOL1741 SACOL0428 GidA GlpD GlyA GuaC GyrB HprK HslU Icd MetE 0.66 1.19 0.47 1.20...”
• The Staphylococcus aureus LytSR two-component regulatory system affects biofilm formation
  Sharma-Kuinkel, Journal of bacteriology 2009
  • “...2017 by University of California, Berkeley SACOL1741 SACOL1449 SACOL1448 SACOL1262 SACOL1782 SACOL2198 SACOL2199 SACOL2553 SACOL2146 SACOL2149 SACOL0175...”
• Complete and SOS-mediated response of Staphylococcus aureus to the antibiotic ciprofloxacin
  Cirz, Journal of bacteriology 2007
  • “...SACOL1160 SACOL1262 SACOL1263 SACOL1385 SACOL1448 SACOL1449 SACOL1741 SACOL1908 SACOL2424 SACOL2426 SACOL2427 SACOL2428 Gene S. AUREUS SOS RESPONSE VOL....”

SAS1622 isocitrate dehydrogenase from Staphylococcus aureus subsp. aureus MSSA476
62% identity, 97% coverage

• Exposure of clinical MRSA heterogeneous strains to β-lactams redirects metabolism to optimize energy production through the TCA cycle
  Keaton, PloS one 2013
  • “...lysine degradation. SA1518 citZ 8.9 citrate synthase Catalyzes the first step in the TCA cycle. SAS1622 citC 11 isocitrate dehydro-genase Involved in the TCA cycle (converts isocitrate to alpha ketoglutarate). SAR1942 citG 2.5 fumarate hydratase, class-II Involved in the TCA cycle (converts (S)-malate to fumarate and...”
  • “...synthase ( citZ , SA1518), aconitate hydratase ( citB , SA11884), isocitrate dehydrogenase ( citC, SAS1622), and a subunit of -ketoglutarate dehydrogenase ( odhB , SA1244). Another gene related to the TCA cycle also found to be up-regulated was acsA (SA1554); this gene codes for the...”

Q5HNL1 Isocitrate dehydrogenase [NADP] from Staphylococcus epidermidis (strain ATCC 35984 / DSM 28319 / BCRC 17069 / CCUG 31568 / BM 3577 / RP62A)
Q8CNX4 Isocitrate dehydrogenase [NADP] from Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200)
62% identity, 97% coverage

• Proteomic Analysis Reveals a Biofilm-Like Behavior of Planktonic Aggregates of Staphylococcus epidermidis Grown Under Environmental Pressure/Stress
  Bottagisio, Frontiers in microbiology 2019
  • “...) (0.0088) LDH_STAEQ Q5HL31 L-lactate dehydrogenase 34.10/34.14 33 68 10/48 (HDMS E ) (0.0053) IDH_STAEQ Q5HNL1 Isocitrate dehydrogenase 46.62/46.64 37 120 16/74 (HDMS E ) (0.0283) a Estimated molecular weight/molecular weight (EMW/MW) expressed in kDa. b Data referring to sequence coverage are expressed as percentage. c...”
• The Extracellular Vesicles from the Commensal Staphylococcus Epidermidis ATCC12228 Strain Regulate Skin Inflammation in the Imiquimod-Induced Psoriasis Murine Model
  Gómez-Chávez, International journal of molecular sciences 2021
  • “...Q8CSL9 COG0508 odhB Dihydrolipoyllysine-residue succinyltransferase C Q8CPH5 COG0045 sucC Succinyl-CoA ligase (ADP-forming) subunit beta C Q8CNX4 COG0538 Icd Isocitrate dehydrogenase (NADP) C Q8CP83 COG0567 odhA 2-Oxoglutarate dehydrogenase E1 component C Q8CPL2 COG1053 sdhA Succinate dehydrogenase flavoprotein subunit C Q8CQA3 COG1249 lpdA Dihydrolipoyl dehydrogenase C Q8CT13 COG0508...”

SXYL_01173 NADP-dependent isocitrate dehydrogenase from Staphylococcus xylosus
61% identity, 97% coverage

• Transcriptomic Analysis of Staphylococcus xylosus in Solid Dairy Matrix Reveals an Aerobic Lifestyle Adapted to Rind
  Leroy, Microorganisms 2020
  • “...system 2.6 * SXYL_01012 fumC Fumarate hydratase class II 2.2 2.7 SXYL_01172 Citrate synthase 2.1 SXYL_01173 icd Isocitrate dehydrogenase [NADP] 2.1 SXYL_01821 pyc Pyruvate carboxylase 0.5 0.3 SXYL_01534 acnA Aconitate hydratase 3.1 2.5 SXYL_00218 gabD Succinate-semialdehyde dehydrogenase 2.2 SXYL_01849-50 cydBA Cytochrome bd-type quinol oxidase 3.3 *...”

Q6GG12 Isocitrate dehydrogenase [NADP] from Staphylococcus aureus (strain MRSA252)
62% identity, 97% coverage

• Antibacterial Activity and Multi-Targeted Mechanism of Action of Suberanilic Acid Isolated from Pestalotiopsis trachycarpicola DCL44: An Endophytic Fungi from Ageratina adenophora
  Wen, Molecules (Basel, Switzerland) 2024
  • “...Up 0.000545771 A0A033V2M2 pfkA ATP-dependent 6-phosphofructokinase 0.828 Down 0.020923953 P64225 gcvT Aminomethyltransferase 1.857 Up 0.000233977 Q6GG12 icd Isocitrate dehydrogenase (NADP) 2.548 Up 2.69982 10 6 Q6GFK5 fumC Fumarate hydratase class II 1.462 Up 8.04802 10 5 Q6GHI9 sucD SuccinateCoA ligase subunit alpha 1.307 Up 0.004931368 A0A8E6CNC9...”
  • “...2 Q5HGY8 pdhD 1.534 0.024147859 1.965 Consistency 3 P64225 gcvT 1.857 0.007774184 3.685 Consistency 4 Q6GG12 icd 2.548 0.000980574 3.874 Consistency 5 Q6GFK5 fumC 1.462 0.000550982 2.589 Consistency 6 A0A0U1MI53 pdhA 1.496 0.00642461 2.194 Consistency 7 P65884 purA 0.576 0.023770336 0.390 Consistency 8 A0A2S6D4J7 glmS 0.799...”

Q8GAX0 isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) from Acidithiobacillus thiooxidans (see paper)
61% identity, 97% coverage

• Induced fit and the catalytic mechanism of isocitrate dehydrogenase.
  Gonçalves, Biochemistry 2012
  • “...2.90 2010 2.24 2.21 - 3lcb:D 55 2.90 2010 2.44 2.08 - Acidithiophilus thiooxidans (UNIPROT Q8GAX0), 60.1% identity 2d4v:A 56 1.90 2008 0.81 1.36 Citrate, NAD + 2d4v:B 0.87 1.37 Citrate, NAD + 2d4v:C 0.77 1.30 Citrate, NAD + 2d4v:D 0.76 1.38 Citrate, NAD + Burkholderia...”

2d4vA / Q8GAX0 Crystal structure of NAD dependent isocitrate dehydrogenase from acidithiobacillus thiooxidans (see paper)
61% identity, 97% coverage

• Ligands: citrate anion; nicotinamide-adenine-dinucleotide (2d4vA)

MXAN_3537 isocitrate dehydrogenase, NADP-dependent from Myxococcus xanthus DK 1622
62% identity, 95% coverage

• Global transcriptome analysis of spore formation in Myxococcus xanthus reveals a locus necessary for cell differentiation
  Müller, BMC genomics 2010
  • “...is in contrast to the observed down regulation of the corresponding gene ( icd ; Mxan_3537). This inconsistency may be caused by post-translational regulation of isocitrate dehydrogenase activity, likely via phosphorylation/dephosphorylation [ 32 ]. Thus, all of the examined glycerol-induced sporulation markers either displayed the predicted...”

AFE_RS02000 NADP-dependent isocitrate dehydrogenase from Acidithiobacillus ferrooxidans ATCC 23270
60% identity, 97% coverage

• Characterize the Growth and Metabolism of <i>Acidithiobacillus ferrooxidans</i> under Electroautotrophic and Chemoautotrophic Conditions
  Wang, Microorganisms 2024
  • “...Clp protease ATP-binding subunit ClpX 1.24 downhill AFE_RS14500 AFE_RS14500 FMN-binding negative transcriptional regulator 1.22 uphill AFE_RS02000 icd NADP-dependent isocitrate dehydrogenase 1.22 uphill AFE_RS14415 rus Rusticyanin 1.21 downhill/uphill AFE_RS14430 AFE_RS14430 cytochrome c oxidase subunit II 1.17 downhill AFE_RS12530 AFE_RS12530 cytochrome bc complex cytochrome b subunit 1.16 uphill...”

lmo1566 highly similar to isocitrate dehyrogenases from Listeria monocytogenes EGD-e
NP_465091 isocitrate dehydrogenase from Listeria monocytogenes EGD-e
LMRG_01401 isocitrate dehydrogenase, NADP-dependent from Listeria monocytogenes 10403S
62% identity, 94% coverage

• c-di-AMP modulates Listeria monocytogenes central metabolism to regulate growth, antibiotic resistance and osmoregulation
  Whiteley, Molecular microbiology 2017
  • “...; pycA , lmo1072 , LMRG_00534 ; citZ , lmo1567 , LMRG_01400 ; citC , lmo1566 , LMRG_01401 ; citB , lmo1641 , LMRG_01325 . L. monocytogenes strain construction Strains were constructed by standard methods ( Reniere et al. , 2016 ). Plasmids were introduced to...”
  • “...DP-L6537 transduced with lysate from DP-L6378 This study DP-L6403 citChimar Transposon mutation in citC (LMRG_01401471, lmo1566) ( Reniere et al. , 2016 ) DP-L6404 dacA-kanR citChimar1 DP-L6403 transduced with lysate from DP-L6378 This study DP-L6540 citB In frame deletion of citB ( lmo1641 ), made with...”
• An In Vivo Selection Identifies Listeria monocytogenes Genes Required to Sense the Intracellular Environment and Activate Virulence Factor Expression
  Reniere, PLoS pathogens 2016 (no snippet)
• The transcriptional response of Listeria monocytogenes during adaptation to growth on lactate and diacetate includes synergistic changes that increase fermentative acetoin production
  Stasiewicz, Applied and environmental microbiology 2011
  • “...(fliG) in the CodY gene set, lmo1246 (deaD), lmo1566 (citC), acetyl-CoA carboxylase gene (lmo1573 accD), lmo2582 (vicK) Regulatory protein genes (lmo0893 rsbV,...”
• Global transcriptional analysis of spontaneous sakacin P-resistant mutant strains of Listeria monocytogenes during growth on different sugars
  Tessema, PloS one 2011
  • “...lmo1251 regulator of the Fnr CRP family (including PrfA) 2.0 10 6 1.6 10 5 lmo1566 ( citC ) isocitrate dehyrogenases 0.7 10 3 0.7 10 3 lmo1567 ( citZ ) citrate synthase subunit II 0.8 10 5 0.8 10 4 lmo1641 aconitate hydratases 0.8 10...”
• Transcriptomic and phenotypic responses of Listeria monocytogenes strains possessing different growth efficiencies under acidic conditions
  Bowman, Applied and environmental microbiology 2010
  • “...CtsR SigB lmo1094 lmo1333, lmo1334 lmo1338, lmo1339 (glk) lmo1566 (citC) lmo1649, lmo1650 CodY lmo1670 SigB lmo1956 (fur) HrcA lmo1966, lmo1967 lmo2054, lmo2055...”
• CcpC-dependent regulation of citrate synthase gene expression in Listeria monocytogenes.
  Mittal, Journal of bacteriology 2009
  • GeneRIF: The citrate synthase (citZ) gene and isocitrate dehydrogenase (citC) gene was part of the same operon.
• c-di-AMP modulates Listeria monocytogenes central metabolism to regulate growth, antibiotic resistance and osmoregulation
  Whiteley, Molecular microbiology 2017
  • “..., lmo1072 , LMRG_00534 ; citZ , lmo1567 , LMRG_01400 ; citC , lmo1566 , LMRG_01401 ; citB , lmo1641 , LMRG_01325 . L. monocytogenes strain construction Strains were constructed by standard methods ( Reniere et al. , 2016 ). Plasmids were introduced to L. monocytogenes...”
• Identification of Listeria monocytogenes determinants required for biofilm formation
  Alonso, PloS one 2014
  • “...900.28 2 1 purL lmrg_02502 1000.21 1 1 purN lmrg_02505 1000.57 1 1 Isocitrate dehydrogenase lmrg_01401 1000.38 1 1 2-oxovalerate dehydrogenase component E1 lmrg_00823 980.35 3 2 Xanthine ribosyltransferase lmrg_01032 900.21 1 1 Aconitate hydratase lmrg_01325 920.12 1 1 Homoserine dehydrogenase lmrg_01700 840.35 1 1 Peptidoglycan...”

Ppro_0452 isocitrate dehydrogenase, NADP-dependent from Pelobacter propionicus DSM 2379
56% identity, 89% coverage

• Evolution from a respiratory ancestor to fill syntrophic and fermentative niches: comparative fenomics of six Geobacteraceae species
  Butler, BMC genomics 2009
  • “...in the cell [ 25 ]. Instead, the Pelobacter species contained non-orthologous isocitrate dehydrogenase genes (Ppro_0452 and Pcar_1038 in cluster 3107) of the more common, homodimeric type [ 25 ]. In addition, both Pelobacter species lacked the dehydrogenase (GSU0509GSU0510) believed to transfer the electrons from NADPH...”

BF638R_3568 NADP-dependent isocitrate dehydrogenase from Bacteroides fragilis 638R
59% identity, 97% coverage

• New functions of pirin proteins and a 2-ketoglutarate: Ferredoxin oxidoreductase ortholog in Bacteroides fragilis metabolism and their impact on antimicrobial susceptibility to metronidazole and amixicile
  Gough, MicrobiologyOpen 2024
  • “...Frd, fumarate reductase, FrdCAB (BF638R_44994501); FumB, fumarate hydratase class I, anaerobic (BF638R_0646); Icd, isocitrate dehydrogenase (BF638R_3568); IM, inner cytoplasmic membrane; Kor1AB, 2Ketoglutarate ferredoxin oxidoreductase (BF638R_43214322); Kor2CDAEBG, 2Ketoglutarate ferredoxin oxidoreductase (BF638R_16601665); LdhA, d Lactate dehydrogenase (BF638R_1473); Lpd1, dihydrolipoamide dehydrogenaseE3 (BF638R_0023); Lpd2, dihydrolipoamide dehydrogenaseE3 (BF638R_1634); MaeB, malate dehydrogenase...”

IDH_HALVD / D4GU92 Isocitrate dehydrogenase [NADP]; ICDH; IDH; IDP; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 from Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2) (Halobacterium volcanii) (see 2 papers)
HVO_2588 isocitrate dehydrogenase (NADP+) from Haloferax volcanii DS2
55% identity, 100% coverage

• function: Catalyzes the oxidative decarboxylation of isocitrate to 2- oxoglutarate and carbon dioxide with the concomitant reduction of NADP(+).
  catalytic activity: D-threo-isocitrate + NADP(+) = 2-oxoglutarate + CO2 + NADPH (RHEA:19629)
  cofactor: Mg(2+) Mn(2+) (Binds 1 Mg(2+) or Mn(2+) ion per subunit.)
  subunit: Homodimer.
• Cas1 and Fen1 Display Equivalent Functions During Archaeal DNA Repair
  Wörtz, Frontiers in microbiology 2022
  • “...periplasmic substrate-binding protein (probable substrate iron-III) 2.45 HVO_B0044 iucA iron transport protein A, iucA 2.43 HVO_2588 isocitrate dehydrogenase, iucD 2.28 Other HVO_1228 halocyanin domain protein (membrane), hcpE 2.92 HVO_2508 carbamoyl-phosphate synthase small subunit, carA 2.56 HVO_2361 carbamoyl-phosphate synthase large subunit, carB 2.04 HVO_B0045 daminobutyrate decarboxylase, bdb...”

icdh / CAC80860.2 NADP-isocitrate dehydrogenase from Haloferax volcanii (see paper)
55% identity, 100% coverage

DOP62_07935 NADP-dependent isocitrate dehydrogenase from Synechococcus elongatus PCC 11801
51% identity, 87% coverage

• Elevated carbon dioxide levels lead to proteome-wide alterations for optimal growth of a fast-growing cyanobacterium, Synechococcus elongatus PCC 11801
  Mehta, Scientific reports 2019
  • “...DOP62_01165 2,3-bisphosphoglycerate-independent phosphoglycerate mutase 3.870.67 5.651.7 5.660.96 Q31NZ1 DOP62_09015 Dihydrolipoyl dehydrogenase 3.451.26 2.260.33 4.061.41 Q31MH0 DOP62_07935 Isocitrate dehydrogenase [NADP] NS 0.250.04 0.340.1 P21577 DOP62_01965 6-phosphogluconate dehydrogenase, decarboxylating 0.120.03 0.080.01 0.160.02 Q31KU2 DOP62_04740 Transaldolase 0.250.03 0.220.03 NS Response to high CO 2 induced cellular stress P22880 DOP62_04920...”

Synpcc7942_1719 isocitrate dehydrogenase, NADP-dependent from Synechococcus elongatus PCC 7942
Q31MH0 Isocitrate dehydrogenase [NADP] from Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)
51% identity, 87% coverage

• Transcriptome landscape of Synechococcus elongatus PCC 7942 for nitrogen starvation responses using RNA-seq
  Choi, Scientific reports 2016
  • “...that consume or produce 2-OG were investigated, expressions of genes encoding for isocitrate dehydrogenase ( Synpcc7942_1719 ) and 2-OG decarboxylase ( Synpcc7942_1435 ) were not changed. Thus, increased levels of 2-OG must be due to high expression of the GS/GOGAT activity in nitrogen starved S. elongatus...”
• The essential gene set of a photosynthetic organism
  Rubin, Proceedings of the National Academy of Sciences of the United States of America 2015
  • “...are shown: acnB (SynPCC7942_0903), icd (SynPCC7942_1719), sdhB (SynPCC7942_1533), fumC (SynPCC7942_1007), gltA (SynPCC7942_0612), maeA (SynPCC7942_1297), and...”
• Blueprint for a minimal photoautotrophic cell: conserved and variable genes in Synechococcus elongatus PCC 7942
  Delaye, BMC genomics 2011
  • “...597 GTP-binding protein TypA 0 1 Synpcc7942_1607 518 porin; major outer membrane protein 0 1 Synpcc7942_1719 475 isocitrate dehydrogenase 0 2 Synpcc7942_1782 430 threonine synthase 0 1 Synpcc7942_1907 358 magnesium-protoporphyrin IX monomethyl ester cyclase 0 0 Synpcc7942_2091 612 NAD(P)H-quinone oxidoreductase subunit F 0 5 Synpcc7942_2093 430...”
• Elevated carbon dioxide levels lead to proteome-wide alterations for optimal growth of a fast-growing cyanobacterium, Synechococcus elongatus PCC 11801
  Mehta, Scientific reports 2019
  • “...Q31R18 DOP62_01165 2,3-bisphosphoglycerate-independent phosphoglycerate mutase 3.870.67 5.651.7 5.660.96 Q31NZ1 DOP62_09015 Dihydrolipoyl dehydrogenase 3.451.26 2.260.33 4.061.41 Q31MH0 DOP62_07935 Isocitrate dehydrogenase [NADP] NS 0.250.04 0.340.1 P21577 DOP62_01965 6-phosphogluconate dehydrogenase, decarboxylating 0.120.03 0.080.01 0.160.02 Q31KU2 DOP62_04740 Transaldolase 0.250.03 0.220.03 NS Response to high CO 2 induced cellular stress P22880...”

SSU1040 isocitrate dehydrogenase [NADP] from Streptococcus suis P1/7
58% identity, 94% coverage

• Precision Genome Engineering in Streptococcus suis Based on a Broad-Host-Range Vector and CRISPR-Cas9 Technology
  Gussak, ACS synthetic biology 2023
  • “...SSU1606 acpP 4.67 SSU1607 fabH 4.05 SSU1608 marR 3.78 SSU1609 phaB 5.05 tircarboxylic acid cycle SSU1040 Icd 2.98 SSU1041 citZ 2.92 SSU1042 acnA 2.93 glycolysis SSU0153 Plr 1.17 SSU0154 Pgk 1.28 SSU0312 Fba 1.56 SSU0483 Tpi 1.12 SSU0927 Ldh 1.34 SSU1308 bglH 1.41 SSU1309 1.54 SSU1320...”
• Characterization of the pivotal carbon metabolism of Streptococcus suis serotype 2 under ex vivo and chemically defined in vitro conditions by isotopologue profiling
  Willenborg, The Journal of biological chemistry 2015
  • “...genome data because the respective S. suis genes SSU1040 -1042 and gdh, which suggest potential biosynthesis pathways, were present in all sequenced S. suis...”

IDH_NOSS1 / P50214 Isocitrate dehydrogenase [NADP]; IDH; IDP; NADP(+)-isocitrate dehydrogenase; NADP(+)-IDH; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (see paper)
alr1827 isocitrate dehydrogenase from Nostoc sp. PCC 7120
51% identity, 87% coverage

• function: Catalyzes the oxidative decarboxylation of isocitrate to 2- oxoglutarate and carbon dioxide with the concomitant reduction of NADP(+).
  catalytic activity: D-threo-isocitrate + NADP(+) = 2-oxoglutarate + CO2 + NADPH (RHEA:19629)
  cofactor: Mg(2+) Mn(2+) (Binds 1 Mg(2+) or Mn(2+) ion per subunit (By similarity). Mn(2+) is the most effective divalent cation in vitro, but the enzyme can also use Mg(2+), Co(2+) and Ni(2+), with lower efficiency (PubMed:8169222).)
  subunit: Homodimer.
  disruption phenotype: Essential, it cannot be deleted.
• Comparative genomics analysis of NtcA regulons in cyanobacteria: regulation of nitrogen assimilation and its coupling to photosynthesis
  Su, Nucleic acids research 2005
  • “...( slr1289 ), and hetC ( alr2817 , P -value < 0.4078) and icd ( alr1827 , P -value < 0.1356) in the training set are not recovered, respectively. The predicted NtcA promoters at a score cutoff with P -value < 0.01 for each genome are...”

Q7V9S5 Isocitrate dehydrogenase [NADP] from Prochlorococcus marinus (strain SARG / CCMP1375 / SS120)
Pro1752 Isocitrate dehydrogenases from Prochlorococcus marinus str. SS120
49% identity, 88% coverage

• Quantitative Proteomics Shows Extensive Remodeling Induced by Nitrogen Limitation in Prochlorococcusmarinus SS120
  Domínguez-Martín, mSystems 2017
  • “...653.17 197.2 471.8 111 Q7VA01 GOGAT 29 27 0.05 1.37 Azaserine 10.56 2.49 15.12 3.55 Q7V9S5 ICDH 12 11 0.63 1.14 Azaserine 3.84 0.65 5.49 1.42 a ANOVA, analysis of variance. b Maximum fold change. c Culture in which the protein reached its highest level. An...”
• Glucose uptake and its effect on gene expression in prochlorococcus
  Gómez-Baena, PloS one 2008
  • “...1.8.1.4 Pro1372 Citrate synthase gltA 2.3.3.1 Pro0185 Aconitase acnB 4.2.1.3 Pro1866 Isocitrate dehydrogenase icd 1.1.1.42 Pro1752 Phosphoenolpyruvate carboxylase ppc 4.1.1.31 Pro1730 Gene codes are shown for the Prochlorococcus SS120 genome, but all of them are present in the available Prochloroccus genomes. Discussion The results presented in...”

E9B494 Isocitrate dehydrogenase [NADP] from Leishmania mexicana (strain MHOM/GT/2001/U1103)
56% identity, 94% coverage

• Identification of differentially expressed proteins from Leishmania amazonensis associated with the loss of virulence of the parasites
  Magalhães, PLoS neglected tropical diseases 2014
  • “...3(3) 5 1.00 3.26 4.40 4.49 4.49 6.96E-03 Protein folding Metabolism [53] 12 Isocitrate dehydrogenase E9B494 5.44/5.51 40/47 16(6) 28 1.00 1.71 1.76 2.51 2.51 2.41E-03 Metabolism Metabolism [54] 303 60S acidic ribosomal subunit protein E8NHJ8 5.07/5.00 33/35 26(21) 45 1.00 3.15 4.72 4.75 4.75 9.76E-05...”

A8YGS2 isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) from Microcystis aeruginosa (see paper)
49% identity, 87% coverage

slr1289 isocitrate dehydrogenase (NADP+) from Synechocystis sp. PCC 6803
50% identity, 88% coverage

• Pyruvate kinase 2 from Synechocystis sp. PCC 6803 increased substrate affinity via glucose-6-phosphate and ribose-5-phosphate for phosphoenolpyruvate consumption
  Karikomi, Plant molecular biology 2024
  • “...2021 ; de Alvarenga et al. 2020 ), isocitrate dehydrogenase (IDH encoded by icd , slr1289) (Muro-Pastor and Florencio 1992 ), malate dehydrogenase (MDH encoded by citH , sll0891) (Takeya et al. 2018 ), malic enzyme (ME encoded by me , sll0721) (Katayama et al. 2022...”
• Photoautotrophic Growth Rate Enhancement of Synechocystis sp. PCC6803 by Heterologous Production of 2-Oxoglutarate:Ferredoxin Oxidoreductase from Chlorobaculum tepidum
  Kim, Biology 2022
  • “...pQE-fd, respectively. To purify Synechocystis isocitrate dehydrogenase (Icd) in E. coli , ORF of Icd (slr1289) was PCR-amplified from the genomic DNA of Synechocystis using the primer set 5-AAAAA AGGAT CCATG TACGA AAAAC TTCAG-3 and 5-AAAAA AAAGC TTTTA ATCAT CGAAA TGACT-3, followed by digestion with Bam...”
• Patterning of the Autotrophic, Mixotrophic, and Heterotrophic Proteomes of Oxygen-Evolving Cyanobacterium Synechocystis sp. PCC 6803
  Muth-Pawlak, Frontiers in microbiology 2022
  • “...). The Glc-supplemented conditions of MT and LAH slightly enhanced the accumulation of Icd ( slr1289 ) that catalyzes the oxidative step leading to 2-OG formation, although all other components of the TCA cycle were moderately downregulated in all the carbon-rich conditions compared to ATLC (...”
• Citrate synthase from Synechocystis is a distinct class of bacterial citrate synthase
  Ito, Scientific reports 2019
  • “...1 ) 43 , 44 . Isocitrate dehydrogenase from Synechocystis 6803 (encoded by icd , slr1289) (Fig. 1 ) is specific to NADP + and generates NADPH but not NADH 45 . Additionally, malate dehydrogenase from Synechocystis 6803 (encoded by citH , sll0891) (Fig. 1 )...”
• A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism
  Sarkar, PLoS computational biology 2019
  • “...degraded in the dark TPMs. Its catabolism occurs via isocitrate dehydrogenase, encoded by the icd (slr1289) gene which has been found to be upregulated in the dark as compared to light in a diurnally cultured Synechocystis by Saha et al. [ 38 ]. Experiments with Synechocystis...”
• Finding novel relationships with integrated gene-gene association network analysis of Synechocystis sp. PCC 6803 using species-independent text-mining
  Kreula, PeerJ 2018
  • “...transhydrogenase alpha subunit slr1434 pntB pyridine nucleotide transhydrogenase beta subunit slr1843 zwf glucose 6-phosphate dehydrogenase slr1289 icdh isocitrate dehydrogenase slr1643 fnr (PetH) ferredoxin-NADP oxidoreductase ssl0020 petF ferredoxin I Iron sulfur cluster metabolism sll0088 sufR hypothetical protein (transcriptional regulator, suf ) slr0074 sufB ABC transporter subunit slr0075...”
  • “...edges): Zwf (slr1834, catalyzing the first committed step of metabolic flux into PPP) and Icd (slr1289), catalyzing the only NADP + -reducing step of the TCA-cycle. 10.7717/peerj.4806/fig-5 Figure 5 Cluster analysis with SigE (sll1689). (A) The first neighbor guilt-by-association (GBA) network using all NADPH-related key genes...”
• Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803
  Giner-Lamia, Nucleic acids research 2017
  • “...protein 874644 N , NH4 slr2002 cphA 1447927 1448046 promoter 3.121 cyanophycin synthetase 1448016 N slr1289 icd 282874 283225 promoter 3.043 isocitrate dehydrogenase (NADP+) 283033 N slr0909 2785363 2785603 intragenic 2.874 unknown protein N slr1912 615686 616010 promoter 2.874 anti-sigma F factor antagonist 615878 N ncl0540/sll1698...”
• Diurnal Regulation of Cellular Processes in the Cyanobacterium Synechocystis sp. Strain PCC 6803: Insights from Transcriptomic, Fluxomic, and Physiological Analyses
  Saha, mBio 2016
  • “...cycling behavior, even though sometimes with opposite phases. For instance, genes such as icd ( slr1289 ), encoding isocitrate dehydrogenase, and mdh ( sll0891 ), encoding malate dehydrogenase, were upregulated almost entirely during the dark period, with peaks at D1 and D11, respectively. In contrast, genes...”
• More

GAH_01703 isocitrate dehydrogenase (NADP(+)) from Geoglobus ahangari
54% identity, 100% coverage

• The complete genome sequence and emendation of the hyperthermophilic, obligate iron-reducing archaeon "Geoglobus ahangari" strain 234(T)
  Manzella, Standards in genomic sciences 2015
  • “...within the G. ahangari All enzymes involved in the formation of oxaloacetate from acetyl-CoA (GAH_00258, GAH_01703, GAH_01110, GAH_02012-02013, GAH_00784-00784, GAH_00779-00782, GAH_00526-00527, and GAH_00039), including putative aconitase proteins (GAH_00857-00858) [ 74 ], were identified in the genome. Also present is a phosphoenolpyruvate carboxylase (GAH_01652), which could catalyze...”

SRU_1973 isocitrate dehydrogenase, NADP-dependent from Salinibacter ruber DSM 13855
55% identity, 98% coverage

• A genome-scale metabolic network reconstruction of extremely halophilic bacterium Salinibacter ruber
  Bagheri, PloS one 2019
  • “...+ 2 Oxoglutarate + 2 Oxidized ferredoxin Key Enzyme 6 R00267 isocitrate dehydrogenase (NADP+) (1.1.1.42) SRU_1973 NADPH + CO 2 + 2 Oxoglutarate NADP + Isocitrate 7 R01900 aconitate hydratase (4.2.1.3) SRU_1866 SRU_1477 Isocitrate H 2 O + cis Aconitate 8 R01325 aconitate hydratase (4.2.1.3) SRU_1866...”

ZMO0544 isocitrate dehydrogenase, NADP-dependent from Zymomonas mobilis subsp. mobilis ZM4
53% identity, 97% coverage

• Genome-Wide Analyses of Proteome and Acetylome in Zymomonas mobilis Under N₂-Fixing Condition
  Nisar, Frontiers in microbiology 2021
  • “...with the KEGG database record of Z. mobilis . In TCA cycle, isocitrate dehydrogenase (CitC, ZMO0544) was upregulated, fumarate hydratase (ZMO1307) was downregulated, and the rest of the proteins were normally regulated under the nitrogen-fixing condition. Whereas, two proteins of the TCA cycle were found acetylated...”
• Transcriptome analysis of Zymomonas mobilis ZM4 reveals mechanisms of tolerance and detoxification of phenolic aldehyde inhibitors from lignocellulose pretreatment
  Yi, Biotechnology for biofuels 2015
  • “...aldolase), ZMO0367 (glucose-6-phosphate 1-dehydrogenase), ZMO0368 (6-phosphogluconate dehydrogenase), ZMO0369 (glucokinase), ZMO0387 (hpcH/hpaI aldolase), ZMO0543 (aconitate hydratase), ZMO0544 (isocitrate dehydrogenase), ZMO0567 (succinyl-CoA synthetase), ZMO0569 (succinate dehydrogenase), ZMO0997 (KDPG aldolase), ZMO1237 ( d -isomer specific 2-hydroxyacid dehydrogenase), ZMO1307 (fumarase), ZMO1360 (pyruvate decarboxylase), ZMO1478 (6-phosphogluconolactonase), ZMO1496 (phosphoenolpyruvate carboxylase), ZMO1596 (Fe-containing...”
• Transcriptome profiling of Zymomonas mobilis under ethanol stress
  He, Biotechnology for biofuels 2012
  • “...ZMO0152 pyk 0.87 ZMO1496 Ppc 0.64 ZMO1237 ldhA 0.54 ZMO1360 pdc 0.76 ZMO1596 AdhB 0.89 ZMO0544 CitC 0.91 ZMO0487 Citrate lyase 0.78 ZMO0569 SdhC 0.95 ZMO0705 BudB 1.03 ZMO1955 YqkJ 0.91 ZMO1307 FumA 0.76 ZMO1963 GltA 0.94 Induction and repression of cell envelope components under ethanol...”

IDH_ARCFU / O29610 Isocitrate dehydrogenase [NADP]; IDH; IDP; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16) (see 2 papers)
2iv0A / O29610 Thermal stability of isocitrate dehydrogenase from archaeoglobus fulgidus studied by crystal structure analysis and engineering of chimers (see paper)
AF_0647 isocitrate dehydrogenase (NADP(+)) from Archaeoglobus fulgidus DSM 4304
54% identity, 100% coverage

• function: Catalyzes the oxidative decarboxylation of isocitrate to 2- oxoglutarate and carbon dioxide with the concomitant reduction of NADP(+) (PubMed:9325430). NAD(+) can replace NADP(+) with low efficiency (PubMed:9325430).
  catalytic activity: D-threo-isocitrate + NADP(+) = 2-oxoglutarate + CO2 + NADPH (RHEA:19629)
  cofactor: Mg(2+) Mn(2+) (Binds 1 Mg(2+) or Mn(2+) ion per subunit (By similarity). Mg(2+) can partially replace Mn(2+), resulting in approximately 70% of the maximal activity with Mn(2+) in vitro (PubMed:9325430).)
  subunit: Homodimer.
• Ligand: zinc ion (2iv0A)
• Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi
  Islam, Microbial biotechnology 2016
  • “...and arrows (strands). Protein accession numbers ( U ni P rot) are: A .fulgidus ( O29610 ), C .noboribetus ( P96318 ), S .aureus ( P99167 ), B .subtilis ( P39126 ), E .coli ( P08200 ), C .maris ( P41560 ), B .taurus ( P41563...”
• A novel methoxydotrophic metabolism discovered in the hyperthermophilic archaeon Archaeoglobus fulgidus
  Welte, Environmental microbiology 2021
  • “...glutamate synthase GltB13 (AF_09524), aspartate aminotransferase AspBC (AF_0409, AF_1623, AF_2129, AF_2366, AF_1417), isocitrate dehydrogenase Icd (AF_0647), aconitase Acn (AF_1963), citrate synthase CitZ (AF_1340), sulfate adenylyltransferase Sat (AF_1667), adenylylsulfate reductase AprAB (AF_166970), dissimilatory sulfite reductase DsrAB (AF_04234), DsrC (AF_2228), quinonemodifying oxidoreductase QmoABC (AF_06613), molybdopterin oxidoreductase DsrMKJOP (AF_0499503),...”

BP951000_0369 NADP-dependent isocitrate dehydrogenase from Brachyspira pilosicoli 95/1000
54% identity, 95% coverage

• The complete genome sequence of the pathogenic intestinal spirochete Brachyspira pilosicoli and comparison with other Brachyspira genomes
  Wanchanthuek, PloS one 2010
  • “...B. murdochii , these being putative citrate synthase (BP951000_0368 and 4083292.C42.orf00523) and putative isocitrate dehydrogenase (BP951000_0369 and 4083292.C42.orf00525). They were not identified in B. hyodysenteriae WA1. The presence of aconitase implies that B. pilosicoli and B murdochii can utilise the TCA to produce glutamate, and this...”
  • “...gltA , BP951000_0367 and 4083292.C42.orf00523), putative isocitrate dehydrogenase ( idh , BP951000_0368 and 4083292.C42.orf00525), aconitase (BP951000_0369 and 4083292.C42.orf00530), malate dehydrogenase ( mdh , BP951000_1737 and 4083292.C15.orf00095), and two copies of fumarate hydratase in B. pilosicoli ( fumA , BP951000_1272 and BP951000_1273): fumA was not indentified in...”

SGO_1611 Isocitrate dehydrogenase from Streptococcus gordonii str. Challis substr. CH1
55% identity, 95% coverage

• Mass Spectrometric Analysis of Whole Secretome and Amylase-precipitated Secretome Proteins from Streptococcus gordonii.
  Maddi, Journal of proteomics & bioinformatics 2014
  • “...beta-N-acetylhexosaminidase (SGO_0405). The non-classical secreted proteins identified in KS1 included: hypothetical protein (SGO_0483), isocitrate dehydrogenase (SGO_1611), and cardiolipin synthase (SGO_2037). YfgQ is a putative protein with a conserved cation-transporting ATPase domain whose exact function is not known. Sortase A is an enzyme that is involved in...”
  • “...physiological and pathological processes [ 36 ]. The non-classical secreted proteins-hypothetical protein (SGO_0483), isocitrate dehydrogenase (SGO_1611), and cardiolipin synthase (SGO_2037) were identified in the KS1 strain and were absent in the AbpA strain. Isocitrate dehydrogenase catalyzes the oxidative decarboxylation of isocitrate to alpha-ketoglutarate and can use...”

icd / Q5UXA4 isocitrate dehydrogenase, NADP (EC 1.1.1.42) from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809) (see 4 papers)
53% identity, 99% coverage

IDH_SYNY3 / P80046 Isocitrate dehydrogenase [NADP]; IDH; IDP; NADP isocitrate dehydrogenase; NADP-IDH; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 from Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa) (see 2 papers)
49% identity, 88% coverage

• function: Catalyzes the oxidative decarboxylation of isocitrate to 2- oxoglutarate and carbon dioxide with the concomitant reduction of NADP(+) (PubMed:1730247). Is specific for NADP(+), cannot use NAD(+) (PubMed:1730247).
  catalytic activity: D-threo-isocitrate + NADP(+) = 2-oxoglutarate + CO2 + NADPH (RHEA:19629)
  cofactor: Mg(2+) Mn(2+) (Binds 1 Mg(2+) or Mn(2+) ion per subunit (By similarity). Can use Mn(2+) or Mg(2+), but the activity is twofold higher in vitro with Mn(2+) (PubMed:1730247).)
  subunit: Homodimer.
  disruption phenotype: Essential, it cannot be deleted.

Q72EU1 isocitrate dehydrogenase (NADP(+)) from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)
56% identity, 92% coverage

• Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough.
  Marbehan, Frontiers in microbiology 2024
  • “...13 TCA cycle Aconitate hydratase CitB Q72D65 DVU_1064 67.5 49 54 23 Isocitrate dehydrogenase CitC Q72EU1 DVU_0477 41.5 24 53 17 Fumarate reductase (Fdr) subunit C FdrC Q726D0 DVU_3261 23.7 Subunit A FdrA Q726C9 DVU_3262 65.9 19 30 14 Subunit B FdrB Q726C8 DVU_3263 27.8 5...”

Q9HLV8 isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) from Thermoplasma acidophilum (see paper)
56% identity, 97% coverage

Q59940 Isocitrate dehydrogenase [NADP] from Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
53% identity, 95% coverage

• Identification of stress-responsive genes in Streptococcus mutans by differential display reverse transcription-PCR
  Chia, Infection and immunity 2001
  • “...0.1 0.1 90/119 (75) 126/131 (96) 38/38 (100) G69599 (7) Q59940 (6) Q59939 (6) a The ratio of induction or repression was estimated by the intensity of the bands...”

sync_0214 isocitrate dehydrogenase, NADP-dependent from Synechococcus sp. CC9311
48% identity, 86% coverage

• Cross-species transcriptional network analysis reveals conservation and variation in response to metal stress in cyanobacteria
  Wang, BMC genomics 2013
  • “...dehydrogenase (NAD+) PMM PMM1596 magenta 0.714 0.4 0.008 PMT PMT1935 turquoise -0.611 -0.2 0.006 SYG sync_0214 pink 0.757 -0.5 0.002 SYW SYNW0166 yellow -0.964 -0.5 0.001 K03588 cell division protein FtsW PMM PMM1458 green 0.661 -0.6 0.023 PMT PMT1475 turquoise -0.611 -0.2 0.027 SYG sync_2326 turquoise...”

cce_3202 NADP-dependent isocitrate dehydrogenase from Crocosphaera subtropica ATCC 51142
49% identity, 87% coverage

• Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles
  Aryal, BMC systems biology 2011
  • “...cycle [ 43 ]. Concurrently, we observed a slight trend in the synthesis of Icd (cce_3202) being increased in the dark and GabD, another enzyme known to participate in glutamate metabolism for the conversion of 2-OG to succinate [ 44 ] in the light cycle (Figure...”

cce_3202 isocitrate dehydrogenase (NADP+) from Cyanothece sp. ATCC 51142
49% identity, 83% coverage

• Analysis of Protein Complexes in the Unicellular Cyanobacterium Cyanothece ATCC 51142
  Aryal, Journal of proteome research 2018
  • “...GltA (cce_1900), succinate dehydrogenase iron-sulfur protein subunit; SdhB (cce_3244), aconitase; AcnB (cce_3280), isocitrate dehydrogenase; Icsd (cce_3202), fumarate hydratase; FumC (cce_0396) and malate dehydrogenase; Mdh (cce_1850), and all but Icd, GabD and Mdh were identified as putative complexes ( Figure 8B ). GltA eluted as a large...”
  • “...Pkt; phosphoketolase (cce_2225), GltA; citrate synthase (cce_1900), AcnB; aconitate hydratase 2 (cce_3280), Icd; isocitrate dehydrogenase (cce_3202), GabD; succinate-semialdehyde dehydrogenase (cce_4228), SucC; succi nyl-CoA synthetase (cce_2357), SdhB; succinate dehydrogenase iron-sulfur protein subunit (cce_3244), FumC; fumarate hydratase (cce_0396), Mdh; malate dehydrogenase (cce_1850). G6P; glucose-6-phosphate; F6P; fructose-6-phosphate, F1,6P; fructose...”
• Multi-Omic Dynamics Associate Oxygenic Photosynthesis with Nitrogenase-Mediated H2 Production in Cyanothece sp. ATCC 51142
  Bernstein, Scientific reports 2015
  • “...key reductant generating reactions of the tricarboxylic acid cycle (TCA), such as isocitrate dehydrogenase (Icd; cce_3202) and succinate dehydrogenase (SdhA; cce_0663), were generally decreased ( Figs 3 E and 4 E); although some variability was observed in the Icd protein profile during the early time points...”
• Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles
  Aryal, BMC systems biology 2011
  • “...cycle [ 43 ]. Concurrently, we observed a slight trend in the synthesis of Icd (cce_3202) being increased in the dark and GabD, another enzyme known to participate in glutamate metabolism for the conversion of 2-OG to succinate [ 44 ] in the light cycle (Figure...”

Dret_0439 Isocitrate dehydrogenase (NADP(+)) from Desulfohalobium retbaense DSM 5692
54% identity, 92% coverage

• Complete genome sequence of Desulfohalobium retbaense type strain (HR(100))
  Spring, Standards in genomic sciences 2010
  • “...carbon precursor 2-oxoglutarate could also be synthesized from citrate by aconitase (Dret_1771) and isocitrate dehydrogenase (Dret_0439). Genes encoding the enzymes ATP-citrate lyase or citrate synthase were not detected in the annotated genome sequence, so that a closing of the TCA cycle is apparently prevented. Defense against...”

PMM1596 Isocitrate dehydrogenase from Prochlorococcus marinus sp. MED4
47% identity, 88% coverage

• Cross-species transcriptional network analysis reveals conservation and variation in response to metal stress in cyanobacteria
  Wang, BMC genomics 2013
  • “...turquoise -0.806 -0.4 0.0001 SYW SYNW0249 greenyellow -0.957 -0.6 0.029 K00030 isocitrate dehydrogenase (NAD+) PMM PMM1596 magenta 0.714 0.4 0.008 PMT PMT1935 turquoise -0.611 -0.2 0.006 SYG sync_0214 pink 0.757 -0.5 0.002 SYW SYNW0166 yellow -0.964 -0.5 0.001 K03588 cell division protein FtsW PMM PMM1458 green...”

SYNW0166 Isocitrate dehydrogenase from Synechococcus sp. WH 8102
48% identity, 88% coverage

• Cross-species transcriptional network analysis reveals conservation and variation in response to metal stress in cyanobacteria
  Wang, BMC genomics 2013
  • “...0.4 0.008 PMT PMT1935 turquoise -0.611 -0.2 0.006 SYG sync_0214 pink 0.757 -0.5 0.002 SYW SYNW0166 yellow -0.964 -0.5 0.001 K03588 cell division protein FtsW PMM PMM1458 green 0.661 -0.6 0.023 PMT PMT1475 turquoise -0.611 -0.2 0.027 SYG sync_2326 turquoise -0.806 -0.3 0.012 SYW SYNW0475 yellow...”
• Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102
  Su, Nucleic acids research 2006
  • “...NarB (SYNW2464), UreGFE (SYNW2443-2445), UreDABC (SYNW2446-2449), CynS (SYNW2490), GOGAT (glutamate synthase), RbcL (SYNW1718) and Icd (SYNW0166), etc. which are not members of the NtcA regulon but are functionally relevant to the network. Some of these proteins are probably regulated by the regulators that are under NtcA...”
  • “...3 glnB 33864998 synw0462 PCC7120, PCC6803 6.422 26 gor 33866067 synw1533 PCC7120 299 icd 33864702 synw0166 PCC7120, PCC6803 618 narB 33866994 synw2464 PCC7120, PCC6803, WH8103 616 nirA 33867007 synw2477 PCC7120, PCC6803, WH8103 11 cynA 33867017 synw2487 synw2485synw2487 PCC7942 5.132 4 cynB 33867016 synw2486 synw2485synw2487 PCC7942 4...”

Q9HNZ7 isocitrate dehydrogenase (NADP(+)) from Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)
50% identity, 99% coverage

• OMICS in ecology: systems level analyses of Halobacterium salinarum reveal large-scale temperature-mediated changes and a requirement of CctA for thermotolerance
  Weng, Omics : a journal of integrative biology 2014
  • “...proteomic study by Shukla (2006). Icd NoxA VNG0582C Q9HNZ7 Q9HP48 Q9HRR3 Energy metabolism Q9HN94 CoxB2 NirD Q9HNW8 Category Uniprot ID Protein name Total no....”

Kole_1227 isocitrate dehydrogenase (NADP(+)) from Kosmotoga olearia TBF 19.5.1
Kole_1227 Isocitrate dehydrogenase (NADP(+)) from Thermotogales bacterium TBF 19.5.1
52% identity, 97% coverage

• Genomic insights into temperature-dependent transcriptional responses of Kosmotoga olearia, a deep-biosphere bacterium that can grow from 20 to 79 °C
  Pollo, Extremophiles : life under extreme conditions 2017
  • “...prolonged cold stress (Alreshidi et al. 2015 ). Alternatively, citrate synthase, together with isocitrate dehydrogenase (Kole_1227), may be involved in converting pyruvate or acetyl-CoA to 2-oxoglutarate, a precursor for several amino acids including arginine, which has been suggested to accumulate in for instance Clostridium (Dahlsten et...”

T303_07275 NADP-dependent isocitrate dehydrogenase from Streptococcus thermophilus ASCC 1275
55% identity, 94% coverage

• Proteomic analysis reveals potential factors associated with enhanced EPS production in Streptococcus thermophilus ASCC 1275
  Padmanabhan, Scientific reports 2020
  • “...acetyl-CoA carboxylase subunit alpha, T303_03125), pyruvate metabolism (isopropylmalate synthase, T303_06880) and citrate cycle (isocitrate dehydrogenase, T303_07275). In glucose medium, there was no significant up/down regulation in other carbohydrate metabolism pathways at 10h when compared to 5h. EPS assembly EPS gene cluster of S. thermophilus 1275 has...”
• Functional Genomic Analyses of Exopolysaccharide-Producing Streptococcus thermophilus ASCC 1275 in Response to Milk Fermentation Conditions
  Wu, Frontiers in microbiology 2019
  • “...protein T303_02740 0.34 NrdR family transcriptional regulator T303_08865 0.49 Aminoglycoside phosphotransferase T303_07285 0.56 Aconitate hydratase T303_07275 0.63 Isocitrate dehydrogenase T303_01900 2.59 Hypothetical protein T303_04110 4.02 Branched-chain amino acid aminotransferase T303_08745 2.85 Copper-binding protein T303_04795 2.24 Cytoplasmic membrane protein T303_01820 0.35 Hypothetical protein T303_03875 2.05 Sulfurtransferase T303_04595...”
• Transcriptomic Insights Into the Growth Phase- and Sugar-Associated Changes in the Exopolysaccharide Production of a High EPS-Producing Streptococcus thermophilus ASCC 1275
  Padmanabhan, Frontiers in microbiology 2018
  • “...to be highly expressed at 5h in M17-L. In L10h, genes involved in citrate cycle (T303_07275, T303_07280, T303_07285), trehalose metabolism (T303_00355, T303_00360, T303_00365) and acetyl CoA carboxylase biotin carrier protein and subunits (T303_03105 T303_03115, T303_03120, T303_03125) were significantly upregulated. FIGURE 7 Changes in expression of genes...”

LAF_0939 isocitrate dehydrogenase from Lactobacillus fermentum IFO 3956
LAF_0939 NADP-dependent isocitrate dehydrogenase from Limosilactobacillus fermentum IFO 3956
51% identity, 95% coverage

• Comparative genome analysis of Lactobacillus reuteri and Lactobacillus fermentum reveal a genomic island for reuterin and cobalamin production
  Morita, DNA research : an international journal for rapid publication of reports on genes and genomes 2008
  • “...only in JCM 1112 T (described later) and genes encoding allantoate amidohydrolase (LAF_0160), isocitrate dehydrogenase (LAF_0939), isopropylmalate isomerase (LAF_0963-0965), and nitric oxide reductase (LAF_1644) are found only in IFO 3956. A COG analysis showed that L. reuteri JCM 1112 T and L. fermentum IFO 3956 contain...”

Tneu_0698 isocitrate dehydrogenase, NADP-dependent from Thermoproteus neutrophilus V24Sta
49% identity, 93% coverage

• Regulation of autotrophic CO2 fixation in the archaeon Thermoproteus neutrophilus
  Ramos-Vera, Journal of bacteriology 2010
  • “...bp). PC, positive-control gene for isocitrate dehydrogenase (Tneu_0698); NC, negative control; noncoding region between the Tneu_0430 and Tneu_0431 genes. (D)...”
• Autotrophic carbon dioxide assimilation in Thermoproteales revisited
  Ramos-Vera, Journal of bacteriology 2009
  • “...Tneu_0176/0177/0178/0179, Tneu_1526/ 1527/1528/1529, Tneu_1795/1796/1797c Tneu_0713 Tneu_0614 Tneu_0698 No gene found No gene found No gene found Tneu_1204 No...”

ST2166 409aa long hypothetical NADP-dependent isocitrate dehydrogenase from Sulfolobus tokodaii str. 7
WP_010980246 NADP-dependent isocitrate dehydrogenase from Sulfurisphaera tokodaii
49% identity, 98% coverage

• Crystal Structures of the Putative Isocitrate Dehydrogenase from Sulfolobus tokodaii Strain 7 in the Apo and NADP⁺-Bound Forms
  Kondo, Archaea (Vancouver, B.C.) 2018
  • “...enzyme that acts during the third step of the tricarboxylic acid cycle. The hypothetical protein ST2166 from the archaeon Sulfolobus tokodaii was isolated and crystallized. It shares high primary structure homology with prokaryotic NADP + -dependent IDHs, suggesting that these enzymes share a common enzymatic mechanism....”
  • “...prokaryotes suggest that prokaryotic NADP-IDHs recognize their cofactors using conserved Lys335, Tyr336, and Arg386 in ST2166 at the opening cleft before the domain closure. Ministry of Education, Culture, Sports, Science and Technology 1. Introduction Isocitrate dehydrogenase (IDH) catalyzes the oxidative decarboxylation of isocitrate to produce -ketoglutarate...”
• Crystal Structures of the Putative Isocitrate Dehydrogenase from Sulfolobus tokodaii Strain 7 in the Apo and NADP+-Bound Forms.
  Kondo, Archaea (Vancouver, B.C.) 2018
  • GeneRIF: Comparisons between the structures of apo and NADP(+)-bound forms and NADP-isocitrate dehydrogenases from other prokaryotes suggest that prokaryotic NADP-isocitrate dehydrogenases recognize their cofactors using conserved Lys335, Tyr336, and Arg386 in ST2166 at the opening cleft before the domain closure.

PMT1935 Isocitrate dehydrogenase from Prochlorococcus marinus str. MIT 9313
44% identity, 88% coverage

• Cross-species transcriptional network analysis reveals conservation and variation in response to metal stress in cyanobacteria
  Wang, BMC genomics 2013
  • “...greenyellow -0.957 -0.6 0.029 K00030 isocitrate dehydrogenase (NAD+) PMM PMM1596 magenta 0.714 0.4 0.008 PMT PMT1935 turquoise -0.611 -0.2 0.006 SYG sync_0214 pink 0.757 -0.5 0.002 SYW SYNW0166 yellow -0.964 -0.5 0.001 K03588 cell division protein FtsW PMM PMM1458 green 0.661 -0.6 0.023 PMT PMT1475 turquoise...”

Q4J6C9 isocitrate-homoisocitrate dehydrogenase (EC 1.1.1.286) from Sulfolobus acidocaldarius (see paper)
Saci_2375 isocitrate dehydrogenase from Sulfolobus acidocaldarius DSM 639
50% identity, 94% coverage

• Early Response of Sulfolobus acidocaldarius to Nutrient Limitation
  Bischof, Frontiers in microbiology 2018
  • “...protein level of TCA cycle proteins, such as Saci_0122 (FumC), Saci_0246 (MDH), Saci_0982 (SDH) and Saci_2375 (aconitase ACN) (Supplementary Table S3 ). Respiratory Chain Organisms can regulate the energy conservation efficiency according to their needs by simultaneously expressing several terminal oxidases. The S. acidocaldarius respiratory chain...”
• Characterization of two β-decarboxylating dehydrogenases from Sulfolobus acidocaldarius
  Takahashi, Extremophiles : life under extreme conditions 2016 (PubMed)
  • “...possesses two -decarboxylating dehydrogenase genes, saci_0600 and saci_2375, in its genome, which suggests that it uses these enzymes for three similar...”
  • “...no activity for homoisocitrate and isocitrate, respectively. Saci_2375 exhibited distinct and similar activities for isocitrate and homoisocitrate, but no...”

Micr_00902 NADP-dependent isocitrate dehydrogenase from Candidatus Micrarchaeum sp.
49% identity, 94% coverage

• Biochemical Characterization of Recombinant Isocitrate Dehydrogenase and Its Putative Role in the Physiology of an Acidophilic Micrarchaeon
  Winkler, Microorganisms 2021
  • “...Shows Conserved Characteristics of Prokaryotic, NADP-Dependent IDHs A_DKE possesses only one gene ( icd2 , Micr_00902) annotated to be encoding a putative NADP-dependent IDH, which is actively expressed, according to available transcriptomic data [ 13 ]. In silico analyses of its amino acid sequence allowed the...”

Q9YE81 isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) from Aeropyrum pernix (see 4 papers)
48% identity, 94% coverage

• Induced fit and the catalytic mechanism of isocitrate dehydrogenase
  Gonçalves, Biochemistry 2012
  • “...(UNIPROT Q3JV82), 74.2% identity 3dms 71 1.65 2011 0.92 0.62 - Aeropyrum pernix ATCC 700893(UNIPROT Q9YE81), 45.2% identity 1kd:A 20 2.3 2005 2.24 1.94 Ca 2+ , ICT, NADP + 1kd:B 0.99 1.33 ICT, NADP + Bacillus subtilis Strain 168 (UNIPROT P39126), 65.0% identity 1hqs:A 72...”

1tyoA / Q9YE81 Isocitrate dehydrogenase from the hyperthermophile aeropyrum pernix in complex with etheno-NADP (see paper)
48% identity, 96% coverage

• Ligand: etheno-nadp (1tyoA)

2e5mA / Q96YK6 Crystal structure of isocitrate dehydrogenase from sulfolobus tokodaii strain 7 (see paper)
48% identity, 98% coverage

• Ligand: nadp nicotinamide-adenine-dinucleotide phosphate (2e5mA)

llmg_0637 isocitrate dehydrogenase from Lactococcus lactis subsp. cremoris MG1363
49% identity, 94% coverage

• Transcriptional response of Lactococcus lactis during bacterial emulsification
  Tarazanova, PloS one 2019
  • “...production and conversion llmg_0635 gltA citrate synthase 6.5 8.1e-4 llmg_0636 citB aconitate hydratase 13.9 6.9e-8 llmg_0637 icd isocitrate dehydrogenase 11.3 4.7e-9 E. Amino acid transport and metabolism llmg_0362 dppA dipeptide-binding protein precursor 45.3 1.9e-7 llmg_pseudo_09 dppP dipeptide-binding protein 4.6 1.1e-6 llmg_pseudo_42 leuB isocitrate/isopropylmalate dehydrogenase 14.9 1.4e-13...”

SSO2182 Isocitrate dehydrogenase, probable (idh) from Sulfolobus solfataricus P2
47% identity, 94% coverage

• Utilization of Phenol as Carbon Source by the Thermoacidophilic Archaeon Saccharolobus solfataricus P2 Is Limited by Oxygen Supply and the Cellular Stress Response
  Wolf, Frontiers in microbiology 2020
  • “...Non-phosphorylating NAD(P)-dependent glyceraldehyde 3-phosphate dehydrogenase 0.23 0.06 1.99E-10 Sso3198 4.2.1.140 Gluconate/galactonate dehydratase 0.24 0.01 2.59E-09 Sso2182 1.1.1.42 Isocitrate dehydrogenase (NADP + ) 0.39 0.04 7.94E-05 Sso3197 4.1.2.20/4.1.2.21 Bifunctional 2-keto-3-deoxy-(6-phospho)gluconate/galactonate aldolase 0.44 0.01 6.58E-04 Genes which are not significantly regulated but discussed in the text were also...”

Q8U488 isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) from Pyrococcus furiosus (see 2 papers)
PF0202 isocitrate dehydrogenase from Pyrococcus furiosus DSM 3638
48% identity, 99% coverage

• Modular architecture of metabolic pathways revealed by conserved sequences of reactions
  Muto, Journal of chemical information and modeling 2013
  • “...17 two gene clusters correspond to the reaction module RM001: the gene cluster (PF0203 PF0201 PF0202) for the RCLASS sequence (RC00067 RC00498+RC00618 RC00084+RC00626) in citrate cycle and the gene cluster (PF0937 PF0938+PF0939 PF0940) for the RCLASS sequence (RC00470 RC01041+RC01046 RC00084+RC00577) in leucine biosynthesis. It is interesting...”
  • “...not share any sequence similarity, the second hydratases (PF0201 and PF0938+PF0939) and the third dehydrogenases (PF0202 and PF0940) form paralogous gene groups with sequence identity of around 35%, suggesting a link between genomic diversity and chemical diversity. Table 4 shows only a few examples of enzyme...”
• Novel multiprotein complexes identified in the hyperthermophilic archaeon Pyrococcus furiosus by non-denaturing fractionation of the native proteome
  Menon, Molecular & cellular proteomics : MCP 2009
  • “...PF0138 PF0139 PF0146 PF0147 PF0160 PF0161 PF0198 PF0199 PF0202 PF0203 PF0390 PF0391 PF0548 PF0549 PF0639 PF0640 PF0641 PF0642 PF0643 PF0753 PF0754 PF0872 PF0873...”
• Impact of substrate glycoside linkage and elemental sulfur on bioenergetics of and hydrogen production by the hyperthermophilic archaeon Pyrococcus furiosus
  Chou, Applied and environmental microbiology 2007
  • “...2.22 3.02 2.42 2.72 2.62 3.32 Glutamate metabolism PF0201 PF0202 PF0203 PF0204 PF0205 PF0206 PF0207 PF0450 PF1602 PF1852 3.42 3.72 5.82 2.82 4.12 2.92 2.12...”
• Whole-genome DNA microarray analysis of a hyperthermophile and an archaeon: Pyrococcus furiosus grown on carbohydrates or peptides
  Schut, Journal of bacteriology 2003
  • “...of California, Berkeley PF0101 TCA cycle PF0201 PF0202 PF0203 [Glutamate biosynthesis] PF0204 PF0205 PF0206 [Arginine biosynthesis] PF0207 PF0208 PF0209 PF0272...”

O67480 Isocitrate dehydrogenase [NADP] from Aquifex aeolicus (strain VF5)
aq_1512 isocitrate dehydrogenase from Aquifex aeolicus VF5
46% identity, 97% coverage

• Carbon Fixation in the Chemolithoautotrophic Bacterium Aquifex aeolicus Involves Two Low-Potential Ferredoxins as Partners of the PFOR and OGOR Enzymes
  Prioretti, Life (Basel, Switzerland) 2023
  • “...OgcB (CfiB) O67483 aq_1517 pycB 52.8 244 74 33 Oxalosuccinate reductase (OSR) Oxalosuccinate Isocitrate Icd O67480 aq_1512 icd 46.9 54 48 23 Aconitase Isocitrate Aconitate Citrate Aco O67656 aq_1784 aco 72.5 133 67 38 Citryl-CoA synthetase (CCS) Citrate Citryl-CoA CcsA O67330 aq_1306 sucC1 48.3 231 77...”
• Carbon Fixation in the Chemolithoautotrophic Bacterium Aquifex aeolicus Involves Two Low-Potential Ferredoxins as Partners of the PFOR and OGOR Enzymes
  Prioretti, Life (Basel, Switzerland) 2023
  • “...(CfiB) O67483 aq_1517 pycB 52.8 244 74 33 Oxalosuccinate reductase (OSR) Oxalosuccinate Isocitrate Icd O67480 aq_1512 icd 46.9 54 48 23 Aconitase Isocitrate Aconitate Citrate Aco O67656 aq_1784 aco 72.5 133 67 38 Citryl-CoA synthetase (CCS) Citrate Citryl-CoA CcsA O67330 aq_1306 sucC1 48.3 231 77 35...”

IDH_CALNO / P96318 Isocitrate dehydrogenase [NADP]; ICDH; IDH; IDP; NADP(+)-specific ICDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 from Caldococcus noboribetus (see paper)
P96318 isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) from Caldococcus noboribetus (see 2 papers)
49% identity, 92% coverage

• function: Catalyzes the oxidative decarboxylation of isocitrate to 2- oxoglutarate and carbon dioxide with the concomitant reduction of NADP(+).
  catalytic activity: D-threo-isocitrate + NADP(+) = 2-oxoglutarate + CO2 + NADPH (RHEA:19629)
  cofactor: Mg(2+) Mn(2+) (Binds 1 Mg(2+) or Mn(2+) ion per subunit.)
  subunit: Homodimer.
• Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi.
  Islam, Microbial biotechnology 2016
  • “...numbers ( U ni P rot) are: A .fulgidus ( O29610 ), C .noboribetus ( P96318 ), S .aureus ( P99167 ), B .subtilis ( P39126 ), E .coli ( P08200 ), C .maris ( P41560 ), B .taurus ( P41563 ) and H .sapiens (...”

icd / Q76LM6 oxalosuccinate reductase subunit from Hydrogenobacter thermophilus (see 3 papers)
47% identity, 97% coverage

DET0450 isocitrate dehydrogenase, putative from Dehalococcoides ethenogenes 195
43% identity, 93% coverage

• Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi
  Islam, Microbial biotechnology 2016
  • “...expressed in Escherichia coli . The orthologs of these genes in pure strains of D.mccartyi (DET0450, cbdbA408, DehaBAV_0427, DhcVS_392, DehalGT_0391, btf_415, dcmb_461, GY50_0375 and DET0509, cbdbA472, DehaBAV1_0485, DhcVS_0450, DehalGT_0448, btf_472, dcmb_518, GY50_0435) are 98100% similar at the amino acid level (Markowitz etal ., 2012 ). Although...”

cbdbA408 isocitrate/isopropylmalate dehydrogenase family protein from Dehalococcoides mccartyi CBDB1
DehalGT_0391 Isocitrate dehydrogenase (NAD(+)) from Dehalococcoides sp. GT
42% identity, 93% coverage

• Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi
  Islam, Microbial biotechnology 2016
  • “...in Escherichia coli . The orthologs of these genes in pure strains of D.mccartyi (DET0450, cbdbA408, DehaBAV_0427, DhcVS_392, DehalGT_0391, btf_415, dcmb_461, GY50_0375 and DET0509, cbdbA472, DehaBAV1_0485, DhcVS_0450, DehalGT_0448, btf_472, dcmb_518, GY50_0435) are 98100% similar at the amino acid level (Markowitz etal ., 2012 ). Although IDH...”
• Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi
  Islam, Microbial biotechnology 2016
  • “.... The orthologs of these genes in pure strains of D.mccartyi (DET0450, cbdbA408, DehaBAV_0427, DhcVS_392, DehalGT_0391, btf_415, dcmb_461, GY50_0375 and DET0509, cbdbA472, DehaBAV1_0485, DhcVS_0450, DehalGT_0448, btf_472, dcmb_518, GY50_0435) are 98100% similar at the amino acid level (Markowitz etal ., 2012 ). Although IDH is an important...”

btf_415 isocitrate/isopropylmalate dehydrogenase family protein from Dehalococcoides mccartyi BTF08
42% identity, 93% coverage

• Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi
  Islam, Microbial biotechnology 2016
  • “...The orthologs of these genes in pure strains of D.mccartyi (DET0450, cbdbA408, DehaBAV_0427, DhcVS_392, DehalGT_0391, btf_415, dcmb_461, GY50_0375 and DET0509, cbdbA472, DehaBAV1_0485, DhcVS_0450, DehalGT_0448, btf_472, dcmb_518, GY50_0435) are 98100% similar at the amino acid level (Markowitz etal ., 2012 ). Although IDH is an important TCAcycle...”

dcmb_461 isocitrate/isopropylmalate dehydrogenase family protein from Dehalococcoides mccartyi DCMB5
42% identity, 93% coverage

• Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi
  Islam, Microbial biotechnology 2016
  • “...orthologs of these genes in pure strains of D.mccartyi (DET0450, cbdbA408, DehaBAV_0427, DhcVS_392, DehalGT_0391, btf_415, dcmb_461, GY50_0375 and DET0509, cbdbA472, DehaBAV1_0485, DhcVS_0450, DehalGT_0448, btf_472, dcmb_518, GY50_0435) are 98100% similar at the amino acid level (Markowitz etal ., 2012 ). Although IDH is an important TCAcycle enzyme...”

DhcVS_392, GY50_0375 isocitrate/isopropylmalate dehydrogenase family protein from Dehalococcoides mccartyi GY50
42% identity, 93% coverage

• Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi
  Islam, Microbial biotechnology 2016
  • “...coli . The orthologs of these genes in pure strains of D.mccartyi (DET0450, cbdbA408, DehaBAV_0427, DhcVS_392, DehalGT_0391, btf_415, dcmb_461, GY50_0375 and DET0509, cbdbA472, DehaBAV1_0485, DhcVS_0450, DehalGT_0448, btf_472, dcmb_518, GY50_0435) are 98100% similar at the amino acid level (Markowitz etal ., 2012 ). Although IDH is an...”
  • “...of these genes in pure strains of D.mccartyi (DET0450, cbdbA408, DehaBAV_0427, DhcVS_392, DehalGT_0391, btf_415, dcmb_461, GY50_0375 and DET0509, cbdbA472, DehaBAV1_0485, DhcVS_0450, DehalGT_0448, btf_472, dcmb_518, GY50_0435) are 98100% similar at the amino acid level (Markowitz etal ., 2012 ). Although IDH is an important TCAcycle enzyme catalysing...”

Mal4_26830 isocitrate/isopropylmalate dehydrogenase family protein from Maioricimonas rarisocia
41% identity, 93% coverage

• Maioricimonas rarisocia gen. nov., sp. nov., a novel planctomycete isolated from marine sediments close to Mallorca Island
  Rivas-Marin, Antonie van Leeuwenhoek 2020
  • “...Y Aconitate hydratase A 4.2.1.3 acnA Mal4_15300 Y Y Y Isocitrate dehydrogenase [NADP] 1.1.1.42 icd Mal4_26830 Y Y Y 2-Oxoglutarate dehydrogenase complex 1.2.4.2/2.3.1.61 sucAB Mal4_26900/Mal4_26910 Y Y Y Succinate-CoA ligase complex 6.2.1.5 sucCD Mal4_08670/Mal4_08660 Y Y Y Succinate dehydrogenase complex 1.3.5.1 sdhABC Mal4_42560/ Mal4_42550/Mal4_42570 Y Y...”

Mal48_24210 isocitrate/isopropylmalate dehydrogenase family protein from Thalassoglobus polymorphus
40% identity, 93% coverage

• Thalassoglobus polymorphus sp. nov., a novel Planctomycete isolated close to a public beach of Mallorca Island
  Rivas-Marin, Antonie van Leeuwenhoek 2020
  • “...Y Y Aconitate hydratase A 4.2.1.3 acnA Mal48_48270 Y Y Isocitrate dehydrogenase [NADP] 1.1.1.42 icd Mal48_24210 Y Y 2-oxoglutarate dehydrogenase complex 1.2.4.2/ sucAB Mal48_06600 Y Y 2.3.1.61 Mal48_24080 Succinate-CoA ligase complex 6.2.1.5 sucCD Mal48_27760/ Y Y Mal48_48200 Succinate dehydrogenase complex 1.3.5.1 sdhABC Mal48_12710/Mal48_12720/ Y Y Mal48_12700...”

CA54_25060 isocitrate/isopropylmalate dehydrogenase family protein from Symmachiella macrocystis
40% identity, 93% coverage

• Three Planctomycetes isolated from biotic surfaces in the Mediterranean Sea and the Pacific Ocean constitute the novel species Symmachiella dynata gen. nov., sp. nov. and Symmachiella macrocystis sp. nov
  Salbreiter, Antonie van Leeuwenhoek 2020
  • “...Aconitate hydratase A 4.2.1.3 acnA Pan258_21500 Mal52_21950 CA54_47570 Isocitrate dehydrogenase [NADP] 1.1.1.42 icd Pan258_54730 Mal52_56040 CA54_25060 2-oxoglutarate dehydrogenase E1 component 1.2.4.2 sucA Pan258_54450 Mal52_55760 CA54_25310 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex 2.3.1.61 sucB Pan258_17100 Mal52_17290 CA54_02340 SuccinateCoA ligase [ADP-forming] subunit alpha 6.2.1.5 sucD Pan258_35790 Mal52_36710...”

Pan258_54730 isocitrate/isopropylmalate dehydrogenase family protein from Symmachiella dynata
40% identity, 93% coverage

• Three Planctomycetes isolated from biotic surfaces in the Mediterranean Sea and the Pacific Ocean constitute the novel species Symmachiella dynata gen. nov., sp. nov. and Symmachiella macrocystis sp. nov
  Salbreiter, Antonie van Leeuwenhoek 2020
  • “...Mal52_00570 CA54_18160 Aconitate hydratase A 4.2.1.3 acnA Pan258_21500 Mal52_21950 CA54_47570 Isocitrate dehydrogenase [NADP] 1.1.1.42 icd Pan258_54730 Mal52_56040 CA54_25060 2-oxoglutarate dehydrogenase E1 component 1.2.4.2 sucA Pan258_54450 Mal52_55760 CA54_25310 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex 2.3.1.61 sucB Pan258_17100 Mal52_17290 CA54_02340 SuccinateCoA ligase [ADP-forming] subunit alpha 6.2.1.5 sucD...”

Mal52_56040 isocitrate/isopropylmalate dehydrogenase family protein from Symmachiella dynata
40% identity, 93% coverage

• Three Planctomycetes isolated from biotic surfaces in the Mediterranean Sea and the Pacific Ocean constitute the novel species Symmachiella dynata gen. nov., sp. nov. and Symmachiella macrocystis sp. nov
  Salbreiter, Antonie van Leeuwenhoek 2020
  • “...CA54_18160 Aconitate hydratase A 4.2.1.3 acnA Pan258_21500 Mal52_21950 CA54_47570 Isocitrate dehydrogenase [NADP] 1.1.1.42 icd Pan258_54730 Mal52_56040 CA54_25060 2-oxoglutarate dehydrogenase E1 component 1.2.4.2 sucA Pan258_54450 Mal52_55760 CA54_25310 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex 2.3.1.61 sucB Pan258_17100 Mal52_17290 CA54_02340 SuccinateCoA ligase [ADP-forming] subunit alpha 6.2.1.5 sucD Pan258_35790...”

ELEN_RS11715 isocitrate/isopropylmalate dehydrogenase family protein from Eggerthella lenta DSM 2243
41% identity, 92% coverage

• Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta
  Noecker, PLoS biology 2023
  • “...required for conversion of acetyl-CoA to glutamate are colocated (aconitate hydratase and isocitrate dehydrogenase, ELEN_RS11710, ELEN_RS11715). Genes for another partial component of the citric acid cyclefumarate hydratase and malate dehydrogenaseare colocated in another region of the genome ELEN_RS056[70-90], suggesting that they may act in a separate...”

Csac_0751 Isocitrate dehydrogenase (NAD(+)) from Caldicellulosiruptor saccharolyticus DSM 8903
40% identity, 93% coverage

• Hydrogenomics of the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus
  van, Applied and environmental microbiology 2008
  • “...aconitate hydratase (Csac_0750), isocitrate dehydrogenase (Csac_0751), and the 2-oxoglutarate:ferredoxin oxidoreductase complex (Csac_1548 to Csac_1551). In the...”
  • “...NADPH-producing reaction is the isocitrate dehydrogenase (Csac_0751) reaction. However, based on sequence homology, the isocitrate dehydrogenase is likely...”

CAC0972 Isocitrate dehydrogenase from Clostridium acetobutylicum ATCC 824
CA_C0972 isocitrate dehydrogenase (NAD(+)) from Clostridium acetobutylicum ATCC 824
40% identity, 84% coverage

• A universal mariner transposon system for forward genetic studies in the genus Clostridium
  Zhang, PloS one 2015
  • “...gene of a putative tricistronic operon, comprising citrate synthase (CAC0970), aconitase (CAC0971) and isocitrate dehydrogenase (CAC0972), which is expressed at higher levels at stationary phase [ 43 ]. Accordingly, the mutant, together with C . acetobutylicum CRG3011, was plated onto P2 minimal agar medium, individually supplemented...”
  • “...Characterization of the found auxotroph mutant with different additives in P2 minimal medium. Supplementation citB (CAC0972) mutant C acetobutylicum CRG3011 Citrate ++ Iso-citrate ++ -Ketoglutarate ++ Glutamate ++ ++ Glutamine + ++ Proline ++ Arginine ++ Without supplementation ++ No growth(), slight growth(+) and normal growth(++)....”
• Complex and extensive post-transcriptional regulation revealed by integrative proteomic and transcriptomic analysis of metabolite stress response in Clostridium acetobutylicum
  Venkataramanan, Biotechnology for biofuels 2015
  • “...(CAC0897 - aro, CAC3171 - LeuB, CAC3243 - chemotaxis protein, CAC0827 - fructose bisphosphate aldolase, CAC0972 - isocitrate dehydrogenase) proteins were found at medium and high stress, respectively, while two (CAC3598 - rubrerythrin and CAC0316 - ArgF/I) were found under both medium and high stress. Similarly,...”
• Transcriptional analysis of spo0A overexpression in Clostridium acetobutylicum and its effect on the cell's response to butanol stress
  Alsaker, Journal of bacteriology 2004
  • “...include citBC (CAC0971, encoding aconitase A, and CAC0972, encoding isocitrate dehydrogenase; earlier annotations of the C. acetobutylicum genome list these...”
• Quantitative proteomic analysis of the influence of lignin on biofuel production by Clostridium acetobutylicum ATCC 824
  Raut, Biotechnology for biofuels 2016
  • “...the lignin stress condition. Interestingly, tricarboxylic acid (TCA) cycle proteins aconitase (CA_C0971) and NAD-isocitrate dehydrogenase (CA_C0972) were up-regulated in the exponential phase of CL grown cells (ExpCL/ExpC). These proteins are involved in energy harvesting via NADH/NADPH generation [ 40 ]. Therefore, it can be possible that...”
• A Quantitative System-Scale Characterization of the Metabolism of Clostridium acetobutylicum
  Yoo, mBio 2015
  • “...NADPH (0.12 0.01) CA_C0970 citA Re- citrate synthase 1.9 0.14 CA_C0971 citB Aconitase 6.5 0.52 CA_C0972 citC Isocitrate dehydrogenase NADH (104 6.8), NADPH (7.1 0.43) CA_C1589 malS1 Malic enzyme NADH (156 9.6), NADPH (3.4 0.24) CA_C1596 malS2 Malic enzyme NADH (142 12.7), NADPH (2.9 0.34) a...”
  • “...dependent ( 53 , 54 ). The functions of the three genes (CA_C0970, CA_C0971, and CA_C0972) proposed ( 55 ) to encode the first three steps of the oxidative branch of the tricarboxylic acid (TCA) cycle were unambiguously characterized. CA_C0970, CA_C0971, and CA_C0972 were individually expressed...”

Clocel_2469 isocitrate/isopropylmalate dehydrogenase family protein from Clostridium cellulovorans 743B
38% identity, 93% coverage

• Clostridium cellulovorans Proteomic Responses to Butanol Stress
  Costa, Frontiers in microbiology 2021
  • “...addition, two enzymes of the tricarboxylic (TCA) cycle, namely citrate synthase (Clocel_3688) and isocitrate dehydrogenase (Clocel_2469) were up-regulated in butanol-challenged C. cellulovorans . Up-regulation of isocitrate dehydrogenase was reported as part of the butanol response of other gram positive bacteria ( Alsaker et al., 2010 ;...”

CAETHG_2753 isocitrate/isopropylmalate dehydrogenase family protein from Clostridium autoethanogenum DSM 10061
38% identity, 83% coverage

• Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia
  Brown, Biotechnology for biofuels 2014
  • “...lyase CAETHG_1052-54, 18981901, 2480-83, T 3 Aconitase (Aco) CAETHG_1051, 2752, T 4 Isocitrate dehydrogenase (Idh) CAETHG_2753, T 5 Malate dehydrogenase (Mdh) CAETHG_1702, 2478, 2689, T 6 Fumarase CAETHG_1902-03, 2062, 2479, T 7 Fumarate reductase CAETHG_0344, 1032, 2961. Glycolysis/Gluconeogenesis. PTS Fructose phosphotransferase system (PTS) CAETHG_0142, 0676-73, G...”

CD0834 putative isocitrate/3-isopropylmalate dehydrogenase from Clostridium difficile 630
Q18A33 Isocitrate dehydrogenase NAD-dependent from Clostridioides difficile (strain 630)
41% identity, 83% coverage

• c-di-AMP signaling is required for bile salt resistance, osmotolerance, and long-term host colonization by Clostridioides difficile
  Oberkampf, Science signaling 2022
  • “...10 03 CD2883 ( celB ) PTS system, cellobiose-specific IIC component 2.16 1.01 10 03 CD0834 ( icd ) Isocitrate dehydrogenase 2.15 8.14 10 03 CD0723 ( lpdA ) Dihydrolipoyl dehydrogenase 2.13 5.02 10 05 CD0722 ( metF ) 5,10-Methylenetetrahydrofolate reductase 2.11 5.32 10 05 CD0203...”
• Mining Autoimmune-Disorder-Linked Molecular-Mimicry Candidates in Clostridioides difficile and Prospects of Mimic-Based Vaccine Design: An In Silico Approach
  Alshamrani, Microorganisms 2023
  • “...QWS55239.1 Q18CT5 3 AGDGTTTATVLA VVAVKAPGFGD DALNATRAAVEEGIV 1.22 3.61 18 Isocitrate/isopropylmalate dehydrogenase family protein P50213 QWS55807.1 Q18A33 5 VTLIPGDGIGPE VMPNLYGDILSDL AGDGTTTATVLA VVAVKAPGFGD DALNATRAAVEEGIV 0.89 1.48 19 Phosphoribosylaminoimidazolecarboxamide formyltransferase P31939 QWS55813.1 Q18A34 5 WQLVKELKEA SFKHVSPAGAAVG REVSDGIIAPGY KYTQSNSVCYAK GAGQQSRIHCTRLAG 0.73 1.23 20 Acyl-CoA dehydrogenase P16219 QWS55947.1 Q18AQ1 2 LIFEDCRIPK...”

CLJU_c06630 isocitrate/isopropylmalate dehydrogenase family protein from Clostridium ljungdahlii DSM 13528
38% identity, 83% coverage

• Pleiotropic Regulator GssR Positively Regulates Autotrophic Growth of Gas-Fermenting Clostridium ljungdahlii
  Zhang, Microorganisms 2023
  • “...metabolism 10 CLJU_c20480 urea carboxylase 4.98 Hydrolase 11 CLJU_c37390 pyruvate carboxylase 3.69 Carbohydrate metabolism 12 CLJU_c06630 isocitrate dehydrogenase (NAD + ) 4.36 Carbohydrate metabolism 13 CLJU_c25360 malate dehydrogenase (oxaloacetate-decarboxylating) 4.10 Carbohydrate metabolism 14 CLJU_c15270 (S)-ureidoglycine aminohydrolase 4.16 Nucleotide metabolism 15 CLJU_c22770 biotin synthase 3.59 Metabolism of...”

6lkyA / Q602J2 Crystal structure of isocitrate dehydrogenase from methylococcus capsulatus
37% identity, 88% coverage

• Ligand: nicotinamide-adenine-dinucleotide (6lkyA)

GOX1336 Isocitrate dehydrogenase [NADP] from Gluconobacter oxydans 621H
38% identity, 84% coverage

• Global mRNA decay and 23S rRNA fragmentation in Gluconobacter oxydans 621H
  Kranz, BMC genomics 2018
  • “..., gluconokinase (GOX1709); gno , gluconate 5-dehydrogenase (GOX2187); gpm phosphoglyceromutase (GOX0330); icd , isocitrate dehydrogenase (GOX1336); lpd , dihydrolipoamide dehydrogenase (GOX2292); mqo , malate:quinone oxidoreductase (GOX2070); odhA , 2-oxoglutarate dehydrogenase E1 component (GOX0882); odhB , dihydrolipoamide succinyltransferase E2 component of 2-oxoglutarate dehydrogenase complex (GOX1073); pdc ,...”
• Combined fluxomics and transcriptomics analysis of glucose catabolism via a partially cyclic pentose phosphate pathway in Gluconobacter oxydans 621H
  Hanke, Applied and environmental microbiology 2013
  • “...GOX1704 GOX1705 GOX0145 GOX1381 GOX1643 GOX0431 GOX1335 GOX1336 mRNA ratio of 45 genes, 2.0; 66 genes, 0.5 Triosephosphate isomerase Ribose-5-phosphate...”
  • “...(acn, GOX1335, ratio of 0.4), isocitrate dehydrogenase (icd, GOX1336, ratio of 0.3), and fumarate hydratase (fumC, GOX1643, ratio of 0.5). Genes involved in...”

P33197 isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) from Thermus thermophilus (see 2 papers)
icd / RF|YP_144801.1 isocitrate dehydrogenase (NADP(+)); EC 1.1.1.42 from Thermus thermophilus HB8 (see 2 papers)
TTHA1535 isocitrate dehydrogenase from Thermus thermophilus HB8
37% identity, 70% coverage

• Lysine propionylation is a prevalent post-translational modification in Thermus thermophilus
  Okanishi, Molecular & cellular proteomics : MCP 2014
  • “...TTHA1146 TTHA1272 TTHA1273 TTHA1275 TTHA1279 TTHA1343 TTHA1378 TTHA1454 TTHA1535 K250 K73 K22 K274 K299, K317 K59 K115, K357, K415 K55, K120 K62 K176...”
  • “...TTHA0543, Spot No. 46; TTHA1028, Spot Nos. 180 and 181; TTHA1535, Spot No. 47; TTHA1838, Spot No. 150; TTHA1839, Spot Nos. 24 and 25; TTHA1840, Spot Nos. 60 and...”

2d1cA / P33197 Crystal structure of tt0538 protein from thermus thermophilus hb8
37% identity, 71% coverage

• Ligand: nadp nicotinamide-adenine-dinucleotide phosphate (2d1cA)

TTC1172 No description from Thermus thermophilus HB27
36% identity, 70% coverage

• In vitro transcription-translation using bacterial genome as a template to reconstitute intracellular profile
  Fujiwara, Nucleic acids research 2017
  • “...( 33 , 34 ). For the compatibility assay, three promoter-SD sequences sets (TTC1532, TTC0834, TTC1172) were amplified from Thermus thermophilus HB27 genome (Tth genome) by PCR. Then, the amplified fragment was fused with sfGFP gene by overlap PCR. The PCR product was cloned into pUC19...”
  • “...) Plasmid harbouring sets of promoter and SD sequence of three Thermus genes (TTC1532, TTC0834, TTC1172) fused with upstream of the reporter, sfGFP gene, were constructed for the compatibility assay. ( B ) GFP synthesized by EcoS30 and the reporter plasmids were detected from fluorescent signals...”

NP_728257 isocitrate dehydrogenase 3a, isoform C from Drosophila melanogaster
35% identity, 93% coverage

• The Krebs Cycle Enzyme Isocitrate Dehydrogenase 3A Couples Mitochondrial Metabolism to Synaptic Transmission.
  Ugur, Cell reports 2017
  • GeneRIF: A role for isocitrate dehydrogenase 3a (idh3a), a Krebs cycle enzyme, in neurotransmission, is reported.

Q9VWH4 Probable isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial from Drosophila melanogaster
35% identity, 93% coverage

• A proteomic approach reveals the differential protein expression in Drosophila melanogaster treated with red ginseng extract (Panax ginseng)
  Liu, Journal of ginseng research 2018
  • “...cytoskeleton Increase 15 P13706 Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic (GPDA) 396 39.2/6.17 NAD binding Decrease 16 Q9VWH4 Probable isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (IDH3A) 202 38.9/6.96 Isocitrate dehydrogenase (NAD+) activity Decrease 17 Q9W0T1 Nucleosome-remodeling factor subunit NURF301 (NU301) gene E(bx) 291 32.7/5.58 Ligand-dependent nuclear receptor binding...”
• Temporal regulation of proteome profile in the fruit fly, Drosophila melanogaster
  Subramanian, PeerJ 2016
  • “...15 34 155 Glycerol-3-phosphate dehydrogenase P13706 39659 6.17 96 7 26 35 156 Isocitrate dehydrogenase Q9VWH4 40818 6.96 63 7 21 36 157 Glyceraldehyde-3-phosphate dehydrogenase P07486 35328 8.26 106 2 8 37 159 ATP synthase subunit P35381 59384 9.09 380 10 20 38 161 Thioredoxin reductase...”

APA386B_2558 isocitrate/isopropylmalate dehydrogenase family protein from Acetobacter pasteurianus 386B
36% identity, 85% coverage

• Complete genome sequence and comparative analysis of Acetobacter pasteurianus 386B, a strain well-adapted to the cocoa bean fermentation ecosystem
  Illeghems, BMC genomics 2013
  • “...(39) malate dehydrogenase (APA386B_1600); (40) aconitate hydratase 1 (APA386B_1323); (41) NAD + -dependent isocitrate dehydrogenase (APA386B_2558); (42) NADP + -dependent isocitrate dehydrogenase (APA386B_2121); (43) 2-oxoglutarate dehydrogenase E1 (APA386B_2269); (44) 2-oxoglutarate dehydrogenase E2 (APA386B_2270); (45) fumarate reductase/succinate dehydrogenase (APA386B_1513 - APA386B_1516); (46) fumarate hydratase (APA386B_321 and APA386B_1305);...”

IDH3A_BOVIN / P41563 Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial; Isocitrate dehydrogenase subunits 3/4; Isocitric dehydrogenase subunit alpha; NAD(+)-specific ICDH subunit alpha; EC 1.1.1.41 from Bos taurus (Bovine) (see paper)
31% identity, 93% coverage

• function: Catalytic subunit of the enzyme which catalyzes the decarboxylation of isocitrate (ICT) into alpha-ketoglutarate. The heterodimer composed of the alpha (IDH3A) and beta (IDH3B) subunits and the heterodimer composed of the alpha (IDH3A) and gamma (IDH3G) subunits, have considerable basal activity but the full activity of the heterotetramer (containing two subunits of IDH3A, one of IDH3B and one of IDH3G) requires the assembly and cooperative function of both heterodimers.
  catalytic activity: D-threo-isocitrate + NAD(+) = 2-oxoglutarate + CO2 + NADH (RHEA:23632)
  cofactor: Mg(2+) Mn(2+) (Divalent metal cations; Mn(2+) or Mg(2+). Activity higher in presence of Mn(2+) than of Mg(2+). Binds 1 Mg(2+) or Mn(2+) ion per subunit.)
  subunit: Heterooligomer of subunits alpha (IDH3A), beta (IDH3B), and gamma (IDH3G) in the apparent ratio of 2:1:1. The heterodimer containing one IDH3A and one IDH3B subunit and the heterodimer containing one IDH3A and one IDH3G subunit assemble into a heterotetramer (which contains two subunits of IDH3A, one of IDH3B and one of IDH3G) and further into the heterooctamer.
• New Biological Insights on X and Y Chromosome-Bearing Spermatozoa.
  Rahman, Frontiers in cell and developmental biology 2019
  • “...AAI05544 1.58 Tubulin alpha-3 chain (TUBA3) Q32KN8 1.68 Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (IDH3A) P41563 1.83 Chain A, the structure of crystalline profilin-beta-actin 2BTF_A 1.69 A Chain A, episelection: Novel Ki nanomolar inhibitors of serine proteases 1BTW_A 1.8 LC-MS R Chain R, zinc ion binding...”
• Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi.
  Islam, Microbial biotechnology 2016
  • “...P39126 ), E .coli ( P08200 ), C .maris ( P41560 ), B .taurus ( P41563 ) and H .sapiens ( P50213 ). 2015 Society for Applied Microbiology and John Wiley & Sons Ltd MSA of Dm PMI sequence with its biochemically characterized or manually reviewed...”

XF2596 isocitrate dehydrogenase from Xylella fastidiosa 9a5c
WP_010895014 isocitrate dehydrogenase from Xylella fastidiosa 32
34% identity, 86% coverage

• The iron stimulon of Xylella fastidiosa includes genes for type IV pilus and colicin V-like bacteriocins
  Zaini, Journal of bacteriology 2008
  • “...2 % % % Energy metabolism XF1535 XF2596 XF0942 XF2547 XF2548 XF0290 Citrate synthase Isocitrate dehydrogenase Malate:quinone oxidoreductase Succinyl-CoA...”
• Enzymatic characterization and functional implication of two structurally different isocitrate dehydrogenases from Xylella fastidiosa.
  Lv, Biotechnology and applied biochemistry 2018 (PubMed)
  • GeneRIF: Xylella fastidiosa is a nutritionally fastidious plant pathogen that contains two structurally different isocitrate dehydrogenases (IDHs), an NAD(+) -dependent homodimeric IDH (diXfIDH) and an NADP(+) -dependent monomeric IDH (monoXfIDH). Kinetic characterization showed that diXfIDH displayed 206-fold preferences for NAD(+) over NADP(+) , while monoXfIDH showed 13,800-fold preferences for NADP(+) over NAD(+) .

G3H0B5 Isocitrate dehydrogenase [NAD] subunit, mitochondrial from Cricetulus griseus
31% identity, 93% coverage

• Characterization of glutathione proteome in CHO cells and its relationship with productivity and cholesterol synthesis
  Chevallier, Biotechnology and bioengineering 2020
  • “...(Aconitase; EC 4.2.1.) 0.20 6.3810 5 G3H450 Isocitrate dehydrogenase (NAD) subunit, mitochondrial 0.19 2.0710 3 G3H0B5 Isocitrate dehydrogenase (NAD) subunit, mitochondrial 0.10 1.7010 2 G3HSW9 Isocitrate dehydrogenase (NAD) subunit, mitochondrial 0.13 2.4610 2 G3HU51 Isocitrate dehydrogenase (NADP) 0.34 2.8410 7 G3IHC0 Isocitrate dehydrogenase (NADP) 0.13 2.8710...”

G1TA59 Isocitrate dehydrogenase [NAD] subunit, mitochondrial from Oryctolagus cuniculus
32% identity, 85% coverage

• Proteomic Analyses Reveals the Mechanism of Acupotomy Intervention on the Treatment of Knee Osteoarthritis in Rabbits.
  Liu, Evidence-based complementary and alternative medicine : eCAM 2022
  • “...subunit (SDH1, accession: A0A5F9CIE2), oxoglutarate dehydrogenase (OGDH, accession: A0A5F9CUY0), isocitrate dehydrogenase [NAD] subunit (IDH3s, accession: G1TA59, A0A5F9D9Z6), dihydrolipoamide S-succinyltransferase (DLST, accession: A0A5F9CAW7), ATP synthase subunit alpha (ATP5F1A, accession: G1SKT4), ubiquinol-cytochrome c reductase core protein 1 (UQCRC1, accession: G1SGP1), succinate-CoA ligase subunit alpha (SUCLG1, accession: G1SKD9), acetyltransferase...”
  • “...12 0.64 0.0142 A0A5F9CIE2 Succinate dehydrogenase [ubiquinone] flavoprotein subunit SDH1 60.33 15.00 7 0.69 0.0231 G1TA59 Isocitrate dehydrogenase [NAD] subunit, mitochondrial IDH3A 49.04 11.00 4 0.64 0.0137 A0A5F9D9Z6 Isocitrate dehydrogenase [NAD] subunit, mitochondrial IDH3B 40.96 14.40 4 0.74 0.0108 G1TUX2 Aconitate hydratase, mitochondrial ACO2 87.35 33.10...”

IDH3A_MOUSE / Q9D6R2 Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial; Isocitric dehydrogenase subunit alpha; NAD(+)-specific ICDH subunit alpha; EC 1.1.1.41 from Mus musculus (Mouse) (see paper)
Q9D6R2 isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) from Mus musculus (see paper)
NP_083849 isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor from Mus musculus
31% identity, 93% coverage

• function: Catalytic subunit of the enzyme which catalyzes the decarboxylation of isocitrate (ICT) into alpha-ketoglutarate. The heterodimer composed of the alpha (IDH3A) and beta (IDH3B) subunits and the heterodimer composed of the alpha (IDH3A) and gamma (IDH3G) subunits, have considerable basal activity but the full activity of the heterotetramer (containing two subunits of IDH3A, one of IDH3B and one of IDH3G) requires the assembly and cooperative function of both heterodimers.
  catalytic activity: D-threo-isocitrate + NAD(+) = 2-oxoglutarate + CO2 + NADH (RHEA:23632)
  cofactor: Mg(2+) Mn(2+) (Divalent metal cations; Mn(2+) or Mg(2+). Activity higher in presence of Mn(2+) than of Mg(2+). Binds 1 Mg(2+) or Mn(2+) ion per subunit.)
  subunit: Heterooligomer of subunits alpha (IDH3A), beta (IDH3B), and gamma (IDH3G) in the apparent ratio of 2:1:1. The heterodimer containing one IDH3A and one IDH3B subunit and the heterodimer containing one IDH3A and one IDH3G subunit assemble into a heterotetramer (which contains two subunits of IDH3A, one of IDH3B and one of IDH3G) and further into the heterooctamer.
  disruption phenotype: IDH3A-null homozygous mice do not survive early embryogenesis (PubMed:30478029). Compound heterozygous mice for the IDH3A-null allele and mutant p.E229K are viable and exhibit rapid retinal degeneration (PubMed:30478029).
• Bifenthrin Diminishes Male Fertility Potential by Inducing Protein Defects in Mouse Sperm
  Bae, Toxics 2024
  • “...b 92 25,817 TEPP Q6IMH0 Testis, prostate, and placenta-expressed protein isoform 2 85 12,510 IDH3A Q9D6R2 Isocitrate dehydrogenase (NAD) subunit alpha, mitochondrial 62 40,069 * Protein score is 10 log (p), where p is the probability that the observed match is a random event. Individual scores...”
• Changes in protein fluxes in skeletal muscle during sequential stages of muscle regeneration after acute injury in male mice.
  Bizieff, Scientific reports 2024
  • “...subunit 4 isoform 1 P19783 OxPhos 13.4076.626% 9.1011.772%* 3.7731.137% 91 Isocitrate dehydrogenase [NAD] subunit alpha Q9D6R2 OxPhos 12.6916.118% 5.3502.844% 3.3881.499% 92 Malate dehydrogenase P14152 Cytoplasm 10.2226.133% 9.0543.799%* 3.0490.749% 93 Citrate synthase Q9CZU6 Mitochondria 13.9958.577% 8.7801.445%* 2.5810.272% 94 Cytochrome c oxidase subunit NDUFA4 Q62425 OxPhos 19.2039.895% 13.5293.471%*...”
• Protein crotonylation: Basic research and clinical diseases.
  Li, Biochemistry and biophysics reports 2024
  • “...P16671 Chronic renal failure (CRF) [ 69 ] Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial IDH3a Q9D6R2 K199 Ischemic heart disease (IHD) [ 72 ] Microtubule-associated protein RP/EB family member 1 EB1 Q8WQ86 K66 Spindle positioning [ 94 ] Tropomyosin alpha-1 chain TPM1 P58771 K28 Ishemia-Reperfusion Injury...”
• Neuronal SIRT3 Deletion Predisposes to Female-Specific Alterations in Cellular Metabolism, Memory, and Network Excitability
  Pearson-Smith, The Journal of neuroscience : the official journal of the Society for Neuroscience 2023 (secret)
• Peptidyl arginine deiminase inhibition alleviates angiotensin II-induced fibrosis.
  Ijichi, American journal of translational research 2023
• Multi-Omic Profiling of Macrophages Treated with Phospholipids Containing Omega-3 and Omega-6 Fatty Acids Reveals Complex Immunomodulatory Adaptations at Protein, Lipid and Metabolic Levels
  Maurício, International journal of molecular sciences 2022
  • “...of 13 proteins (O88569, P61164, Q60737, Q9CZ13, P70404, P97807.1, P56480, P05202, Q9DB77, Q8QZT1, Q8BFR5, and Q9D6R2) is strongly downregulated by 6 PC either in the presence or absence of LPS. Among the 37 proteins, five (P41241, P00493, Q00612, Q9ESY9, and Q09014) are involved in the immune...”
• Multiple Herpes Simplex Virus-1 (HSV-1) Reactivations Induce Protein Oxidative Damage in Mouse Brain: Novel Mechanisms for Alzheimer's Disease Progression
  Protto, Microorganisms 2020
  • “...OS = Mus musculus GN = Idh3a PE = 1 SV = 1 - [IDH3A_MOUSE] Q9D6R2 4.5 5.6 9.84 3 39.6 6.73 7204 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 OS=Mus musculus GN = Gnb1 PE = 1 SV = 3 - [GBB1_MOUSE] P62874 45 4.38 7.35...”
• Myeloperoxidase-Derived 2-Chlorohexadecanal Is Generated in Mouse Heart during Endotoxemia and Induces Modification of Distinct Cardiomyocyte Protein Subsets In Vitro.
  Prasch, International journal of molecular sciences 2020
  • “...aldolase A 39,811.6 8.75 P17182 Eno1 Alpha-enolase 47,482.3 6.37 P16858 Gapdh Glyceraldehyde-3-phosphate dehydrogenase 36,094.6 8.76 Q9D6R2 Idh3a Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial 40,094.5 6.27 P06151 Ldha L-lactate dehydrogenase A chain 36,840.2 7.84 Q91WD5 Ndufs2 NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial 53,024.1 6.52 Q9DBJ1 Pgam1...”
• More
• miR-9-5p regulates immunometabolic and epigenetic pathways in β-glucan-trained immunity via IDH3α.
  Su, JCI insight 2021
  • GeneRIF: miR-9-5p regulates immunometabolic and epigenetic pathways in beta-glucan-trained immunity via IDH3alpha.
• Mouse Idh3a mutations cause retinal degeneration and reduced mitochondrial function.
  Findlay, Disease models & mechanisms 2018
  • GeneRIF: the role of IDH3 in retinal disease and mitochondrial function, was investigated.
• Application of fluorescence two-dimensional difference in-gel electrophoresis as a proteomic biomarker discovery tool in muscular dystrophy research
  Carberry, Biology 2013
  • “...2.1 33 Alpha-fetoprotein AAA37190 95 5.47 48,819 2 5 2.1 34 Isocitrate dehydrogenase subunit alpha NP_083849 242 6.27 40,077 6 20 2.1 35 L-lactate dehydrogenase B chain NP_032518 54 5.7 36,839 5 12 2.1 36 Actin, alpha, cardiac gi|387090 51 5.23 42,048 2 7 2.1 37...”
  • “...transferring flavoprotein, alpha AAH03432 449 8.62 35,366 11 44 2.4 56 Isocitrate dehydrogenase subunit alpha NP_083849 167 6.27 40,077 6 19 2.4 57 Malate dehydrogenase 2, mitochondrial ABD77283 85 7.7 32,121 2 8 2.4 58 Creatine kinase, M-type NP_031736 404 6.58 43,250 11 33 2.4 59...”

Q28480 Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (Fragment) from Macaca fascicularis
31% identity, 93% coverage

• Intrinsic protein kinase activity in mitochondrial oxidative phosphorylation complexes.
  Phillips, Biochemistry 2011
  • “...II P23004 2 15 Long-chain specific acyl Coenzyme A dehydrogenase P51174 2 16 Isocitrate dehydrogenase Q28480 3 17 Pyruvate dehydrogenase, E1 beta subunit P11177 2 18 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9, 39kDa Q0MQB3 2 19 Malate dehydrogenase P00346 6 20 Complex V, gamma subunit...”

XAC1046 isocitrate dehydrogenase from Xanthomonas axonopodis pv. citri str. 306
XAUB_41080 isocitrate dehydrogenase from Xanthomonas citri pv. aurantifolii str. ICPB 11122
35% identity, 86% coverage

• Periplasm-enriched fractions from Xanthomonas citri subsp. citri type A and X. fuscans subsp. aurantifolii type B present distinct proteomic profiles under in vitro pathogenicity induction
  Zandonadi, PloS one 2020
  • “...XauB 4,21E-01 Unique 0,00248762 XAUB_41080 Isocitrate dehydrogenase 35.7 5.4 38.4 4.6 401 15 25 I (XAC1046) C XAUB_40770 Outer membrane protein (4) 39.7 4.6 131 14 30 IV (XAC1012) OM+ XAUB_20300 Glyceraldehyde-3-phosphate dehydrogenase (3) 36.2 6.0 40 3 6 I (XAC3352) C 11 XauB 2,15E-01 Unique...”
• Periplasm-enriched fractions from Xanthomonas citri subsp. citri type A and X. fuscans subsp. aurantifolii type B present distinct proteomic profiles under in vitro pathogenicity induction
  Zandonadi, PloS one 2020
  • “...hydrolase (4) 53.2 5.5 100 8 14 I (XAC0804) C 10 XauB 4,21E-01 Unique 0,00248762 XAUB_41080 Isocitrate dehydrogenase 35.7 5.4 38.4 4.6 401 15 25 I (XAC1046) C XAUB_40770 Outer membrane protein (4) 39.7 4.6 131 14 30 IV (XAC1012) OM+ XAUB_20300 Glyceraldehyde-3-phosphate dehydrogenase (3) 36.2...”

IDH3A_PIG / P56471 Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial; Isocitric dehydrogenase subunit alpha; NAD(+)-specific ICDH subunit alpha; EC 1.1.1.41 from Sus scrofa (Pig) (see paper)
31% identity, 93% coverage

• function: Catalytic subunit of the enzyme which catalyzes the decarboxylation of isocitrate (ICT) into alpha-ketoglutarate. The heterodimer composed of the alpha (IDH3A) and beta (IDH3B) subunits and the heterodimer composed of the alpha (IDH3A) and gamma (IDH3G) subunits, have considerable basal activity but the full activity of the heterotetramer (containing two subunits of IDH3A, one of IDH3B and one of IDH3G) requires the assembly and cooperative function of both heterodimers.
  catalytic activity: D-threo-isocitrate + NAD(+) = 2-oxoglutarate + CO2 + NADH (RHEA:23632)
  cofactor: Mg(2+) Mn(2+) (Divalent metal cations; Mn(2+) or Mg(2+). Activity higher in presence of Mn(2+) than of Mg(2+). Binds 1 Mg(2+) or Mn(2+) ion per subunit.)
  subunit: Heterooligomer of subunits alpha (IDH3A), beta (IDH3B), and gamma (IDH3G) in the apparent ratio of 2:1:1. The heterodimer containing one IDH3A and one IDH3B subunit and the heterodimer containing one IDH3A and one IDH3G subunit assemble into a heterotetramer (which contains two subunits of IDH3A, one of IDH3B and one of IDH3G) and further into the heterooctamer.
• Comparative proteomic analysis reveals different responses in porcine lymph nodes to virulent and attenuated homologous African swine fever virus strains
  Herrera-Uribe, Veterinary research 2018
  • “...26 5.1 0.0004 1640 P01009 SERPINA1 Alpha-1-antitrypsin Sus scrofa 5.54 47.4 11 4.2 0.0029 6332 P56471 IDH3A Isocitratedehydrogenase [NAD] subunitalpha Sus scrofa 6.72 40.10 50 4.0 0.0003 1130 P52552 PRDX2 Peroxiredoxin-2 Sus scrofa 4.66 14.10 36 3.6 0.0000 1224 P08758 ANXA5 Annexin A5 Homo sapiens 4.94...”

PADG_02805 isocitrate dehydrogenase [NAD] subunit 2, mitochondrial from Paracoccidioides brasiliensis Pb18
C1G6K0 isocitrate dehydrogenase (NAD(+)) from Paracoccidioides brasiliensis (strain Pb18)
33% identity, 93% coverage

• Effect of Nitrosative Stress on the S-Nitroso-Proteome of Paracoccidioides brasiliensis
  Navarro, Frontiers in microbiology 2020
  • “...40S ribosomal protein S27 639.72 PADG_04440 C1GB04 Uncharacterized protein 634.92 PADG_04516 C1GBZ4 Glutamate dehydrogenase 633.89 PADG_02805 C1G6K0 Isocitrate dehydrogenase [NAD] subunit, mitochondrial 614.55 PADG_00354 C1G0G4 40S ribosomal protein S17 612.26 PADG_00872 C1FYJ6 Histone H4 598.41 PADG_05517 C1GE31 Uncharacterized protein 555.52 PADG_01267 C1G2V1 40S ribosomal protein S11...”
• Effect of Nitrosative Stress on the S-Nitroso-Proteome of Paracoccidioides brasiliensis
  Navarro, Frontiers in microbiology 2020
  • “...ribosomal protein S27 639.72 PADG_04440 C1GB04 Uncharacterized protein 634.92 PADG_04516 C1GBZ4 Glutamate dehydrogenase 633.89 PADG_02805 C1G6K0 Isocitrate dehydrogenase [NAD] subunit, mitochondrial 614.55 PADG_00354 C1G0G4 40S ribosomal protein S17 612.26 PADG_00872 C1FYJ6 Histone H4 598.41 PADG_05517 C1GE31 Uncharacterized protein 555.52 PADG_01267 C1G2V1 40S ribosomal protein S11 502.35...”

PAAG_07729 isocitrate dehydrogenase subunit 2 from Paracoccidioides lutzii Pb01
33% identity, 93% coverage

• Interaction of Isocitrate Lyase with Proteins Involved in the Energetic Metabolism in Paracoccidioides lutzii
  Freitas, Journal of fungi (Basel, Switzerland) 2020
  • “...dihydrolipoyl dehydrogenase 18,252.14 PAAG_00417 succinyl-CoA ligase subunit alpha 15,495.53 PAAG_01463 succinyl-CoA ligase subunit beta 45,050.75 PAAG_07729 isocitrate dehydrogenase subunit 2 29,021.65 PAAG_00053 malate dehydrogenase 64,147.15 PAAG_08449 malate dehydrogenase 40,336.05 PAAG_05048 3-isopropylmalate dehydratase large subunit 24,897.33 Electron transport 16,888.22 PAAG_04820 ATPase alpha subunit 17,866.72 Respiration 82,884.62 PAAG_06796...”
  • “...5375.759 PAAG_08203 phosphoenolpyruvate carboxykinase 4991.925 Tricarboxylic-acid pathway PAAG_01534 pyruvate dehydrogenase E1 component subunit beta 3429.868 PAAG_07729 isocitrate dehydrogenase subunit 2 4581.662 PAAG_08449 malate dehydrogenase 3811.987 PAAG_00053 malate dehydrogenase 2309.6 PAAG_05048 3-isopropylmalate dehydratase large subunit 3299.345 Electron transport PAAG_04820 ATPase alpha subunit 4619.729 Respiration PAAG_08037 ATP synthase...”
• Proteomic profile response of Paracoccidioides lutzii to the antifungal argentilactone
  Prado, Frontiers in microbiology 2015
  • “...dehydrogenase PAAG_08449 7490.87 0.756 Isocitrate dehydrogenase subunit 1 PAAG_00856 1820.37 * Isocitrate dehydrogenase subunit 2 PAAG_07729 1604.29 * Succinate dehydrogenase flavoprotein subunit, mitochondrial PAAG_01725 1798.19 0.827 Oxidation of fatty acids Short-chain specific acyl-CoA dehydrogenase PAAG_05454 1028.15 * Transport Carbonic anhydrase PAAG_05716 854.25 0.795 Clathrin light chain...”

D2VQ70 Isocitrate dehydrogenase from Naegleria gruberi
35% identity, 92% coverage

• Identification of Immunogenic Antigens of Naegleria fowleri Adjuvanted by Cholera Toxin
  Rojas-Hernández, Pathogens (Basel, Switzerland) 2020
  • “...protein (D2VSP0) ; Malate dehydrogenase (D2VZB1) ; Prohibitin (D2W2C5) ; Isocitrate dehydrogenase NAD subunit mitochondrial (D2VQ70) ; Isocitrate dehydrogenase NADP dependent (D2VRD7) ; Mitochondrial trans-2 enoyl CoA reductase (D2VNA9) ; Inosine 5 monophosphate dehydrogenase (D2UY23) ; ATP synthase subunit beta (D2V5T0) ; Predicted protein (D2VKI4) ;...”

Afu1g12800 isocitrate dehydrogenase, NAD-dependent from Aspergillus fumigatus Af293
34% identity, 87% coverage

• Transcriptomic analysis of the exit from dormancy of Aspergillus fumigatus conidia
  Lamarre, BMC genomics 2008
  • “...carbon and nitrogen flux through the 2-ketoglutarate towards amino acid biosynthesis. The NADPH isocitrate dehydrogenase (Afu1g12800) that produces the 2-ketoglutarate was also highly activated. Succinate dehydrogenase (Afu3g07810), also coupling TCA cycle to amino acid synthesis through the intermediary of 2-ketoglutarate was up-regulated. Cellular transport Although the...”

IDH3A / P50213 Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (EC 1.1.1.286) from Homo sapiens (see 2 papers)
IDH3A_HUMAN / P50213 Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial; Isocitric dehydrogenase subunit alpha; NAD(+)-specific ICDH subunit alpha; EC 1.1.1.41 from Homo sapiens (Human) (see 5 papers)
P50213 isocitrate dehydrogenase (NAD+) (subunit 2/2) (EC 1.1.1.41) from Homo sapiens (see paper)
31% identity, 93% coverage

• function: Catalytic subunit of the enzyme which catalyzes the decarboxylation of isocitrate (ICT) into alpha-ketoglutarate. The heterodimer composed of the alpha (IDH3A) and beta (IDH3B) subunits and the heterodimer composed of the alpha (IDH3A) and gamma (IDH3G) subunits, have considerable basal activity but the full activity of the heterotetramer (containing two subunits of IDH3A, one of IDH3B and one of IDH3G) requires the assembly and cooperative function of both heterodimers.
  catalytic activity: D-threo-isocitrate + NAD(+) = 2-oxoglutarate + CO2 + NADH (RHEA:23632)
  cofactor: Mg(2+) Mn(2+) (Divalent metal cations; Mn(2+) or Mg(2+). Activity higher in presence of Mn(2+) than of Mg(2+). Binds 1 Mg(2+) or Mn(2+) ion per subunit.)
  subunit: Heterooligomer of subunits alpha (IDH3A), beta (IDH3B), and gamma (IDH3G) in the apparent ratio of 2:1:1. The heterodimer containing one IDH3A and one IDH3B subunit and the heterodimer containing one IDH3A and one IDH3G subunit assemble into a heterotetramer (which contains two subunits of IDH3A, one of IDH3B and one of IDH3G) and further into the heterooctamer.
• Proteomic analysis reveals changes in the proteome of human THP-1 macrophages infected with <i>Paracoccidioides brasiliensis</i>
  de, Frontiers in cellular and infection microbiology 2023
  • “...synthase 1520.56 * O75390 Citrate synthase_ mitochondrial 12200.29 * A2A274 Aconitate hydratase_ mitochondrial 916.17 * P50213 Isocitrate dehydrogenase [NAD] subunit alpha_ mitochondrial 1918.82 * O75874 Isocitrate dehydrogenase [NADP] cytoplasmic 975.87 * P09622 Dihydrolipoyl dehydrogenase_ mitochondrial 1686.78 * P53597 SuccinateCoA ligase [ADP/GDP-forming] subunit alpha_ mitochondrial 651.86 *...”
• Mining Autoimmune-Disorder-Linked Molecular-Mimicry Candidates in Clostridioides difficile and Prospects of Mimic-Based Vaccine Design: An In Silico Approach.
  Alshamrani, Microorganisms 2023
  • “...GroEL P10809 QWS55239.1 Q18CT5 3 AGDGTTTATVLA VVAVKAPGFGD DALNATRAAVEEGIV 1.22 3.61 18 Isocitrate/isopropylmalate dehydrogenase family protein P50213 QWS55807.1 Q18A33 5 VTLIPGDGIGPE VMPNLYGDILSDL AGDGTTTATVLA VVAVKAPGFGD DALNATRAAVEEGIV 0.89 1.48 19 Phosphoribosylaminoimidazolecarboxamide formyltransferase P31939 QWS55813.1 Q18A34 5 WQLVKELKEA SFKHVSPAGAAVG REVSDGIIAPGY KYTQSNSVCYAK GAGQQSRIHCTRLAG 0.73 1.23 20 Acyl-CoA dehydrogenase P16219 QWS55947.1 Q18AQ1...”
  • “...] H. pylori [ 117 ], P. aeruginosa and S. aureus [ 118 ] 16 P50213 Isocitrate dehydrogenase [NAD] subunit alpha Psoriasis - Huntingtons disease, Parkinsons disease EpsteinBarr virus, HCV, Legionellosis Atherosclerosis [ 119 ], Type I diabetes [ 120 ] H. pylori [ 117 ]...”
• Distinct or Overlapping Areas of Mitochondrial Thioredoxin 2 May Be Used for Its Covalent and Strong Non-Covalent Interactions with Protein Ligands.
  Ntallis, Antioxidants (Basel, Switzerland) 2023
  • “...15 P00395 Cytochrome c oxidasesubunit 1 5z62 (chain A) 17.92 1utrAB 9.9 58 NC 16 P50213 Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial 7ce3 (chain A) 17.46 1f9mAB 5.8 58,000 C 17 P49247 Ribose 5-phosphateisomerase A AF 15.87 3md9AB 9.3 150 NM BioGRID 18 P08559 Pyruvate dehydrogenase...”
• CLPX regulates mitochondrial fatty acid β-oxidation in liver cells.
  Suzuki, The Journal of biological chemistry 2023
  • “...enzyme subunit alpha, mitochondrial 10 17 P55084 HADHB Trifunctional enzyme subunit beta, mitochondrial 2 2 P50213 IDH3A Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial 1 6 Q92552 MRPS27 28S ribosomal protein S27, mitochondrial 2 2 P52815 MRPL12 39S ribosomal protein L12, mitochondrial 2 7 P00403 MT-CO2 Cytochrome...”
• Radiobiological effects of wound fluid on breast cancer cell lines and human-derived tumor spheroids in 2D and microfluidic culture.
  Jeibouei, Scientific reports 2022
  • “...P-value Genes hsa01200:Carbon metabolism 11 14.10256 8.49E09 Q6NVY1, P08559, P36957, O75874, P40925, Q02252, P11766, P05166, P50213, Q96I99, Q9P2R7 hsa00020:Citrate cycle (TCA cycle) 7 8.974359 7.17E08 P08559, P36957, O75874, P40925, P50213, Q96I99, Q9P2R7 hsa00071:Fatty acid degradation 8 10.25641 2.05E08 P42765, Q16836, P49189, P00325, P11766, P55084, P49419, P49748...”
• Identification of Predictive Biomarkers of Response to HSP90 Inhibitors in Lung Adenocarcinoma
  Marrugal, International journal of molecular sciences 2021
  • “...protein B1 P09429 HMGB1 Hydroxymethylglutaryl-CoA synthase, cytoplasmic Q01581 HMGCS1 Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial P50213 IDH3A Isocitrate dehydrogenase [NADP], mitochondrial P48735 IDH2 Magnesium transporter protein 1 Q9H0U3 MAGT1 Mediator of RNA polymerase II transcription subunit 14 O60244 MED14 Mitotic interactor and substrate of PLK1 Q8IVT2...”
• Isoform-specific dysregulation of AMP-activated protein kinase signaling in a non-human primate model of Alzheimer's disease.
  Wang, Neurobiology of disease 2021
  • “...protein Ral-A RALA P11233 23.6 6.00 7.33 1.22 Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial IDH3A P50213 39.6 13.33 16.33 1.23 Dynein light chain 2, cytoplasmic DYNLL2 Q96FJ2 10.3 5.67 7.00 1.24 Ras-related protein Rap-1A RAP1A P62834 21.0 6.67 8.67 1.30 Guanine nucleotide-binding protein G(q) subunit alpha...”
• Impact of Cryopreservation on Spermatozoa Freeze-Thawed Traits and Relevance OMICS to Assess Sperm Cryo-Tolerance in Farm Animals.
  Khan, Frontiers in veterinary science 2021
  • “...taurus O43236 Down Annulus Flagella- related ( 85 ) Isocitrate dehydrogenase subunit IDH3A Bos taurus P50213 Down Mitochondria Energy- Related ( 139 ) Izumo sperm-egg fusion 1 IZUMO1 Bos taurus/Capra hircus/Sus scrofa Q9D9J7 Sperm cell-surface protein Fertilization ( 64 ) Prostaglandin D2 synthase PTGDS Ovis aries...”
• More

6kdeA / P50213 Crystal structure of the alpha beta heterodimer of human idh3 in complex with ca(2+) (see paper)
31% identity, 93% coverage

• Ligand: calcium ion (6kdeA)

6m3sB / A0A0H2XBX7 Dimeric isocitrate dehydrogenase from xanthomonas campestris pv. Campestris 8004
34% identity, 86% coverage

• Ligands: nicotinamide-adenine-dinucleotide; isocitrate calcium complex (6m3sB)

Q55BI2 Isocitrate dehydrogenase [NAD] regulatory subunit A, mitochondrial from Dictyostelium discoideum
31% identity, 95% coverage

• Proteomic and Transcriptomic Profiling Identifies Early Developmentally Regulated Proteins in Dictyostelium Discoideum
  González-Velasco, Cells 2019
  • “...synthase (SQS) Q55DU3 Actobindin-A Q553V1 Citrate synthase Q65YR7 Cystatin-A2 Q54KB7 Glutamate dehydrogenase Q1ZXH5 Calcium-binding protein Q55BI2 Isocitrate dehydrogenase subunit A P54653 Calcium-binding protein 2 O97470 Substrate carrier family protein ancA Q54RF4 Calcium-binding protein 4a Q54JP5 Probable ornithine aminotransferase P54679 Probable membrane ATPase Q8MP58 Uncharacterized protein Q86AA1...”

NP_446090 isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor from Rattus norvegicus
31% identity, 93% coverage

• A proteomic survey of rat cerebral cortical synaptosomes
  Witzmann, Proteomics 2005
  • “...DESTGSIAK; LQSIGTEN TEENR 1 2 additional peptides - 79 3408 NP_446090 AB047541* 2.43 6.5 40.1 33 - 80 4401 NP_620266 Y15068* 1.56 6.1 40.7 31 - 81 5402 P26284...”

SO1538 isocitrate dehydrogenase, NAD-dependent from Shewanella oneidensis MR-1
34% identity, 85% coverage

• Transcriptional analysis of Shewanella oneidensis MR-1 with an electrode compared to Fe(III)citrate or oxygen as terminal electron acceptor
  Rosenbaum, PloS one 2012
  • “...oxidoreductase, L-lactate dehydrogenase 0.0296 Lactate metabolism 1.413225 SO1521 D-lactate dehydrogenase (dld) 0.0035 Lactate metabolism 1.487265 SO1538 isocitrate dehydrogenase 0.0000 TCA-cycle 1.61607 SO1678 methylmalonate-semialdehyde dehydrogenase 0.0132 1.572969 SO1748 hypothetical protein 0.0075 One type c heme binding motif 2.960933 SO1776 MtrB 0.0000 Outer membrane protein MtrB 2.167019 SO1777...”
• Snapshot of iron response in Shewanella oneidensis by gene network reconstruction
  Yang, BMC genomics 2009
  • “...These genes include methylcitrate synthase (PrpC), 2-methylisocitrate lyase (PrpB), 2-methyl citrate dehydratase (AcnD), isocitrate dehydrogenase (SO1538), and malate dehydrogenase (SfcA). Table 4 Other selected genes differentially expressed during iron depletion and repletion a Gene Annotation Change in expression at: C1' C5' C10' C20' C40' C60' F1'...”
  • “...2-methylisocitrate lyase (PrpB) 0.73 0.70 0.71 2.54 4.35 8.07 1.05 0.45 0.24 0.15 0.33 0.33 SO1538 isocitrate dehydrogenase 0.69 0.95 1.01 5.25 4.04 4.08 0.73 0.44 0.62 0.55 0.66 0.59 SO3855 malate dehydrogenase (SfcA) 0.88 0.92 1.14 3.16 2.73 2.48 1.03 0.97 1.11 1.30 1.17 1.37...”
• Characterization of the Shewanella oneidensis Fur gene: roles in iron and acid tolerance response
  Yang, BMC genomics 2008
  • “...aerobic energy transport, including TCA cycle enzymes malate dehydrogenase (Mdh), succinate dehydrogenase (SdhC), isocitrate dehydrogenase (SO1538) and citrate synthase (GltA). Other related genes include succinylarginine dihydrolase(AstB) and isovaleryl-CoA dehydrogenase (Ivd). Notably, in contrast to the genes involved in anaerobic energy transport, these genes were induced by...”

F1LNF7 Isocitrate dehydrogenase [NAD] subunit, mitochondrial from Rattus norvegicus
31% identity, 93% coverage

• The mitochondrial proteomic changes of rat hippocampus induced by 28-day simulated microgravity.
  Ji, PloS one 2022
  • “...0.006727 KNG1_RAT P08934 Kng1 Kininogen-1 1.68 0.038332 G3V7I0_RAT G3V7I0 Prdx3 Peroxiredoxin 3 1.67 0.003211 F1LNF7_RAT F1LNF7 Idh3a Isocitrate dehydrogenase [NAD] subunit, mitochondrial 1.67 0.005636 Q6IMX3_RAT Q6IMX3 Acads Acetyl-Coenzyme A dehydrogenase, short chain, isoform CRA_a 1.67 0.01089 A0A0G2JVM0_RAT A0A0G2JVM0 Aldh4a1 Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial 1.66 0.007541 D4A8N2_RAT D4A8N2...”
• Global Proteome Changes in the Rat Diaphragm Induced by Endurance Exercise Training
  Sollanek, PloS one 2017
  • “...C D4A5L9 LOC679794 74.5 7.8 83.6 7.5 12 0.035 Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial F1LNF7 Idh3a 75.2 5 83.3 6.4 11 0.015 NADH dehydrogenase (Ubiquinone) flavoprotein 1 Q5XIH3 Ndufv1 102.7 8.6 114.1 9.8 11 0.023 Secreted Proteins Fibrinopeptide A P14480 Fgb 2.6 0.4 3.2 0.5...”

U3I2P1 Isocitrate dehydrogenase [NAD] subunit, mitochondrial from Anas platyrhynchos platyrhynchos
31% identity, 93% coverage

• Maternal diet deficient in riboflavin induces embryonic death associated with alterations in the hepatic proteome of duck embryos
  Tang, Nutrition & metabolism 2019
  • “...DLST 31.87 12 12 1.94 2.55E-02 R0L7Q0 Fumarate hydratase FH 59.83 26 26 1.62 3.80E-03 U3I2P1 Isocitrate dehydrogenase [NAD] subunit, mitochondrial IDH3A 28.88 8 8 3.48 6.67E-03 Fatty acid beta-oxidation R0L018 Carnitine O-palmitoyltransferase I, liver isoform CPT1A 46.10 35 35 5.45 2.10E-14 U3INM7 Carnitine palmitoyltransferase 2...”

TERG_07814 isocitrate dehydrogenase, NAD-dependent from Trichophyton rubrum CBS 118892
34% identity, 83% coverage

• Relevance of Nutrient-Sensing in the Pathogenesis of Trichophyton rubrum and Trichophyton interdigitale
  Cruz, Frontiers in fungal biology 2022
  • “...hydrogenase [NAD] subunit 1, mitochondrial TERG_01670 F: TAAGGACCAGGCTAACCC R: GACGGCTCGGGTGAAC idh2 Isocitratede hydrogenase, NAD-dependent, mitochondrial TERG_07814 F: GGTTCCGCTCCCGATA R:TGTTTTTGATGATGGCGT idhp Isocitrate dehydrogenase [NADP], mitochondrial TERG_06075 F: TCCTGAAGAAATACGATGGC R:CGGCAGGGGTGGTCA icl Isocitrate lyase TERG_00825 F: ACCGACTTGTAGCCATCC R: GTTCTTGCCCGCTTGCTCT meicl Mitochondrial 2-methylisocitrate lyase ( Trichophyton tonsurans ) TERG_01271 F:...”

Q53GF8 Isocitrate dehydrogenase [NAD] subunit, mitochondrial (Fragment) from Homo sapiens
31% identity, 93% coverage

• Proteomics identification of ITGB3 as a key regulator in reactive oxygen species-induced migration and invasion of colorectal cancer cells
  Lei, Molecular & cellular proteomics : MCP 2011
  • “...26 27 28 29 30 31 32 33 Q9Y570 Q15019 Q9Y617 Q53GF8 P07355 P37837 P05198 Q15293 P09525 P60891 P11908 P05388 P52907 Q15181 P00491 P45880 34 35 36 37 38 39 40 41...”
  • “...2.235 2.349 Membrane Mitochondrion 7 16 21 P08670 P07339 Q53GF8 0.343 2.372 2.945 Cytoplasm Lysosome Mitochondrion 35 39 43 45 47 Q13162 P18669 Q99714 P62993...”

MCP_0437 isocitrate/isopropylmalate dehydrogenase family protein from Methanocella paludicola SANAE
32% identity, 87% coverage

• Genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultivated representative of the order Methanocellales
  Sakai, PloS one 2011
  • “...0184). However, as similar to the RC-I MRE50 genome, the only two enzymes, isocitrate dehydrogenase (MCP_0437) and fumarase (MCP_0508 and 0509) seemed to be encoded. Therefore M. paludicola is not able to synthesize 2-oxoglutarate, the precursor of glutamate. Generally, in many methanogens, the incomplete TCA cycle...”

ABO_0296 isocitrate dehydrogenase from Alcanivorax borkumensis SK2
33% identity, 93% coverage

• An impaired metabolic response to hydrostatic pressure explains Alcanivorax borkumensis recorded distribution in the deep marine water column
  Scoma, Scientific reports 2016
  • “...1.98 224.4 56.9 1871 ABO_1201 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase + 1.15 186.7 84.2 1441 ABO_0296 isocitrate dehydrogenase + 0.92 559.4 295.7 1344 ABO_1493 succinyl-CoA synthetase subunit beta + 0.79 77.5 45.0 691 ABO_1540 fumarate hydratase + 0.73 75.5 45.4 2058 ABO_0275 phosphoenolpyruvate carboxykinase + 0.53...”

CG32026 uncharacterized protein from Drosophila melanogaster
32% identity, 54% coverage

• Single-cell RNA sequencing reveals cell landscape following antimony exposure during spermatogenesis in Drosophila testes
  Yu, Cell death discovery 2023
  • “...Drosophila testes, and found that representative DEGs of carbon metabolism related factors ( CG7059 , CG32026 and CG9314 ), SCP-Containing Proteins [SCP-containing protein A ( scpr-A ), SCP-containing protein B ( scpr-B ), and SCP-containing protein C ( scpr-C )], S-LAPs [Sperm-Leucylaminopeptidase 1 ( S-Lap1 )...”
• Dietary Sugar Shifts Mitochondrial Metabolism and Small RNA Biogenesis in Sperm
  Ramesh, Antioxidants & redox signaling 2023
  • “...( Fig. 1B , clusters 1 & 2). Proteins involved in TCA cycle (CS, Fum2, CG32026, Irp-1B) and pyruvate metabolism (PyK, Gapdh, and Menl-2) were enriched in cluster 1, whereas translation-related proteins dominated cluster 2 (RpL22-like, RpL7, RpL8, eIF4A, eEF2) ( Fig. 1C ). To gain...”
• Transcriptional coupling of distant regulatory genes in living embryos
  Levo, Nature 2022
  • “...CG2865 CG2865 CG2915 CG2915 CG3036 CG3036 CG3097 CG3097 CG31038 CG31038 CG31431 CG31431 CG31871 CG31371 CG32G26 CG32026 CG32399 CG32399 CG32982 CG32932 CG33099 CG33099 CG3625 CG3625 CG4133 CG4133 CG4702 CG4702 CG5002 CG5002 CG5522 CG5522 CG5888 CG5888 CG6051 CG6051 CG6398 CG6398 CG6885 CG6885 CG7800 CG7800 CG8001 CG8001 CG8066 CG8066...”

IDH3A_CAEEL / Q93714 Probable isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial; Isocitric dehydrogenase subunit alpha; NAD(+)-specific ICDH subunit alpha; EC 1.1.1.41 from Caenorhabditis elegans (see paper)
NP_492330 putative isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial from Caenorhabditis elegans
35% identity, 85% coverage

• catalytic activity: D-threo-isocitrate + NAD(+) = 2-oxoglutarate + CO2 + NADH (RHEA:23632)
  cofactor: Mg(2+) Mn(2+) (Binds 1 Mg(2+) or Mn(2+) ion per subunit.)
  subunit: Heterooligomer of subunits alpha, beta, and gamma in the apparent ratio of 2:1:1.
  disruption phenotype: RNAi-mediated knockdown causes accumulation of citrate, leading to induction of the citrate-induced mitochondrial unfolded protein response (mtUPR).
• Isocitrate Dehydrogenase Alpha-1 Modulates Lifespan and Oxidative Stress Tolerance in Caenorhabditis elegans.
  Lin, International journal of molecular sciences 2022
  • GeneRIF: Isocitrate Dehydrogenase Alpha-1 Modulates Lifespan and Oxidative Stress Tolerance in Caenorhabditis elegans.

IDH3A_RAT / Q99NA5 Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial; Isocitric dehydrogenase subunit alpha; NAD(+)-specific ICDH subunit alpha; EC 1.1.1.41 from Rattus norvegicus (Rat) (see paper)
Q99NA5 isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) from Rattus norvegicus (see paper)
31% identity, 93% coverage

• function: Catalytic subunit of the enzyme which catalyzes the decarboxylation of isocitrate (ICT) into alpha-ketoglutarate. The heterodimer composed of the alpha (IDH3A) and beta (IDH3B) subunits and the heterodimer composed of the alpha (IDH3A) and gamma (IDH3G) subunits, have considerable basal activity but the full activity of the heterotetramer (containing two subunits of IDH3A, one of IDH3B and one of IDH3G) requires the assembly and cooperative function of both heterodimers.
  catalytic activity: D-threo-isocitrate + NAD(+) = 2-oxoglutarate + CO2 + NADH (RHEA:23632)
  cofactor: Mg(2+) Mn(2+) (Divalent metal cations; Mn(2+) or Mg(2+). Activity higher in presence of Mn(2+) than of Mg(2+). Binds 1 Mg(2+) or Mn(2+) ion per subunit.)
  subunit: Heterooligomer of subunits alpha (IDH3A), beta (IDH3B), and gamma (IDH3G) in the apparent ratio of 2:1:1. The heterodimer containing one IDH3A and one IDH3B subunit and the heterodimer containing one IDH3A and one IDH3G subunit assemble into a heterotetramer (which contains two subunits of IDH3A, one of IDH3B and one of IDH3G) and further into the heterooctamer.
• Identification of proteins regulated by chlorogenic acid in an ischemic animal model: a proteomic approach.
  Shah, Laboratory animal research 2023
  • “...subunit A P63331 35.60 5.30 13/110 45 16 Unknown 17 Isocitrate dehydrogenase (NAD+) subunit alpha Q99NA5 39.59 6.47 7/93 31 18 Isocitrate dehydrogenase (NAD+) subunit alpha Q99NA5 39.59 6.47 7/108 21 19 Isocitrate dehydrogenase (NAD+) subunit alpha Q99NA5 39.59 6.47 7/93 31 20 Dynamin-like protein 1...”
• Global Proteomic Profile of Aluminum-Induced Hippocampal Impairments in Rats: Are Low Doses of Aluminum Really Safe?
  Bittencourt, International journal of molecular sciences 2022
  • “...using copper in the hippocampus, have observed changes in mitochondrial metabolic proteins such as IDH3A (Q99NA5) associated with mitochondrial encephalopathy [ 72 ] and UCRI (P20788), suggesting that altered mitochondrial energy metabolism is possibly associated with increased damage [ 73 ]. In vitro studies observed that...”
• Proteomic analysis of rat colonic mucosa following acupuncture treatment for irritable bowel syndrome with diarrhea
  Liu, PloS one 2022
  • “...domain-containing protein 1 Isoc1 -1.6 0.048 P23965 Enoyl-CoA delta isomerase 1, mitochondrial Eci1 -1.5 0.0010 Q99NA5 Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial Idh3a -1.5 0.00087 P29266 3-hydroxyisobutyrate dehydrogenase, mitochondrial Hibadh -1.4 0.048 P49432 Pyruvate dehydrogenase E1 component subunit beta, mitochondrial Pdhb -1.4 0.029 Functional distribution of...”
• Brown Adipose Tissue Sheds Extracellular Vesicles That Carry Potential Biomarkers of Metabolic and Thermogenesis Activity Which Are Affected by High Fat Diet Intervention.
  Camino, International journal of molecular sciences 2022
  • “...THIL_RAT P17764 Acetyl-CoA acetyltransferase, mitochondrial 0.006 2.12 PYC_RAT P52873 Pyruvate carboxylase, mitochondrial 0.003 2.10 IDH3A_RAT Q99NA5 Isocitrate dehydrogenase [NAD] subunit Alpha, mitochondrial 0.027 2.07 HSP74_RAT O88600 Heat shock 70 kDa protein 4 0.044 2.04 FETA_RAT P02773 Alpha-fetoprotein 0.029 2.01 DECR_RAT Q64591 2,4-dienoyl-CoA reductase [(3E)-enoyl-CoA-producing], mitochondrial 0.033...”
• Identification of changed proteins by retinoic acid in cerebral ischemic damage: a proteomic study.
  Kang, The Journal of veterinary medical science 2022
  • “...11 Adenosylhomocysteinase P10760 47.53 6.07 15/132 33 *** 12 Isocitrate dehydrogenase [NAD + ] subunit Q99NA5 39.58 6.47 8/93 31 ** 13 Rab GDP dissociation inhibitor P50399 50.50 5.90 9/150 23 *** 14 Glycerol-3-phosphate dehydrogenase O35077 37.43 6.16 8/105 25 ** 15 14-3-3 Gamma P61983 28.28...”
• Alterations in the Proteome and Phosphoproteome Profiles of Rat Hippocampus after Six Months of Morphine Withdrawal: Comparison with the Forebrain Cortex
  Ujcikova, Biomedicines 2021
  • “...3.9 2.0 0.0478 2 P37377 Snca Alpha-synuclein 1287.2 16 80 14.5 4.6 1.4 0.0114 3 Q99NA5 Idh3a Isocitrate dehydrogenase [NAD] subunit 830.1 9 28 39.6 6.5 2.4 0.0252 alpha, mitochondrial a sequence coverage, b theoretical molecular weight, c theoretical isoelectric point. biomedicines-10-00080-t002_Table 2 Table 2 Subcellular...”
  • “...Chaperone, response to oxidative stress, regulation of synaptic vesicle trafficking, regulation of neurotransmitter release 3 Q99NA5 Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial 2.4 Mitochondrion Krebs cycle biomedicines-10-00080-t003_Table 3 Table 3 GO enrichment analysis for significantly upregulated and downregulated proteins identified in the rat hippocampus isolated from...”
• Identification of regulated proteins by epigallocatechin gallate treatment in an ischemic cerebral cortex animal model: a proteomics approach.
  Park, The Journal of veterinary medical science 2021
  • “...phosphatase 2A, subunit B P58389 36.59 5.88 9/56 29 11 Isocitrate dehydrogenase (NAD+) subunit alpha Q99NA5 39.58 6.47 8/93 31 12 14-3-3 gamma P61983 28.28 4.80 8/77 35 13 Thioredoxin Q920J4 32.23 4.84 8/87 42 14 Ubiquitin carboxy-terminal hydrolase L1 Q7TQI3 31.25 4.85 11/66 50 15...”
• Identification of regulated proteins by resveratrol in glutamate-induced cortical injury of newborn rats.
  Gim, The Journal of veterinary medical science 2021
  • “...11/88 30 21 Tubulin-specific chaperone A 25 22 Unknown 23 Isocitrate dehydrogenase (NAD+) subunit alpha Q99NA5 39.58 6.47 8/93 31 24 Rab GDP dissociation inhibitor beta P50399 50.50 5.90 16/138 46 25 Protein phosphatase 2A, subunit B P58389 36.59 5.88 9/56 29 26 Proteasome subunit alpha...”
• More

An08g05580 uncharacterized protein from Aspergillus niger
34% identity, 83% coverage

• Comprehensively dissecting the hub regulation of PkaC on high-productivity and pellet macromorphology in citric acid producing Aspergillus niger
  Zheng, Microbial biotechnology 2022
  • “...encoding citric acid synthase citA (An09g06680) and two isocitrate dehydrogenases ( icdA , An02g12430 and An08g05580). Moreover, this module was enriched with genes associated with the mitochondria ( P =0.001), further supporting the role of this module in organic acid synthesis. The hypothesis that genes within...”
• Functional exploration of co-expression networks identifies a nexus for modulating protein and citric acid titres in Aspergillus niger submerged culture
  Cairns, Fungal biology and biotechnology 2019
  • “...(GO:0006099) kgdA An04g04750 Oxoglutarate dehydrogenase mdhA An07g02160 Mitochondrial malate dehydrogenase idh1 An18g06760 Isocitrate dehydrogenase idh2 An08g05580 Isocitrate dehydrogenase ico2 An09g03870 Aconitate hydratase citA An09g06680 Citrate synthase aclA An11g00530 Cytoplasmic ATP-citrate lyase kgd2 An11g11280 Dihydrolipoamide S-succinyl transferase fumR An12g07850 Fumarate hydratase aclB An11g00510 ATP:citrate oxaloacetate lyase Predicted...”
  • “...genes passing Spearman correlation coefficients above 0.5 were retrieved for query genes citA (An09g06680), idh2 (An08g05580), fumR (An12g07850), copA (An16g02460), sec13 (An04g00360) and sec26 (An08g03270). Next, genes common to all 6 sub-networks were identified, giving 259 candidates. GO-enriched biological processes in this list were identified relative...”
• Identification of novel citramalate biosynthesis pathways in Aspergillus niger
  Hossain, Fungal biology and biotechnology 2019
  • “...6 ANI_1_906164 An18g06760 Isocitrate dehydrogenase (NAD+) subunit 1 Mito 189.71 209.47 167.93 190.84 6 ANI_1_798074 An08g05580 Isocitrate dehydrogenase [NAD] subunit 2 Mito 165.29 175.80 165.81 151.75 6 ANI_1_3136024 An02g12430 Isocitrate dehydrogenase [NADP] Per 53.93 50.46 43.22 64.47 7 ANI_1_826184 An04g04750 2-Oxoglutarate dehydrogenase Mito 115.53 103.38 107.27...”
• The amyR-deletion strain of Aspergillus niger CICC2462 is a suitable host strain to express secreted protein with a low background
  Zhang, Microbial cell factories 2016
  • “...fumarate hydratase (An12g07850), succinate dehydrogenase (ubiquinone) flavoprotein subunit (An02g12770), and isocitrate dehydrogenase (NAD) subunit 2 (An08g05580). The transcriptome data showed that most of these genes related to these two central metabolic pathways are constitutively expressed. Normal cellular metabolism and the generation and utilization of energy were...”
  • “...acid cycle An07g02160 282.02 924.35 1.71 Malate dehydrogenase activity An12g07850 166.48 428.02 1.36 Hydro-lyase activity An08g05580 386.02 899.66 1.22 Isocitrate dehydrogenase activity An02g12770 389.46 891.41 1.19 Succinate dehydrogenase activity An18g06760 594 1299.36 1.13 Isocitrate dehydrogenase activity An14g04400 390.85 854.72 1.13 Succinate dehydrogenase activity Influence of the...”
• Trancriptional landscape of Aspergillus niger at breaking of conidial dormancy revealed by RNA-sequencing
  Novodvorska, BMC genomics 2013
  • “...transaminase 4.63 7.63 0 n/a An14g02870 succinic semialdehyde dehydrogenase 31.91 274.43 2.34 117.27 TCA cycle An08g05580 isocitrate dehydrogenase 2.71 10.85 69.17 6.37 An18g06760 isocitrate dehydrogenase 3.17 55.23 354.46 6.41 An04g04750 oxoglutarate dehydrogenase 2.23 22.9 109.76 4.79 An17g01670 succinyl-CoA synthetase 5.36 24.29 128.98 5.31 Metabolism of internal...”
  • “...increased expression of tricarboxylic acid cycle (TCA cycle) genes. Genes coding for putative isocitrate dehydrogenases (An08g05580, An18g06760), -ketoglutarate dehydrogenase An04g04750) and succinyl-CoA synthetase (An17g01670) exhibited increased transcript levels at the breaking of dormancy. After the onset of germination, we detected increased transcript levels of genes encoding...”

AO090012000629 No description from Aspergillus oryzae RIB40
34% identity, 87% coverage

• Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing
  Wang, Nucleic acids research 2010
  • “...key regulator genes of the TCA cycle, citrate synthase (AO090102000627), isocitrate dehydrogenase (AO090003000008, AO090005001404 and AO090012000629) and succinate dehydrogenase (AO090010000505, AO090020000415 and AO090020000596), were upregulated on SC ( Supplementary Table S10 ), as well as some important genes of oxidative phosphorylation (AO090001000657, AO090005000617, AO090005000749, AO090005000888, AO090010000482...”

aksF / Q58991 NAD-dependent threo-isocitrate dehydrogenase (EC 1.1.1.87) from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (see paper)
AKSF_METJA / Q58991 Homoisocitrate dehydrogenase; HICDH; Homo(2)-isocitrate/homo(3)-isocitrate dehydrogenase; Isohomocitrate dehydrogenase; IHDH; NAD-dependent threo-isohomocitrate dehydrogenase; EC 1.1.1.87; EC 1.1.1.- from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii) (see 2 papers)
Q58991 methanogen homoaconitase (EC 4.2.1.114) from Methanocaldococcus jannaschii (see paper)
29% identity, 87% coverage

• function: Catalyzes the NAD-dependent oxidation and decarboxylation of (2R,3S)-homoisocitrate, (2R,3S)-homo(2)-isocitrate and (2R,3S)-homo(3)- isocitrate, into 2-oxoadipate, 2-oxopimelate (2-oxoheptanedioate), and 2-oxosuberate, respectively. All these substrates are intermediates in the biosynthesis of biotin and of 7-mercaptoheptanoate, a moiety of coenzyme B in methanoarchaea (PubMed:10940051, PubMed:18765671). Is also able to produce 2-oxoazelate from (2R,3S)-homo(4)-isocitrate in vitro, but this substrate is probably not physiologically relevant (PubMed:18765671). Is unable to use any isomer of isocitrate or isopropylmalate as a substrate, and NADP as an oxidant (PubMed:10940051).
  catalytic activity: (2R,3S)-homoisocitrate + NAD(+) = 2-oxoadipate + CO2 + NADH (RHEA:11900)
  catalytic activity: (2R,3S)-iso(homo)2citrate + NAD(+) = 2-oxoheptanedioate + CO2 + NADH (RHEA:68404)
  catalytic activity: (2R,3S)-iso(homo)3citrate + NAD(+) = 2-oxosuberate + CO2 + NADH (RHEA:68408)
  cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)

IDH-V / Q945K7 NAD+-dependent isocitrate dehydrogenase catalytic subunit (EC 1.1.1.286) from Arabidopsis thaliana (see 3 papers)
IDH5_ARATH / Q945K7 Isocitrate dehydrogenase [NAD] catalytic subunit 5, mitochondrial; IDH-V; Isocitric dehydrogenase 5; NAD(+)-specific ICDH 5; EC 1.1.1.41 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
Q945K7 isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) from Arabidopsis thaliana (see 2 papers)
NP_568113 isocitrate dehydrogenase V from Arabidopsis thaliana
AT5G03290 isocitrate dehydrogenase, putative / NAD+ isocitrate dehydrogenase, putative from Arabidopsis thaliana
33% identity, 84% coverage

• function: Performs an essential role in the oxidative function of the citric acid cycle.
  catalytic activity: D-threo-isocitrate + NAD(+) = 2-oxoglutarate + CO2 + NADH (RHEA:23632)
  cofactor: Mg(2+) Mn(2+) (Binds 1 Mg(2+) or Mn(2+) ion per subunit.)
  subunit: Heterooligomer of catalytic and regulatory subunits.
• A new anaplerotic respiratory pathway involving lysine biosynthesis in isocitrate dehydrogenase-deficient Arabidopsis mutants.
  Boex-Fontvieille, The New phytologist 2013 (PubMed)
  • GeneRIF: A substantial reduction in leaf isocitrate dehydrogenase activity did not lead to changes in the respiration efflux rate but respiratory metabolism was reorchestrated.
• NAD-dependent isocitrate dehydrogenase mutants of Arabidopsis suggest the enzyme is not limiting for nitrogen assimilation.
  Lemaitre, Plant physiology 2007
  • GeneRIF: Leaf IDH activity is reduced by 92% in mutant
• Integrative Omics Analysis of Three Oil Palm Varieties Reveals (Tanzania × Ekona) TE as a Cold-Resistant Variety in Response to Low-Temperature Stress
  Saand, International journal of molecular sciences 2022
  • “...(P49298), and isocitrate dehydrogenase [NAD] (Q8LFC0) proteins were suppressed in BE. Nonetheless, isocitrate dehydrogenase [NAD] (Q945K7) was suppressed in OG, and isocitrate dehydrogenase [NADP] (P50218) was expressed in TE only. The isocitrate dehydrogenase [NADP] proteins were suppressed in brassica and coconut leaf proteomic under cold stress...”
• Maternal environment alters dead pericarp biochemical properties of the desert annual plant Anastatica hierochuntica L
  Khadka, PloS one 2020
  • “...insulinase AT1G51980 0.000993 8.49 proteolysis A8MS83 Ribosomal protein L23AB AT3G55280 0.00376 8.08 respons to stress Q945K7 Isocitrate dehydrogenase [NAD] catalytic subunit 5, mitochondrial AT5G03290 0.00374 7.73 TCA cycle F4K3R8 Voltage dependent anion channel 2 AT5G67500 0.00285 7 transmembrane transport F4III4 MALE GAMETOPHYTE DEFECTIVE 1 AT2G21870 0.00448...”
• Characterization of the Isocitrate Dehydrogenase Gene Family and Their Response to Drought Stress in Maize
  Wei, Plants (Basel, Switzerland) 2023
  • “...into two clusters based on their catalytic activity. Previous studies showed that the genes AtIDH4 (At5g03290) and AtIDH8 (At3g09805) in Arabidopsis encoded proteins with catalytic subunits [ 30 ]. Based on this, ZmIDH1.1, ZmIDH1.2, and ZmIDH1.5, which clustered with AtIDH4 and AtIDH8, may be catalytically active,...”
• Molecular Characterization of NDL1-AGB1 Mediated Salt Stress Signaling: Further Exploration of the Role of NDL1 Interacting Partners
  Gupta, Cells 2021
  • “...ID Primers (5 to 3) 1. ANNAT1 AT1G35720 Forward CACCATGGCGACTCTTAAGGT Reverse AGCATCATCTTCACC GAGAA 2. IDH-V AT5G03290 Forward CACCATGACCATGGCAGCAAA Reverse GAGATGATCACAGATTGCCTTTG 3. SLT1 AT2G37570 Forward CACCATGGAGAATCATCATCCTTCT Reverse TTAAGTCAGCATAAGATCGTTTCC cells-10-02261-t002_Table 2 Table 2 NDL1 interactome showed twenty-four interactors specifically involved during salt stress responses. We refer to them...”
• Transcriptomic Landscape of Herbivore Oviposition in Arabidopsis: A Systematic Review
  Ojeda-Martinez, Frontiers in plant science 2021
  • “...urticae main drivers were involved in secondary metabolite processes such as SHM4 (AT4G13930) and IDH5 (AT5G03290) ( Proietti et al., 2013 ; Yoshida and Hisabori, 2014 ). Other mechanisms associated with molecule trafficking were represented by genes such as PTR4 (AT2G02020) and SAR1 (AT2G33120) ( Zhang...”
• Central Metabolism in Mammals and Plants as a Hub for Controlling Cell Fate
  Selinski, Antioxidants & redox signaling 2021
  • “...(EC 1.1.1.42) NAD-IDH2 AT2G17130 (EC 1.1.1.41) NAD-IDH3 AT4G35650 (EC 1.1.1.41) NAD-IDH4 AT1G32480 (EC 1.1.1.41) NAD-IDH5 AT5G03290 (EC 1.1.1.41) NAD-IDH6 AT3G09810 (EC 1.1.1.41) Malate dehydrogenase mtNAD-MDH1 AT1G53240 (EC 1.1.1.37) HGNC:6971 (EC 1.1.1.37) YKL085W (EC 1.1.1.37) mtNAD-MDH2 AT3G15020 (EC 1.1.1.37) Malic enzyme NAD-ME1 AT2G13560 (EC 1.1.1.39) HGNC:6984 (EC...”
• Target of Rapamycin Regulates Genome Methylation Reprogramming to Control Plant Growth in Arabidopsis
  Zhu, Frontiers in genetics 2020
  • “...phosphate-dependent transferase AT1G74030 1.6688 Hyper Exon/intron/utr3 ENO1| Enolase AT3G49360 1.9074 Hyper Promoter PGL2| 6-phosphogluconolactonase, DevB-type AT5G03290 1.9497 Hyper Exon IDH5| Isocitrate dehydrogenase NAD-dependent AT3G12780 1.9568 Hyper Exon/intron PGK1| Phosphoglycerate kinase AT1G01090 2.0177 Hyper Exon/intron PDH-E1| Pyruvate dehydrogenase E1 component AT1G17650 2.6505 Hyper Exon/intron GLYR2| 6-phosphogluconate dehydrogenase...”
  • “...DapA AT4G01850 1.7869 Hyper Exon SAM2| S-adenosylmethionine synthetase AT4G23590 1.9377 Hyper Exon Pyridoxal phosphate-dependent transferase AT5G03290 1.9497 Hyper Exon IDH5| Isocitrate dehydrogenase NAD-dependent AT3G12780 1.9568 Hyper Exon/intron PGK1| Phosphoglycerate kinase Ribosome AT4G27490 0.2287 Hypo Promoter Ribosomal protein S5 domain 2-type fold AT1G23280 0.2364 Hypo Promoter Mak16|...”
• Recent Findings Unravel Genes and Genetic Factors Underlying Leptosphaeria maculans Resistance in Brassica napus and Its Relatives
  Cantila, International journal of molecular sciences 2020
  • “..., 76 ] BnaA10g23040D RLK AT5G08440 Unknown protein [ 70 , 76 ] BnaA10g26650D RLK AT5G03290 Isocitrate dehydrogenase (NAD) catalytic subunit 5, mitochondrial [ 70 , 76 ] BLMR1 (A10 in Bna) BnaA10g21910D - AT5G10360 40S ribosomal protein S6 (RPS6B) [ 85 ] BnaA10g19660D - AT3G17620...”
• Maternal environment alters dead pericarp biochemical properties of the desert annual plant Anastatica hierochuntica L
  Khadka, PloS one 2020
  • “...L23AB AT3G55280 0.00376 8.08 respons to stress Q945K7 Isocitrate dehydrogenase [NAD] catalytic subunit 5, mitochondrial AT5G03290 0.00374 7.73 TCA cycle F4K3R8 Voltage dependent anion channel 2 AT5G67500 0.00285 7 transmembrane transport F4III4 MALE GAMETOPHYTE DEFECTIVE 1 AT2G21870 0.00448 6.34 pollen development Q9SR73 40S ribosomal protein S28-1...”
• Proteomic and metabolomic analyses provide insight into the off-flavour of fruits from citrus trees infected with 'Candidatus Liberibacter asiaticus'
  Yao, Horticulture research 2019
  • “...5 EC 5.1.3.2 0.51 2.93E02 gi|568849997 AT3G59480 FRK3 Fructokinase 3 EC 2.7.1.4 0.55 1.02E04 gi|568855816 AT5G03290 IDH-V NAD + -dependent isocitric dehydrogenase V EC 1.1.1.41 0.55 1.28E03 gi|568856679 AT2G36530 ENO2 Enolase 2 EC 4.2.1.11 0.62 1.85E10 gi|568864726 AT1G74030 ENO1 Enolase 1 EC 4.2.1.11 0.59 3.20E02 gi|568868208...”
• More

MJ1596 3-isopropylmalate dehydrogenase 2 (leuB2) from Methanocaldococcus jannaschii DSM 2661
29% identity, 87% coverage

• Methanogen homoaconitase catalyzes both hydrolyase reactions in coenzyme B biosynthesis
  Drevland, The Journal of biological chemistry 2008
  • “...water to produce (2R,3S)-homoisocitrate. Finally, HICDH (MJ1596) catalyzes an oxidative ancestors, respectively. Direct assays decarboxylation reaction forming...”
  • “...in the supplemental materials. T378C) compared with the MJ1596 sequence reported by the 2-Oxoadipic Acid--Diethyl glutarate (4.7 g, 25 mmol) was genome...”

B6TJM1 3-isopropylmalate dehydrogenase from Zea mays
32% identity, 91% coverage

• The Difference of Physiological and Proteomic Changes in Maize Leaves Adaptation to Drought, Heat, and Combined Both Stresses
  Zhao, Frontiers in plant science 2016
  • “...K7V2K6 + + Indole-3-acetate beta-glucosyltransferase/ B6TB13 + Uncharacterized protein (HSP70)/ K7VJF3 + + 3-isopropylmalate dehydrogenase/ B6TJM1 + Uncharacterized protein (Fragment)/ K7VZF7 + + Aspartate aminotransferase/ B4FUH2 + Heat shock protein 82/ Q08277 + + Stachyose synthase/ B6UBW7 + Heat shock protein 17.2/ Q43701 + + Glutathione...”

Q6CA33 isocitrate dehydrogenase (NAD(+)) from Yarrowia lipolytica (strain CLIB 122 / E 150)
30% identity, 93% coverage

• Proteomic Study of Response to Copper, Cadmium, and Chrome Ion Stress in Yarrowia lipolytica Strains Isolated from Andean Mine Tailings in Peru
  Sánchez-Rojas, Microorganisms 2022
  • “...proteins that were modulated upon chromium treatment, such as glycerol-3-phosphate dehydrogenase (Q6CEQ0), isocitrate dehydrogenase [NAD] (Q6CA33), aldehyde dehydrogenase (Q6C2W9), and HSPs. As already reported, Cr +6 can affect the structure and degradation of proteins, as well as DNA, lipids, and other supramolecular biological compounds due to...”

AL01_06250 isocitrate/isopropylmalate dehydrogenase family protein from Bombella intestini
33% identity, 86% coverage

• Whole-Genome Sequence Analysis of Bombella intestini LMG 28161T, a Novel Acetic Acid Bacterium Isolated from the Crop of a Red-Tailed Bumble Bee, Bombus lapidarius
  Li, PloS one 2016
  • “...(AL01_01980, AL01_07015); 20, citrate synthase (AL01_06255); 21, aconitate hydratase 1 (AL01_06260); 22, NADP+-dependent isocitrate dehydrogenase (AL01_06250); 23, 2-oxoglutarate dehydrogenase E1 (AL01_08340); 24, dihydrolipoyllysine succinyltransferase (AL01_07740); 25, dihydrolipoamide dehydrogenase (AL01_00930); 26, fumarate hydratase (AL01_05840); 27, PQQ-dependent glucose dehydrogenase (AL01_09305); 28, gluconolactonase (AL01_06230); 29, lactate dehydrogenase (AL01_06935); 30,...”

IDH2 / P28241 isocitrate dehydrogenase [NAD] β subunit (EC 1.1.1.286) from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (see paper)
IDH2_YEAST / P28241 Isocitrate dehydrogenase [NAD] subunit 2, mitochondrial; Isocitric dehydrogenase; NAD(+)-specific ICDH; EC 1.1.1.41 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 2 papers)
P28241 isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) from Saccharomyces cerevisiae (see paper)
NP_014779 isocitrate dehydrogenase (NAD(+)) IDH2 from Saccharomyces cerevisiae S288C
YOR136W Idh2p from Saccharomyces cerevisiae
30% identity, 93% coverage

• function: Performs an essential role in the oxidative function of the citric acid cycle. Also binds RNA; specifically to the 5'-untranslated leaders of mitochondrial mRNAs
  catalytic activity: D-threo-isocitrate + NAD(+) = 2-oxoglutarate + CO2 + NADH (RHEA:23632)
  cofactor: Mg(2+) Mn(2+) (Binds 1 Mg(2+) or Mn(2+) ion per subunit.)
  subunit: Octamer of two non-identical subunits IDH1 and IDH2
• Basis for half-site ligand binding in yeast NAD(+)-specific isocitrate dehydrogenase.
  Lin, Biochemistry 2011
  • GeneRIF: On the basis of a potential interaction between side chains of Cys-150 residues in IDH2 subunits in each tetramer of the enzyme, ligand binding assays of wild-type (IDH1/IDH2) and IDH1/IDH2(C150S) octameric enzymes were conducted.
• Disulfide bond formation in yeast NAD+-specific isocitrate dehydrogenase.
  Garcia, Biochemistry 2009
  • GeneRIF: Structural features of a ligand-free form of IDH2 suggest that formation of a disulfide bond during stationary phase in yeast transformants might stabilize an inactive form of the enzyme.
• Allosteric motions in structures of yeast NAD+-specific isocitrate dehydrogenase.
  Taylor, The Journal of biological chemistry 2008
  • GeneRIF: analysis of allosteric motion in the IDH1 and IDH2 subunits of NAD+-specific isocitrate dehydrogenase
• Structural studies of Saccharomyces cerevesiae mitochondrial NADP-dependent isocitrate dehydrogenase in different enzymatic states reveal substantial conformational changes during the catalytic reaction.
  Peng, Protein science : a publication of the Protein Society 2008
  • GeneRIF: Structural studies of Saccharomyces cerevisiae mitochondrial NADP-dependent IDH2 in different enzymatic states reveal substantial conformational changes during the catalytic reactiion.
• Improving Identification of In-organello Protein-Protein Interactions Using an Affinity-enrichable, Isotopically Coded, and Mass Spectrometry-cleavable Chemical Crosslinker
  Makepeace, Molecular & cellular proteomics : MCP 2020
  • “...15 3 32 38 P00830 ATP2 P09457 ATP5 72 Yes Yes 10 27 19 26 P28241 IDH2 P28834 IDH1 72 Yes Yes 5 44 11 17 P09624 LPD1 P12695 LAT1 67 No No 27 7 1 59 P05626 ATP4 P30902 ATP7 64 No Yes 9 4...”
• Regulation of xylose metabolism in recombinant Saccharomyces cerevisiae
  Salusjärvi, Microbial cell factories 2008
  • “...2.9 10.7 -0.5 8.1 -3.4 P04807 Hxk2p_b YGL253W hexokinase 0.7 2.9 -1.1 -0.5 -1.8 -3.4 P28241 Idh2p YOR136W isocitrate dehydrogenase (NAD+) -0.9 -0.5 0.7 0.2 1.7 0.7 P00817 Ipp1p YBR011C inorganic diphosphatase -1.7 -0.5 -1.5 -0.9 0.3 -0.5 P53598 Lsc1p YOR142W succinate-CoA ligase (ADP-forming) -0.5 -0.4...”
• Data integration uncovers the metabolic bases of phenotypic variation in yeast
  Petrizzelli, PLoS computational biology 2021
  • “...10.1371/journal.pcbi.1009157.t002 Table 2 Reactions associated to protein complexes with an AND Boolean relationship. Proteins Reactions (YOR136W AND YNL037C) Icit_Akg_m_nad (YIL125W AND YDR148C AND YFL018C ) Akg_Succoa_m ( YGR240C AND YMR205C ) F6p_Fdp (YBR221C AND YER178W AND YFL018C AND YGR193C AND YNL071W ) Pyr_Accoa_m ( YGR244C AND...”
• Central Metabolism in Mammals and Plants as a Hub for Controlling Cell Fate
  Selinski, Antioxidants & redox signaling 2021
  • “...AT4G35260 (EC 1.1.1.41) HGNC:5384 (EC 1.1.1.41) HGNC:5385 (EC 1.1.1.41) HGNC:5386 (EC 1.1.1.41) YNL037C (EC 1.1.1.41) YOR136W (EC 1.1.1.41) YDL066W (EC 1.1.1.42) NAD-IDH2 AT2G17130 (EC 1.1.1.41) NAD-IDH3 AT4G35650 (EC 1.1.1.41) NAD-IDH4 AT1G32480 (EC 1.1.1.41) NAD-IDH5 AT5G03290 (EC 1.1.1.41) NAD-IDH6 AT3G09810 (EC 1.1.1.41) Malate dehydrogenase mtNAD-MDH1 AT1G53240 (EC...”
• Yeast screen for modifiers of C9orf72 poly(glycine-arginine) dipeptide repeat toxicity
  Chai, FEMS yeast research 2018
  • “...metabolic pathways (12/133) aco2 YJL200C flx1 YIL134W idh2 YOR136W oxa1 YER154W rcf2 zwf1 YNR018W YNL241C gor1 YNL274C gpd2 YOL059W gph1 YPR160W stb5 YHR178W...”
• A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models
  Reimers, Metabolites 2017
  • “...An example is the enzyme isocitrate dehydrogenase in yeast, composed of the gene products of YOR136W and YNL037C, where the corresponding gene products both participate as dimers. Hence the amino acid counts for each gene product should be multiplied by two and then added up when...”
  • “...acid counts for the gene products involved in the synthesis of isocitrate dehydrogenase in yeast. YOR136W YNL037C Ala 29 29 Arg 18 18 Asn 21 19 Asp 15 18 Cys 3 0 Gln 7 8 Glu 19 22 Gly 28 32 His 7 10 Ile 29...”
• Transcriptional profiling reveals molecular basis and novel genetic targets for improved resistance to multiple fermentation inhibitors in Saccharomyces cerevisiae
  Chen, Biotechnology for biofuels 2016
  • “...YCR005C, YDL182W, YDR135C, YGL196W, YIR034C, YJR078W, YJR103W, YJR109C, YJR137C, YLR142W, YMR250W, YNL037C, YNL073W, YNR001C, YOL086C, YOR136W, YOR202W, YPL160W, YPR035W Nucleobase-containing small molecule metabolic process (GO:0055086) YCR021C, YDR135C, YDR529C, YEL021W, YEL024W, YEL041W, YER036C, YER037W, YJR078W, YJR103W, YKL073W, YMR145C, YNL088W, YNL220W, YOL059W, YOL081W, YOL086C, YOR204W, YPL036W, YPR181C Since...”
• Systematic chemical-genetic and chemical-chemical interaction datasets for prediction of compound synergism
  Wildenhain, Scientific data 2016
  • “...by Rgt1p when glucose is limiting Null mutant is viable, decreased transport of glucose S000001136 YOR136W IDH2 + Subunit of mitochondrial NAD(+)-dependent isocitrate dehydrogenase, which catalyzes the oxidation of isocitrate to alpha-ketoglutarate in the TCA cycle Null mutant is viable, G1 delay, increased thermotolerance S000005662 YLR384C...”
• RSC Chromatin-Remodeling Complex Is Important for Mitochondrial Function in Saccharomyces cerevisiae
  Imamura, PloS one 2015
  • “...YDL198C GGC1 GDP/GTP Carrier YJR144W MGM101 Mitochondrial Genome Maintenance Mitochondrial enzyme YAL044C GCV3 GlyCine cleaVage YOR136W IDH2 Isocitrate DeHydrogenase YBR221C PDB1 Pyruvate Dehydrogenase Beta subunit YPL188W POS5 PerOxide Sensitive YMR267W PPA2 PyroPhosphatAse YJR104C SOD1 SuperOxide Dismutase General metabolism Amino acid biosynthesis YLR027C AAT2 Aspartate AminoTransferase YJL071W...”
• Adjustment of trehalose metabolism in wine Saccharomyces cerevisiae strains to modify ethanol yields
  Rossouw, Applied and environmental microbiology 2013
  • “...LSC1 LSC2 YNR001c YCR005c YPR001w YLR304c YJL200C YNL037c YOR136w YIL125w YDR148c YOR142w YGR244c Y15376 Y13485 Y12828 Y15212 Y17022 Y15362 Y12392 Y12284 Y13506...”
• More

LOC103934973 isocitrate dehydrogenase [NAD] catalytic subunit 5, mitochondrial from Pyrus x bretschneideri
31% identity, 92% coverage

• Comparative physiological, metabolomic and transcriptomic analyses reveal the mechanisms of differences in pear fruit quality between distinct training systems
  Liu, BMC plant biology 2024
  • “...PpME (encoding the malic enzyme, LOC103934506 and LOC103944816) and PpIDH (encoding isocitrate dehydrogenase, LOC103926949 and LOC103934973), which contribute to their degradation, was upregulated in the PpPOD -TRV fruitlets (Fig. 7 B). These results indicate that PpPOD appears to have a positive regulatory effect on major organic...”

P29696 3-isopropylmalate dehydrogenase, chloroplastic from Solanum tuberosum
31% identity, 82% coverage

• Proteomic and Metabolic Analysis of Pinus halepensis Mill. Embryonal Masses Induced under Heat Stress
  Pereira, International journal of molecular sciences 2023
  • “...beta-4, chloroplastic Q10G39 Oryza sativa subsp. japonica 0.80 1.48 1.63 0.025 2.13 3-isopropylmalate dehydrogenase, chloroplastic P29696 Solanum tuberosum 0.82 1.32 1.46 0.038 2.35 Trifunctional UDP-glucose 4.6-dehydratase/UDP-4-keto-6-deoxy-D-glucose 3.5-epimerase/UDP-4-keto-L-rhamnose-reductase RHM1 Q9SYM5 Arabidopsis thaliana 0.68 1.49 1.60 0.009 2.39 NADPH--cytochrome P450 reductase 1 Q9SB48 Arabidopsis thaliana 1.07 1.58 1.34...”
• Hydrogen Peroxide Response in Leaves of Poplar (Populus simonii × Populus nigra) Revealed from Physiological and Proteomic Analyses
  Yu, International journal of molecular sciences 2017
  • “...lyase family protein OAS-TL Uncertain XP_006389317 70 2 3747 3-isopropyl malate dehydrogenase, chloroplastic IPMDH Chl P29696 117 2 3402 Alanine aminotransferase family protein ALT Uncertain ALT55639 239 6 3515 Aldolase superfamily protein isoform 1, delta-aminolevulinic acid dehydratase 1, chloroplastic* ALAD1 Chl EOY16322 92 3 3587 Uroporphyrinogen...”

M1CHE3 3-isopropylmalate dehydrogenase, chloroplastic from Solanum tuberosum
31% identity, 82% coverage

• Transcriptomic and proteomic data provide new insights into cold-treated potato tubers with T- and D-type cytoplasm
  Szajko, Planta 2022
  • “...0.02927 45 M1C0N9 Sulfurtransferase 0.37 0.03869 26 M0ZWY7, M1B641 Elongation factor Tu 0.33 0.00004 79 M1CHE3 Isocitrate dehydrogenase [NAD] subunit d 0.32 0.00094 43 M1BT60 CBS domain-containing protein 0.31 0.00004 38 M1AUM5 e , M1AUM6 Gamma aminobutyrate transaminase isoform1 0.28 0.00827 46 P52903 f Pyruvate dehydrogenase...”

LOC18035427 isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial from Citrus x clementina
32% identity, 93% coverage

• Transcriptome analysis of Harumi tangor fruits: Insights into interstock-mediated fruit quality
  Liao, Frontiers in plant science 2022
  • “...GAUT15 , LOC18045452) were grouped in profile 9. Genes encoding isocitrate dehydrogenase ( IDH1 , LOC18035427), 2-oxoglutarate dehydrogenase ( 2-OGDH , LOC18048455), phosphoenolpyruvate carboxylase ( ATPPC4 , LOC18043504), and succinate dehydrogenase ( SDH2 , LOC18037039) belonged to profile 10. Finally, genes encoding ,-trehalose-phosphate synthase ( ATTPS7...”

IDH1_ARATH / Q8LFC0 Isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial; IDH-I; Isocitric dehydrogenase 1; NAD(+)-specific ICDH 1 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
Q8LFC0 isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) from Arabidopsis thaliana (see 2 papers)
AT4G35260, NP_195252 isocitrate dehydrogenase 1 from Arabidopsis thaliana
NP_195252 IDH1 (ISOCITRATE DEHYDROGENASE 1); isocitrate dehydrogenase (NAD+)/ oxidoreductase, acting on the CH-OH group of donors, NAD or NADP as acceptor from Arabidopsis thaliana
32% identity, 93% coverage

• function: Performs an essential role in the oxidative function of the citric acid cycle.
  subunit: Heterooligomer of catalytic and regulatory subunits
• Rewiring of primary metabolism for ammonium recycling under short-term low CO₂ treatment - its implication for C₄ evolution
  Miao, Frontiers in plant science 2024
  • “...tricarboxylic acid cycle (TCA) were markedly upregulated, specifically aconitase (ACO1, AT4G35830), isocitrate dehydrogenase 1 (IDH1, AT4G35260), 2-oxoglutarate dehydrogenase (OGDC, AT3G55410), succinate dehydrogenase (SDH, AT5G66760), and mMDH1 ( Figure3A ; Supplementary Dataset S1 ). However, we observed a significant reduction of the succinate and fumarate in comparison...”
• Nucleotide Imbalance, Provoked by Downregulation of Aspartate Transcarbamoylase Impairs Cold Acclimation in Arabidopsis
  Bellin, Molecules (Basel, Switzerland) 2023
  • “...AT3G55410 E1-OGDH1 0.33 0.99 1.37 Mt dehydrogenase AT5G55070 E2-OGDH2 0.62 1.06 1.63 0.43 Mt dehydrogenase AT4G35260 IDH1 0.51 0.80 1.04 Mt dehydrogenase AT3G27380 SDH2-1 0.43 1.68 2.22 1.14 1.59 Mt dehydrogenase AT3G03250 UGP2 0.57 1.19 0.95 0.40 0.52 Ct, PM pyrophosphorylase AT5G51830 FRK1 0.53 2.46 3.27...”
• Integrative Analysis of Transcriptomic and Proteomic Changes Related to Cytoplasmic Male Sterility in Spring Stem Mustard (Brassica juncea var. tumida Tsen et Lee)
  Shen, International journal of molecular sciences 2022
  • “...+ ) AT4G35650 DOWN DAP BjuB024174 K00026 Malate dehydrogenase AT2G22780 DOWN DAP BjuA003018 K00030 IDH1 AT4G35260 UP DAP BjuA003018 K00030 IDH1 AT4G35260 UP DAP BjuB019661 K00026 Malate dehydrogenase, chloroplastic AT3G47520 UP DAP BjuB040953 K01899 SuccinateCoA ligase AT5G08300 DOWN DAP BjuB027452 K03963 Uncharacterized protein AT2G02050 UP DAP...”
• Investigation of proteins' interaction network and the expression pattern of genes involved in the ABA biogenesis and antioxidant system under methanol spray in drought-stressed rapeseed
  Mohsenzadeh, 3 Biotech 2022
  • “...AT3G54660 AT2G41680 AT2G27150 AT3G14440 AT5G17230 AT4G35260 AT3G52200 GR NTRC AAO3 NCED3 PSY IDH1 LTA3 https://www.uniprot.org/uniprot/P42770...”
• Autophagy Contributes to the Quality Control of Leaf Mitochondria
  Nakamura, Plant & cell physiology 2021
  • “...upstream from the start codon to the region just before the stop codon of IDH1 (At4g35260) was amplified from Arabidopsis genomic DNA by PCR using the primers IDH1-F and IDH1-R ( Supplementary Table S1 ), cloned into pENTR/D/TOPO and transferred to the vector pGWB553 ( Nakagawa...”
• The Phosphofructokinase Isoform AtPFK5 Is a Novel Target of Plastidic Thioredoxin-f-Dependent Redox Regulation
  Hess, Antioxidants (Basel, Switzerland) 2021
  • “...phloem loading or a phloem-related process. The co-expression with the isocitrate dehydrogenase genes IDH1 ( At4g35260 ), IDH2 ( At2g17130 ) and IDH-VI (At3g09810) ( http://atted.jp/ , accessed on 23 February 2021), which are also highly expressed in this cell type [ 67 ], might hint...”
• Central Metabolism in Mammals and Plants as a Hub for Controlling Cell Fate
  Selinski, Antioxidants & redox signaling 2021
  • “...1.1.1.27) HGNC:6535 (EC 1.1.1.27) HGNC:6541 (EC 1.1.1.27) HGNC:6544 (EC 1.1.1.27) n.e. Mitochondrion Isocitrate dehydrogenase NAD-IDH1 AT4G35260 (EC 1.1.1.41) HGNC:5384 (EC 1.1.1.41) HGNC:5385 (EC 1.1.1.41) HGNC:5386 (EC 1.1.1.41) YNL037C (EC 1.1.1.41) YOR136W (EC 1.1.1.41) YDL066W (EC 1.1.1.42) NAD-IDH2 AT2G17130 (EC 1.1.1.41) NAD-IDH3 AT4G35650 (EC 1.1.1.41) NAD-IDH4 AT1G32480...”
• Gel-based proteomic map of Arabidopsis thaliana root plastids and mitochondria
  Grabsztunowicz, BMC plant biology 2020
  • “...dehydrogenase, represented by isocitrate dehydrogenase family protein (At5g14590 in spot 65) and regulatory subunits 1 (At4g35260, spot 72) and 2 (At2g17130, spots 62 and 63). 2-oxoglutarate, in turn, is decarboxylated to succinyl-CoA (by alpha-ketoglutarate dehydrogenase), which is then converted to succinate by the action of succinyl-CoA...”
• More
• Integrative Omics Analysis of Three Oil Palm Varieties Reveals (Tanzania × Ekona) TE as a Cold-Resistant Variety in Response to Low-Temperature Stress
  Saand, International journal of molecular sciences 2022
  • “...apetala under chilling stress [ 80 ]. Citrate synthase, mitochondrial (P49298), and isocitrate dehydrogenase [NAD] (Q8LFC0) proteins were suppressed in BE. Nonetheless, isocitrate dehydrogenase [NAD] (Q945K7) was suppressed in OG, and isocitrate dehydrogenase [NADP] (P50218) was expressed in TE only. The isocitrate dehydrogenase [NADP] proteins were...”
• Mild reductions in mitochondrial NAD-dependent isocitrate dehydrogenase activity result in altered nitrate assimilation and pigmentation but do not impact growth
  Sienkiewicz-Porzucek, Molecular plant 2010
  • “...tabacum , CAA74776, Y14431) and 66% identity to IDH1 in Arabidopsis ( Arabidopsis thaliana , NP_195252, At4g35260). In silico predictions indicate that Sl IDH1 bears characteristics of a mitochondrial transit peptide sequence, indicating a mitochondrial location, whereas Sl ICDH1 and 2 have a cytosolic location (data...”

3asjA / Q5SIJ1 Crystal structure of homoisocitrate dehydrogenase in complex with a designed inhibitor (see paper)
33% identity, 84% coverage

• Ligand: 3-[(carboxymethyl)sulfanyl]-2-oxopropanoic acid (3asjA)

hicdh / Q5SIJ1 homoisocitrate dehydrogenase subunit (EC 1.1.1.87) from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (see paper)
HICDH_THET8 / Q5SIJ1 Isocitrate/homoisocitrate dehydrogenase; Homoisocitrate dehydrogenase; HICDH; EC 1.1.1.286 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (see paper)
HICDH_THET2 / Q72IW9 Isocitrate/homoisocitrate dehydrogenase; Homoisocitrate dehydrogenase; HICDH; EC 1.1.1.286 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27) (see 4 papers)
Q5SIJ1 homoisocitrate dehydrogenase (EC 1.1.1.87) from Thermus thermophilus (see paper)
TTC1012 No description from Thermus thermophilus HB27
TTHA1378 homoisocitrate dehydrogenase from Thermus thermophilus HB8
33% identity, 84% coverage

• function: Catalyzes the NAD(+)-dependent oxidative decarboxylation of homoisocitrate to 2-oxoadipate (alpha-ketoadipate), a reaction involved in lysine biosynthesis through the alpha-aminoadipate pathway (PubMed:21813504). In addition, has high activity with isocitrate, but is inactive with 3-isopropylmalate (By similarity).
  catalytic activity: (2R,3S)-homoisocitrate + NAD(+) = 2-oxoadipate + CO2 + NADH (RHEA:11900)
  catalytic activity: D-threo-isocitrate + NAD(+) = 2-oxoglutarate + CO2 + NADH (RHEA:23632)
  cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
  subunit: Homotetramer. Dimer of dimers. The homotetramer can transiently dissociate into homodimers.
• function: Catalyzes the NAD(+)-dependent oxidative decarboxylation of homoisocitrate to 2-oxoadipate (alpha-ketoadipate), a reaction involved in lysine biosynthesis through the alpha-aminoadipate pathway. In addition, has high activity with isocitrate, but is inactive with 3- isopropylmalate.
  catalytic activity: (2R,3S)-homoisocitrate + NAD(+) = 2-oxoadipate + CO2 + NADH (RHEA:11900)
  catalytic activity: D-threo-isocitrate + NAD(+) = 2-oxoglutarate + CO2 + NADH (RHEA:23632)
  cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
  subunit: Homotetramer. Dimer of dimers. The homotetramer can transiently dissociate into homodimers.
  disruption phenotype: Does not grow on minimal medium. Requires alpha- aminoadipate or lysine for growth.
• Evolution of lysine biosynthesis in the phylum deinococcus-thermus
  Nishida, International journal of evolutionary biology 2012
  • “...5 Enzyme 6 Enzyme 7 Enzyme 8 Enzyme 9 Enzyme 10 Thermus thermophilus HB27 TTC0043 TTC1012 TTC1393 TTC1396 TTC1541* TTC1542* TTC1543* TTC1546* TTC1547* TTC1550* Thermus thermophilus HB8 TTHA0411 TTHA1378 TTHA1755 TTHA1757 TTHA1903* TTHA1904* TTHA1907* TTHA1910* TTHA1911* TTHA1914* Thermus scotoductus TSC_c05810 TSC_c20650 TSC_c03550 TSC_c3520 TSC_c01940* TSC_c01930* TSC_c01920*...”
• Lysine propionylation is a prevalent post-translational modification in Thermus thermophilus
  Okanishi, Molecular & cellular proteomics : MCP 2014
  • “...TTHA0968 TTHA0996 TTHA1146 TTHA1272 TTHA1273 TTHA1275 TTHA1279 TTHA1343 TTHA1378 TTHA1454 TTHA1535 K250 K73 K22 K274 K299, K317 K59 K115, K357, K415 K55, K120...”
• Evolution of lysine biosynthesis in the phylum deinococcus-thermus
  Nishida, International journal of evolutionary biology 2012
  • “...HB27 TTC0043 TTC1012 TTC1393 TTC1396 TTC1541* TTC1542* TTC1543* TTC1546* TTC1547* TTC1550* Thermus thermophilus HB8 TTHA0411 TTHA1378 TTHA1755 TTHA1757 TTHA1903* TTHA1904* TTHA1907* TTHA1910* TTHA1911* TTHA1914* Thermus scotoductus TSC_c05810 TSC_c20650 TSC_c03550 TSC_c3520 TSC_c01940* TSC_c01930* TSC_c01920* TSC_c01890* TSC_c01880* TSC_c01850* Meiothermus ruber Mrub_0871 Mrub_2738 Mrub_0027 Mrub_2721* Mrub_2723* Mrub_2724* Mrub_2727* Mrub_2728*...”
• Degradation of ppGpp by nudix pyrophosphatase modulates the transition of growth phase in the bacterium Thermus thermophilus
  Ooga, The Journal of biological chemistry 2009
  • “...ilvN, leuA, leuB, leuC, leuD, mhpC, mhpD, mhpE, tyrA, ttha1378 fumC, gltA, icdA, korA, korB, lpdA, mdh, sdhA, sdhB, sdhD, sucA, sucB bluB, cbiB, cbiD, cbiG,...”
  • “...Metabolism Amino acid biosynthes ilvD dihydroxyacid dehydratase TTHA1378 462.3 0.45 Metabolism Amino acid biosynthes TTHA1576 391.9 0.48 Metabolism Amino acid...”

FAD_1632 isocitrate/isopropylmalate family dehydrogenase from Ferroplasma acidiphilum
28% identity, 96% coverage

• Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum Y^T
  Golyshina, Scientific reports 2017
  • “...pyruvate: ferredoxin oxidoreductase (FAD_05670568); 6, citrate synthase (FAD_1100); 7, aconitate hydratase (FAD_0701); 8, isocitrate dehydrogenase (FAD_1632); 9,2-oxoglutarate:ferredoxin oxidoreductase (FAD_07120713); 10, succinyl-CoA synthetase (FAD_0709710); 11, succinate dehydrogenase (FAD_07140717); 12, fumarate hydratase (FAD_1630); 13, malate dehydrogenase (FAD_0718); 14, glutamate dehydrogenase (FAD_0434); 15, aspartate aminotransferase (FAD_1098); 16, phosphoenolpyruvate synthase...”

MJ0720 / Q58130 3-isopropylmalate dehydrogenase subunit (EC 1.1.1.85) from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (see 2 papers)
LEU3_METJA / Q58130 3-isopropylmalate/3-methylmalate dehydrogenase; 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; IPMDH; Beta-IPM dehydrogenase; D-malate dehydrogenase [decarboxylating]; EC 1.1.1.85; EC 1.1.1.n5; EC 1.1.1.83 from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii) (see paper)
MJ0720 3-isopropylmalate dehydrogenase 1 (leuB1) from Methanocaldococcus jannaschii DSM 2661
34% identity, 87% coverage

• function: Catalyzes the oxidation of 3-carboxy-2-hydroxy-4- methylpentanoate (3-isopropylmalate) to 3-carboxy-4-methyl-2- oxopentanoate, which decarboxylates to 4-methyl-2-oxopentanoate (2- oxoisocaproate). Also catalyzes the oxidative decarboxylation of 3- methylmalate to 2-oxobutyrate, and that of D-malate to pyruvate. Cannot use NADP(+) instead of NAD(+). Cannot catalyze the oxidation of L- malate, L-tartrate, D-tartrate, DL-isocitrate, or DL-lactate.
  catalytic activity: (2R,3S)-3-isopropylmalate + NAD(+) = 4-methyl-2-oxopentanoate + CO2 + NADH (RHEA:32271)
  catalytic activity: (2R,3S)-3-methylmalate + NAD(+) = 2-oxobutanoate + CO2 + NADH (RHEA:32715)
  catalytic activity: (R)-malate + NAD(+) = pyruvate + CO2 + NADH (RHEA:18365)
  cofactor: Mg(2+) Mn(2+) (Binds 1 Mg(2+) or Mn(2+) ion per subunit.)
  subunit: Homotetramer.
• Methanogen homoaconitase catalyzes both hydrolyase reactions in coenzyme B biosynthesis
  Drevland, The Journal of biological chemistry 2008
  • “...catalyzed the hyisopropylmalate dehydrogenase (IPMDH; MJ0720). The citramalate synthase (MJ1392) replaces isopropyldration of cis-homoaconitate, cismalate...”
• Enzymology and evolution of the pyruvate pathway to 2-oxobutyrate in Methanocaldococcus jannaschii
  Drevland, Journal of bacteriology 2007
  • “...Another broad-specificity enzyme, isopropylmalate dehydrogenase (MJ0720), catalyzed the oxidative decarboxylation of -isopropylmalate, -methylmalate, and...”
  • “...pDG141 to create pDG157. The leuB gene at locus MJ0720 (NP_247705) was amplified using PCR and cloned between the NdeI and BamHI sites of plasmid pET-19b...”
• Modified pathway to synthesize ribulose 1,5-bisphosphate in methanogenic archaea
  Finn, Journal of bacteriology 2004
  • “...2 to 4 were identified as Mj0216 (lane 2), Mj1025 or Mj0720 (lane 3), and Mj0601 (lane 4), the target protein. specific activity of Mj0601 at this stage was 305...”

MA4265 isocitrate/isopropylmalate dehydrogenase family protein from Methanosarcina acetivorans C2A
32% identity, 86% coverage

• A nuclear magnetic resonance based approach to accurate functional annotation of putative enzymes in the methanogen Methanosarcina acetivorans
  Chen, BMC genomics 2011
  • “...a number of these as case studies to illustrate our generalized approach. Case study #1: MA4265 The MA4265 gene is annotated as a putative isocitrate/isopropylmalate dehydrogenase family protein in the DOE Integrated Microbial Genome (IMG) database ( http://img.jgi.doe.gov/ ). The re-annotation to a putative isocitrate/isopropylmalate dehydrogenase,...”
  • “...been verified experimentally [ 15 , 16 ]. In our studies, the gene product of MA4265 (342 aa) was heterologously expressed in E. coli as a soluble protein at 25C and was folded as judged by 1D 1 H NMR spectroscopy. The putative enzymatic annotations, isocitrate...”

Rfer_2380 Isocitrate dehydrogenase (NAD+) from Rhodoferax ferrireducens DSM 15236
32% identity, 95% coverage

• Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens
  Risso, BMC genomics 2009
  • “...dehydrogenase (Rfer_2411), for which there is a lineage-specific gene duplication in the R. ferrireducens genome (Rfer_2380, 97% identity) that resembles homologs of the Betaproteobacteria . Rfer_3489, annotated as a CitB, a citrate-utilization protein, might also be involved in this metabolism. The in silico model predicted that...”

Sb04g024840 No description from Sorghum bicolor
31% identity, 93% coverage

• Characterization of the Isocitrate Dehydrogenase Gene Family and Their Response to Drought Stress in Maize
  Wei, Plants (Basel, Switzerland) 2023
  • “..., while ZmIDH1.4 is orthologous to the rice gene LOC Os02g38200 and the sorghum gene Sb04g024840 . These genes are annotated as IDH, NAD + -dependent, and are involved in the TCA cycle and L-glutamine biosynthesis III. This suggests that ZmIDH1.2 , ZmIDH1.5, and ZmIDH1.4 may...”

LIC13328 isocitrate dehydrogenase from Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
Q72M63 Isocitrate dehydrogenase [NADP] from Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130)
32% identity, 78% coverage

• Surface proteomics and label-free quantification of Leptospira interrogans serovar Pomona
  Techawiwattanaboon, PLoS neglected tropical diseases 2021
  • “...proteinase K shaving. Abundance ranking a Gene ID Gene names Protein IDs Protein names 1 LIC13328 lic13328 Q72M63 Isocitrate dehydrogenase 2 LIC11335 groEL P61438 GroEL protein 3 LIC12082 cysK Q72QN1 Cysteine synthase 4 LIC12966 lipL41 Q72N71 LipL41 5 LIC11352 lipL32 Q72SM7 LipL32 6 LIC10175 lic10175 Q72VX0...”
• Pathogenic Leptospira interrogans exoproteins are primarily involved in heterotrophic processes
  Eshghi, Infection and immunity 2015
  • “...LIC11698 LIC12422 LIC10852 LIC10763 LIC10750 LIC13328 LIC10065 Fumarate hydratase (aspartate ammonia-lyase) Sulfate adenylyltransferase subunit 2 (transcription...”
• Surface proteomics and label-free quantification of Leptospira interrogans serovar Pomona
  Techawiwattanaboon, PLoS neglected tropical diseases 2021
  • “...shaving. Abundance ranking a Gene ID Gene names Protein IDs Protein names 1 LIC13328 lic13328 Q72M63 Isocitrate dehydrogenase 2 LIC11335 groEL P61438 GroEL protein 3 LIC12082 cysK Q72QN1 Cysteine synthase 4 LIC12966 lipL41 Q72N71 LipL41 5 LIC11352 lipL32 Q72SM7 LipL32 6 LIC10175 lic10175 Q72VX0 Uncharacterized protein...”

Rfer_2411 Isocitrate dehydrogenase (NAD+) from Rhodoferax ferrireducens DSM 15236
32% identity, 93% coverage

• Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens
  Risso, BMC genomics 2009
  • “...to Gammaproteobacteria and Alphaproteobacteria homologs (see Additional file 5 ). An exception is isocitrate dehydrogenase (Rfer_2411), for which there is a lineage-specific gene duplication in the R. ferrireducens genome (Rfer_2380, 97% identity) that resembles homologs of the Betaproteobacteria . Rfer_3489, annotated as a CitB, a citrate-utilization...”

LOC112172665 isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial from Rosa chinensis
33% identity, 83% coverage

• Reactive Oxygen and Related Regulatory Factors Involved in Ethylene-Induced Petal Abscission in Roses
  Han, Plants (Basel, Switzerland) 2024
  • “...Our data indicated that the expressions of these genes ( RhRHS17 , LOC112172931; RhIDH1 , LOC112172665; RhIDH-III , LOC112188192; RhERS , LOC112174439; RhPBL32 , LOC112174003; RhFRS5 , LOC112170513; RhRAC5 , LOC112173840; RhRAC1 , LOC112172302; RhRBOHD , LOC112196847; RhRBOHC , LOC112179306; RhPLATZ9 , LOC112179143; RhWRKY33a , LOC112192343)...”

RHTO_01290 isocitrate dehydrogenase (NAD+) from Rhodotorula toruloides NP11
32% identity, 93% coverage

• Systems analysis of phosphate-limitation-induced lipid accumulation by the oleaginous yeast Rhodosporidium toruloides
  Wang, Biotechnology for biofuels 2018
  • “...pMD18-T, resulting in T-IDH1 and T-IDH2. The full-length cDNA fragments coding Idh1 (RHTO_01289) and Idh2 (RHTO_01290) were individually cloned into the plasmid pET28a by RF cloning method, and the plasmids including Idh1 and Idh2 were transformed into E. coli BL21(DE3). Recombinant Idh1 and Idh2 were produced...”

G1APK3 isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) from Rhodotorula toruloides (see paper)
32% identity, 93% coverage

IDH6_ARATH / Q8LG77 Isocitrate dehydrogenase [NAD] catalytic subunit 6, mitochondrial; IDH-VI; Isocitric dehydrogenase 6; NAD(+)-specific ICDH 6; EC 1.1.1.41 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
Q8LG77 isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) from Arabidopsis thaliana (see paper)
AT3G09810 isocitrate dehydrogenase, putative / NAD+ isocitrate dehydrogenase, putative from Arabidopsis thaliana
32% identity, 84% coverage

• function: Catalytic subunit of the NAD(+)-dependent isocitrate dehydrogenase involved in the oxidative decarboxylation of isocitrate to 2-oxoglutarate (Probable). Performs an essential role in the oxidative function of the citric acid cycle.
  catalytic activity: D-threo-isocitrate + NAD(+) = 2-oxoglutarate + CO2 + NADH (RHEA:23632)
  cofactor: Mg(2+) Mn(2+) (Binds 1 Mg(2+) or Mn(2+) ion per subunit.)
  subunit: Heterooligomer of catalytic and regulatory subunits.
• The Phosphofructokinase Isoform AtPFK5 Is a Novel Target of Plastidic Thioredoxin-f-Dependent Redox Regulation
  Hess, Antioxidants (Basel, Switzerland) 2021
  • “...with the isocitrate dehydrogenase genes IDH1 ( At4g35260 ), IDH2 ( At2g17130 ) and IDH-VI (At3g09810) ( http://atted.jp/ , accessed on 23 February 2021), which are also highly expressed in this cell type [ 67 ], might hint at a function in energy production in leaf...”
• Central Metabolism in Mammals and Plants as a Hub for Controlling Cell Fate
  Selinski, Antioxidants & redox signaling 2021
  • “...(EC 1.1.1.41) NAD-IDH3 AT4G35650 (EC 1.1.1.41) NAD-IDH4 AT1G32480 (EC 1.1.1.41) NAD-IDH5 AT5G03290 (EC 1.1.1.41) NAD-IDH6 AT3G09810 (EC 1.1.1.41) Malate dehydrogenase mtNAD-MDH1 AT1G53240 (EC 1.1.1.37) HGNC:6971 (EC 1.1.1.37) YKL085W (EC 1.1.1.37) mtNAD-MDH2 AT3G15020 (EC 1.1.1.37) Malic enzyme NAD-ME1 AT2G13560 (EC 1.1.1.39) HGNC:6984 (EC 1.1.1.39) HGNC:6985 (EC 1.1.1.40)...”
• iTRAQ Mitoproteome Analysis Reveals Mechanisms of Programmed Cell Death in Arabidopsis thaliana Induced by Ochratoxin A
  Wang, Toxins 2017
  • “...AT3G58750 Citrate synthase 2 (CSY2) 2.0 (1.0) AT2G17130 Isocitrate dehydrogenase subunit 2 (IDH2) 9.1 (3.2) AT3G09810 Isocitrate dehydrogenase, putative 5.2 (2.4) AT5G03290 Isocitrate dehydrogenase, putative 4.7 (2.4) AT4G26910 2-oxoacid dehydrogenase family protein 3.8 (1.9) AT2G05710 Aconitate hydratase (Aconitase) 4.0 (2.0) AT5G23250 Succinyl-CoA ligase, putative 2.2 (1.3)...”
• Respiratory electron transfer pathways in plant mitochondria
  Schertl, Frontiers in plant science 2014
  • “...kDa/53 kDa Lancien et al., 1998 At4g35650 At3g09810: 138 kDa/40 kDa Lin et al., 2004 At3g09810 At5g03290: 138 kDa/40 kDa Lemaitre and Hodges, 2006 At5g03290 Lemaitre et al., 2007 At2g17130 -Ketoglutarate dehydrogenase complex At3g55410 (E1) -Ketoglutarate + coenzyme A + NAD + succinyl-CoA + CO 2...”
• Label-free shotgun proteomics and metabolite analysis reveal a significant metabolic shift during citrus fruit development
  Katz, Journal of experimental botany 2011
  • “...7.19 7 8.92 0 0.744 1.03 2385 At1g65930 2 8.40 3923 At1g65930 3 4.43 24612 At3g09810 2 1.31 0 1.16 2.03 2 0.80 0 1.57 1.95 149 At4g35260 3 0.53 0 4.43 2.77 0 0.80 1.28 2-oxoglutarate dehydrogenase E1 53498 At3g55410 0 1.76 3.59 2 335.26...”
• Global protein interactome exploration through mining genome-scale data in Arabidopsis thaliana
  Xu, BMC genomics 2010
  • “...putative), At3G28710 (H+-transporting two-sector ATPase, putative), AT3G47520 (Encodes a protein with NAD-dependent malate dehydrogenase activity), AT3G09810 (isocitrate dehydrogenase, putative / NAD+ isocitrate dehydrogenase, putative). When mapping the At2G44350 gene to the orthologs in mouse and S. pombe, which we did not applied in our predictive process,...”
• Diurnal changes in mitochondrial function reveal daily optimization of light and dark respiratory metabolism in Arabidopsis
  Lee, Molecular & cellular proteomics : MCP 2010
  • “...2-Oxoglutarate--The abundance of protein spot 45, which contained IDH3 (At3g09810), declined by 2-fold at the end of the dark period (12 h) and then increased...”
• The rules of gene expression in plants: organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana
  Aceituno, BMC genomics 2008
  • “...1); isocitrate dehydrogenase (NAD+) 2 U At1g65930 isocitrate dehydrogenase, putative/NADP+ isocitrate dehydrogenase, putative 1 U At3g09810 isocitrate dehydrogenase, putative/NAD+ isocitrate dehydrogenase, putative 0 M At4g35650 isocitrate dehydrogenase, putative/NAD+ isocitrate dehydrogenase, putative 0 U At5g14590 isocitrate dehydrogenase, putative/NADP+ isocitrate dehydrogenase, putative 0 M At1g54340 ICDH (ICDH); isocitrate...”

Q6ZI55 NAD-dependent isocitrate dehydrogenase c2 from Oryza sativa subsp. japonica
32% identity, 93% coverage

• Proteomic changes associated with expression of a gene (ipt) controlling cytokinin synthesis for improving heat tolerance in a perennial grass species
  Xu, Journal of experimental botany 2010
  • “...545 Q40676 252 0.6 0.7 NAD-dependent isocitrate dehydrogenase [ Oryza sativa ] Mitochondrion 40629/8.14 386 Q6ZI55 264 1.2 GAPDH (phosphorylation) [ Hordeum vulgare ] Cytoplasm 33235/6.20 850 P08477 267 1.7 GAPDH (phosphorylation) [ Hordeum vulgare ] Cytoplasm 33235/6.20 880 P08477 291 0.4 Ferredoxin-NADP reductase precursor [...”

TSC_c20650 homoisocitrate dehydrogenase from Thermus scotoductus SA-01
32% identity, 84% coverage

• Evolution of lysine biosynthesis in the phylum deinococcus-thermus
  Nishida, International journal of evolutionary biology 2012
  • “...thermophilus HB8 TTHA0411 TTHA1378 TTHA1755 TTHA1757 TTHA1903* TTHA1904* TTHA1907* TTHA1910* TTHA1911* TTHA1914* Thermus scotoductus TSC_c05810 TSC_c20650 TSC_c03550 TSC_c3520 TSC_c01940* TSC_c01930* TSC_c01920* TSC_c01890* TSC_c01880* TSC_c01850* Meiothermus ruber Mrub_0871 Mrub_2738 Mrub_0027 Mrub_2721* Mrub_2723* Mrub_2724* Mrub_2727* Mrub_2728* Meiothermus silvanus Mesil_2567 Mesil_1337 Mesil_0348 Mesil_0347 Mesil_0435* Mesil_0436* Mesil_0438* Mesil_0441* Mesil_0442* Oceanithermus...”

RHTO_01289 isocitrate dehydrogenase (NAD+) from Rhodotorula toruloides NP11
33% identity, 83% coverage

• Systems analysis of phosphate-limitation-induced lipid accumulation by the oleaginous yeast Rhodosporidium toruloides
  Wang, Biotechnology for biofuels 2018
  • “...and ligated with pMD18-T, resulting in T-IDH1 and T-IDH2. The full-length cDNA fragments coding Idh1 (RHTO_01289) and Idh2 (RHTO_01290) were individually cloned into the plasmid pET28a by RF cloning method, and the plasmids including Idh1 and Idh2 were transformed into E. coli BL21(DE3). Recombinant Idh1 and...”
  • “...consumption (Fig. 2 d). The levels of proteins associated with the TCA cycle, including Idh1 (RHTO_01289), Sdh1 (RHTO_05714), Sdh2 (RHTO_06068), and Mdh1 (RHTO_04363), decreased in the Pi-limited sample, namely, P 0/ F 3 value below 0.8, indicating that the TCA cycle activity was reduced under Pi-limitation....”

idh2 / RF|NP_595203.1 isocitrate dehydrogenase (NAD+) subunit 2; EC 1.1.1.41 from Schizosaccharomyces pombe (see 2 papers)
SPBC902.05c isocitrate dehydrogenase (NAD+) subunit 2 from Schizosaccharomyces pombe
30% identity, 84% coverage

• CharProtDB Source (per GeneDB): GeneDB_Spombe
• Key function for the CCAAT-binding factor Php4 to regulate gene expression in response to iron deficiency in fission yeast
  Mercier, Eukaryotic cell 2008
  • “...encoded by distinct genes: SPAC11G7.03 and SPBC902.05c for the NAD-dependent isocitrate dehydrogenase; SPBC3H7.03, SPBC776.15c, and SPAC1002.09c for the...”

IDH2_SCHPO / Q9USP8 Isocitrate dehydrogenase [NAD] subunit 2, mitochondrial; Isocitric dehydrogenase; NAD(+)-specific ICDH; EC 1.1.1.41 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see 3 papers)
30% identity, 84% coverage

• function: Performs an essential role in the oxidative function of the citric acid cycle and is involved in glutamate biosynthesis (PubMed:7903653). Also binds RNA; specifically to the 5'-untranslated leaders of mitochondrial mRNAs (PubMed:10975257).
  catalytic activity: D-threo-isocitrate + NAD(+) = 2-oxoglutarate + CO2 + NADH (RHEA:23632)
  cofactor: Mg(2+) Mn(2+) (Binds 1 Mg(2+) or Mn(2+) ion per subunit.)
  subunit: Octamer of two non-identical subunits IDH1 and IDH2.

LOC107804365 isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial-like precursor from Nicotiana tabacum
31% identity, 93% coverage

• Differential proteomics of tobacco seedling roots at high and low potassium concentrations
  Dai, Scientific reports 2021
  • “...KOG.Fun Metabolism related LOC107808039 4 Cytochrome b 4.72 C LOC107822887 11 Glutamate synthase 4 E LOC107804365 3 Isocitrate dehydrogenase 18.75 E LOC107797411 5 delta-1-pyrroline-5-carboxylate synthase 6.46 E LOC107798726 5 Peroxisomal 4.74 I LOC107832497 4 Phospholipase 4.72 I LOC107783543 3 Acyl-CoA synthetase 23.41 I LOC107768675 2 Copper...”

M1BEG6 NAD-dependent isocitrate dehydrogenase from Solanum tuberosum
30% identity, 93% coverage

• Transcriptomic and proteomic data provide new insights into cold-treated potato tubers with T- and D-type cytoplasm
  Szajko, Planta 2022
  • “...isoform d 0.21 0.00004 88 M1A0Z7 f Mitochondrial small heat shock protein 0.21 0.00095 43 M1BEG6 NAD-dependent isocitrate dehydrogenase d 0.21 0.0081 33 M1CL95 e, f Chaperonin-60kD, ch60 0.19 0.00004 70 M1BCZ5, P54260 Aminomethyltransferase 0.19 0.00008 52 M1A028 Dihydrolipoyl dehydrogenase 0.18 0.00004 50 M1C9T0 Aldehyde dehydrogenase...”

3blwF / P28241 Yeast isocitrate dehydrogenase with citrate and amp bound in the regulatory subunits (see paper)
29% identity, 93% coverage

• Ligand: citrate anion (3blwF)

IDH3_ARATH / O81796 Isocitrate dehydrogenase [NAD] regulatory subunit 3, mitochondrial; IDH-III; Isocitric dehydrogenase 3; NAD(+)-specific ICDH 3 from Arabidopsis thaliana (Mouse-ear cress) (see 3 papers)
O81796 isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) from Arabidopsis thaliana (see paper)
AT4G35650 isocitrate dehydrogenase, putative / NAD+ isocitrate dehydrogenase, putative from Arabidopsis thaliana
NP_195290 isocitrate dehydrogenase III from Arabidopsis thaliana
32% identity, 83% coverage

• function: Performs an essential role in the oxidative function of the citric acid cycle.
  subunit: Heterooligomer of catalytic and regulatory subunits. Interacts with 14-3-3-like proteins GRF1 GRF3 and GRF8 (PubMed:22104211).
• Mapping the Influence of Light Intensity on the Transgenerational Genetic Architecture of Arabidopsis thaliana
  Mei, Current issues in molecular biology 2024
  • “...related to stress response. AT4G35890 , AT4G36590, and AT4G36650 are related to transcriptional regulation, and AT4G35650 , AT4G35640, and AT4G36090 are related to anabolism. The genes duplicated under low light also included AT1G16440 and AT2G27520 , which are related to developmental regulation; AT1G16670 , AT2G27580, and...”
  • “...upstream_gene MADS-box transcription factor family protein AT4G36650 17285093 4 T/T synonymous Plant-specific TFIIB-related protein Anabolism AT4G35650 16910021 4 T/T 3_prime_UTR Isocitrate dehydrogenase III AT4G35640 16911160 4 A/A upstream_gene Serine acetyltransferase 3;2 AT4G36090 17079871 4 T/T synonymous Oxidoreductase, 2OG-Fe(II) oxygenase family protein AT4G36250 17151190 4 A/A synonymous...”
• Integrative Analysis of Transcriptomic and Proteomic Changes Related to Cytoplasmic Male Sterility in Spring Stem Mustard (Brassica juncea var. tumida Tsen et Lee)
  Shen, International journal of molecular sciences 2022
  • “...+ transporting ATPase subunit G - DOWN DAP BjuA029659 K00030 isocitrate dehydrogenase (NAD + ) AT4G35650 DOWN DAP BjuB024174 K00026 Malate dehydrogenase AT2G22780 DOWN DAP BjuA003018 K00030 IDH1 AT4G35260 UP DAP BjuA003018 K00030 IDH1 AT4G35260 UP DAP BjuB019661 K00026 Malate dehydrogenase, chloroplastic AT3G47520 UP DAP BjuB040953...”
• SWATH-MS based quantitive proteomics reveal regulatory metabolism and networks of androdioecy breeding system in Osmanthus fragrans
  Duan, BMC plant biology 2021
  • “...protein 75.664 ofr.gene29794 AT1G24020 MLP-like protein 423 55.531 ofr.gene19061 AT4G29270 Acid phosphatase-like protein 53.622 ofr.gene44766 AT4G35650 isocitrate dehydrogenase III 50.243 ofr.gene33663 AT1G70830 MLP-like protein 28 39.128 ofr.gene28906 AT2G20420 ATP citrate lyase (ACL) family protein 37.688 ofr.gene20390 AT5G63190 MA3 domain-containing protein 34.902 ofr.gene43330 AT1G53240 Lactate/malate dehydrogenase 34.634...”
• Central Metabolism in Mammals and Plants as a Hub for Controlling Cell Fate
  Selinski, Antioxidants & redox signaling 2021
  • “...1.1.1.41) YNL037C (EC 1.1.1.41) YOR136W (EC 1.1.1.41) YDL066W (EC 1.1.1.42) NAD-IDH2 AT2G17130 (EC 1.1.1.41) NAD-IDH3 AT4G35650 (EC 1.1.1.41) NAD-IDH4 AT1G32480 (EC 1.1.1.41) NAD-IDH5 AT5G03290 (EC 1.1.1.41) NAD-IDH6 AT3G09810 (EC 1.1.1.41) Malate dehydrogenase mtNAD-MDH1 AT1G53240 (EC 1.1.1.37) HGNC:6971 (EC 1.1.1.37) YKL085W (EC 1.1.1.37) mtNAD-MDH2 AT3G15020 (EC 1.1.1.37)...”
• Analysis of Promoters of Arabidopsis thaliana Divergent Gene Pair SERAT3;2 and IDH-III Shows SERAT3;2 Promoter is Nested Within the IDH-III Promoter
  Raipuria, Molecular biotechnology 2017 (PubMed)
  • “...gene pair SERAT3;2 and IDH-III encoded by At4g35640 and At4g35650 genes, respectively. As per TAIR annotation, these two genes are separated by a 161 bp IGR,...”
  • “...the divergent gene pair At4g35640 and At4g35650 coding, respectively, for Serine acetyl transferase (SERAT3;2) and isocitrate dehydrogenase (IDH-III),...”
• Analysis of Microtubule-Associated-Proteins during IBA-Mediated Adventitious Root Induction Reveals KATANIN Dependent and Independent Alterations of Expression Patterns
  Abu-Abied, PloS one 2015
  • “...different MAPs was normalized to the mean expression of two housekeeping genes IDH (isocitrate dehydrogenase At4g35650) and Alcohol oxidase (At1g03990). To cluster genes that are similar by their expression profile, we scaled the gene-expression signals by subtracting their mean of the log 2 signals over all...”
• Respiratory electron transfer pathways in plant mitochondria
  Schertl, Frontiers in plant science 2014
  • “...kDa/42 kDa Behal and Oliver, 1998 At5g14590 At5g14590: 140 kDa/53 kDa Lancien et al., 1998 At4g35650 At3g09810: 138 kDa/40 kDa Lin et al., 2004 At3g09810 At5g03290: 138 kDa/40 kDa Lemaitre and Hodges, 2006 At5g03290 Lemaitre et al., 2007 At2g17130 -Ketoglutarate dehydrogenase complex At3g55410 (E1) -Ketoglutarate +...”
• Evidence for extensive heterotrophic metabolism, antioxidant action, and associated regulatory events during winter hardening in Sitka spruce
  Collakova, BMC plant biology 2013
  • “...expression as LPD1. A putative regulatory subunit of the mitochondrial NAD-dependent isocitrate dehydrogenase III ( At4g35650 ) increased 2-fold in TP1 and showed a stable 4.4-fold increase in transcript levels in TP2 through TP4. Malic enzyme gene ( At4g00570 ) showed only a moderate 2.2-fold up-regulation...”
  • “...operational. For example, a putative regulatory subunit of the mitochondrial NAD-dependent isocitrate dehydrogenase III ( At4g35650 ) [ 72 , 73 ] showed a stable 4.4-fold increase in transcript levels in TP2 through TP4. Malic enzyme has been implicated in generating NADH and pyruvate needed for...”
• More
• Analysis of Promoters of Arabidopsis thaliana Divergent Gene Pair SERAT3;2 and IDH-III Shows SERAT3;2 Promoter is Nested Within the IDH-III Promoter.
  Raipuria, Molecular biotechnology 2017 (PubMed)
  • GeneRIF: Study has identified a unique bidirectional promoter capable of driving gene expression in Arabidopsis thaliana, and showed for the first time, that SERAT3;2 promoter is nested in the IDH-III promoter.
• Expression analysis of Arabidopsis thaliana NAD-dependent isocitrate dehydrogenase genes shows the presence of a functional subunit that is mainly expressed in the pollen and absent from vegetative organs.
  Lemaitre, Plant & cell physiology 2006 (PubMed)
  • GeneRIF: Four of the IDH genes were expressed in all plant organs tested. One gene (At4g35650) was expressed mainly in the pollen. In leaves, the IDH genes were highly expressed in the veins, and to a lesser extent in mesophyll cells.
• Sex differences in brain proteomes of neuron-specific STAT3-null mice after cerebral ischemia/reperfusion.
  Di, Journal of neurochemistry 2012
  • “...3/8 Calreticulin (CALR) P14211 7e-006 1/3 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) P16858 2e-007 3/3 Isocitrate dehydrogenase (IDH) O81796 2e-004 2/2 Peroxiredoxin 6 (PRDX6) O08709 1e-006 1/3 Synapsin II (SYN2) Q64332 7e-014 3/7 Table 2 Expression levels changes of proteins identified in all the groups compared Up Down Ipsilateral...”
• Involvement of Stat3 in mouse brain development and sexual dimorphism: a proteomics approach.
  Di, Brain research 2010
  • “...GAPDH P16858 2.00E-07 272% 0.0002 Energy metabolism VDAC2 Q60930 9.00E-06 328% 0.007 mitochondrial exchange IDH O81796 2.00E-04 29% 0.007 energy metabolism B) STAT 3 KO Female vs STAT3 KO Male Syn Q91ZZ3 5.00E-09 188% 0.012 Synaptic Syn O55042-1 1.00E-11 154% 0.036 Synaptic VDAC 2 Q60930 2.00E-06...”
  • “...MnSOD P09671 3.00E-06 172% 0.042 antioxidant VDAC 3 Q60931 2.00E-05 68% 0.002 mitochondrial exchange IDH O81796 2.00E-04 49% 0.016 energy metabolism...”

NP_001234366 isocitrate dehydrogenase [NAD] regulatory subunit 1 from Solanum lycopersicum
31% identity, 93% coverage

• Mild reductions in mitochondrial NAD-dependent isocitrate dehydrogenase activity result in altered nitrate assimilation and pigmentation but do not impact growth.
  Sienkiewicz-Porzucek, Molecular plant 2010
  • GeneRIF: Studies show that even small changes in mitochondrial NAD-dependent isocitrate dehydrogenase activity lead to noticeable alterations in nitrate assimilation. [NAD Isocitrate Dehydrogenase]
• Mild reductions in cytosolic NADP-dependent isocitrate dehydrogenase activity result in lower amino acid contents and pigmentation without impacting growth.
  Sulpice, Amino acids 2010
  • GeneRIF: Study demonstrated that minor changes in activity of cytosolic NADP-isocitrate dehydrogenase in tomato leaves has dramatic metabolic consequences but these have little effect on growth or plant performance. [SlICDH1]

G1APK2 isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) from Rhodotorula toruloides (see paper)
33% identity, 83% coverage

IDH-II / P93032 NAD+-dependent isocitrate dehydrogenase regulatory subunit (EC 1.1.1.286) from Arabidopsis thaliana (see paper)
IDH2_ARATH / P93032 Isocitrate dehydrogenase [NAD] regulatory subunit 2, mitochondrial; IDH-II; Isocitric dehydrogenase 2; NAD(+)-specific ICDH 2 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
P93032 isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) from Arabidopsis thaliana (see 2 papers)
AT2G17130 IDH2 (ISOCITRATE DEHYDROGENASE SUBUNIT 2); isocitrate dehydrogenase (NAD+)/ oxidoreductase, acting on the CH-OH group of donors, NAD or NADP as acceptor from Arabidopsis thaliana
32% identity, 88% coverage

• function: Performs an essential role in the oxidative function of the citric acid cycle.
  subunit: Heterooligomer of catalytic and regulatory subunits
• Insights into physiological roles of flavonoids in plant cold acclimation
  Kitashova, The Plant journal : for cell and molecular biology 2024
  • “...positively correlated with plastidial pyruvate dehydrogenase (AT1G01090) while it correlated negatively with the mitochondrial IDH2 (AT2G17130) and the mitochondrial PDH component subunit alpha1 (AT1G59900; Figure 2 ). Figure 2 Pearson correlation of pyruvate dehydrogenases and isocitrate dehydrogenases. Numbers show Pearson correlation coefficients; blank fields were not...”
• The boundary of life and death: changes in mitochondrial and cytosolic proteomes associated with programmed cell death of Arabidopsis thaliana suspension culture cells
  Schwarze, Frontiers in plant science 2023
  • “...fraction greater than that observed for the matrix protein isocitrate dehydrogenase [NADP(+)] type 2 (IDH2; AT2G17130, log2FC = 2.09762) that is frequently used as mitochondrial structural marker ( Rikhvanov etal., 2007 ; Lopez-Huertas and del Ro, 2014 ; Lee etal., 2019 ; Supplementary Table S4A ,...”
• The Phosphofructokinase Isoform AtPFK5 Is a Novel Target of Plastidic Thioredoxin-f-Dependent Redox Regulation
  Hess, Antioxidants (Basel, Switzerland) 2021
  • “...phloem-related process. The co-expression with the isocitrate dehydrogenase genes IDH1 ( At4g35260 ), IDH2 ( At2g17130 ) and IDH-VI (At3g09810) ( http://atted.jp/ , accessed on 23 February 2021), which are also highly expressed in this cell type [ 67 ], might hint at a function in...”
• Central Metabolism in Mammals and Plants as a Hub for Controlling Cell Fate
  Selinski, Antioxidants & redox signaling 2021
  • “...(EC 1.1.1.41) HGNC:5386 (EC 1.1.1.41) YNL037C (EC 1.1.1.41) YOR136W (EC 1.1.1.41) YDL066W (EC 1.1.1.42) NAD-IDH2 AT2G17130 (EC 1.1.1.41) NAD-IDH3 AT4G35650 (EC 1.1.1.41) NAD-IDH4 AT1G32480 (EC 1.1.1.41) NAD-IDH5 AT5G03290 (EC 1.1.1.41) NAD-IDH6 AT3G09810 (EC 1.1.1.41) Malate dehydrogenase mtNAD-MDH1 AT1G53240 (EC 1.1.1.37) HGNC:6971 (EC 1.1.1.37) YKL085W (EC 1.1.1.37)...”
• Gel-based proteomic map of Arabidopsis thaliana root plastids and mitochondria
  Grabsztunowicz, BMC plant biology 2020
  • “...family protein (At5g14590 in spot 65) and regulatory subunits 1 (At4g35260, spot 72) and 2 (At2g17130, spots 62 and 63). 2-oxoglutarate, in turn, is decarboxylated to succinyl-CoA (by alpha-ketoglutarate dehydrogenase), which is then converted to succinate by the action of succinyl-CoA synthetase (or ligase) [ 58...”
• Consequences of Oxidative Stress on Plant Glycolytic and Respiratory Metabolism
  Dumont, Frontiers in plant science 2019
  • “...17 [Cys 961 ] Isocitrate dehydrogenase IDH1 (At4g35260) 8 13 22 [ C128/216 ] IDH2 (At2g17130) 8 13 NADP-IDH (At1g65930) 10 [Cys 75/262/363 ], 11 [Cys 75/363 ] 13 17 [Cys 116 ], 18 [Cys 75/116/131/269 ] Succinyl-CoA ligase SCS (At2g20420, At5g23250) 13 SCS (At5g08300) 13...”
• iTRAQ Mitoproteome Analysis Reveals Mechanisms of Programmed Cell Death in Arabidopsis thaliana Induced by Ochratoxin A
  Wang, Toxins 2017
  • “...(1.2) AT2G44350 ATP citrate synthase (ATCS) 3.8 (1.9) AT3G58750 Citrate synthase 2 (CSY2) 2.0 (1.0) AT2G17130 Isocitrate dehydrogenase subunit 2 (IDH2) 9.1 (3.2) AT3G09810 Isocitrate dehydrogenase, putative 5.2 (2.4) AT5G03290 Isocitrate dehydrogenase, putative 4.7 (2.4) AT4G26910 2-oxoacid dehydrogenase family protein 3.8 (1.9) AT2G05710 Aconitate hydratase (Aconitase)...”
• Quantitative Proteomic Analysis of the Response to Zinc, Magnesium, and Calcium Deficiency in Specific Cell Types of Arabidopsis Roots
  Fukao, Proteomes 2016
  • “...0.62 0.83 0.72 0.69 0.64 AT2G04305 Magnesium transporter CorA-like family protein N.D. 0.32 0.46 N.D. AT2G17130 isocitrate dehydrogenase subunit 2 0.47 0.41 0.44 0.63 0.63 0.89 AT2G28190 copper/zinc superoxide dismutase 2 N.D. 0.40 0.69 0.35 0.60 AT2G28520 vacuolar proton ATPase A1 0.47 0.66 0.44 0.63 0.50...”
• More

CNAG_07363 isocitrate dehydrogenase, NAD-dependent from Cryptococcus neoformans var. grubii H99
30% identity, 94% coverage

• A PAS Protein Directs Metabolic Reprogramming during Cryptococcal Adaptation to Hypoxia
  Zhao, mBio 2021
  • “...reductive branch of the TCA cycle, including the IDH1 ( CNAG_07851 ) and IDH2 ( CNAG_07363 ) homologs, were upregulated under hypoxia in Cryptococcus ( Fig.1C and Data Set S2 ). In addition, genes involved in the PPP ( CNAG_01984 , CNAG_04025 , and CNAG_06923 /...”
• A Fungal Arrestin Protein Contributes to Cell Cycle Progression and Pathogenesis
  Telzrow, mBio 2019
  • “...CNAG_02928 Large subunit ribosomal protein L5e 4.3 0.0 CNAG_05759 Acetyl-CoA carboxylase/biotin carboxylase c 4.0 0.0 CNAG_07363 Isocitrate dehydrogenase, NAD dependent 4.0 0.0 CNAG_02673 NAD-dependent epimerase/dehydratase 3.7 0.0 CNAG_02811 Small subunit ribosomal protein S29 3.7 0.0 CNAG_07745 MPD1 Alcohol dehydrogenase, propanol preferring 3.3 0.0 CNAG_00176 Glutamate carboxypeptidase...”
• Cryptococcus neoformans can form titan-like cells in vitro in response to multiple signals
  Trevijano-Contador, PLoS pathogens 2018
  • “...and E2 components of ketoglutarate deshydrogenase (CNAG_03674 and CNAG_03596), the two subunits of isocitrate dehydrogenase (CNAG_07363 and CNAG_07851), and CNAG_05653, encoding malate synthase. In addition, genes belonging to the oxidative segment of the pentose-phosphate shunt were also induced, such as glucose-6-phosphate dehydrogenase (CNAG_03245), 6-phosphogluconolactonase (CNAG_02133), and...”
  • “...deHase, E1 component 0.9 3.3E-02 2.3 4.4E-03 CNAG_03596 2-oxoglutarate deHase E2 component 0.6 2.0 2.4E-02 CNAG_07363 isocitrate deHase, NAD-dependent 1.0 3.4E-03 2.8 2.0E-03 CNAG_07851 isocitrate deHase, NAD-dependent 2.1 1.8E-09 2.7 5.7E-04 CNAG_05653 malate synthase A (MLS1) 1.8 2.4E-05 7.8 1.7E-11 Pentose-phosphate shunt (p-value : 5 ....”
• Brain inositol is a novel stimulator for promoting Cryptococcus penetration of the blood-brain barrier
  Liu, PLoS pathogens 2013
  • “...Inositol-1-phosphate synthase (Ino1) 2.79 CNE01560 CNAG_02399 Glutathione reductase 2.72 CND00180 CNAG_00879 Glutamate dehydrogenase 2.63 CNA04610 CNAG_07363 Isocitrate dehydrogenase 2.59 CNL04840 CNAG_05138 Exo-beta-1,3-glucanase 2.54 CNC02410 CNAG_01737 Methyl sterol oxidase 2.54 CNB00990 CNAG_03596 2-Oxoglutarate_dehydrogenase_complex 2.53 CNE02710 CNAG_07639 Triacylglycerol lipase 2.50 Signal transduction CNA01180 CNAG_00130 Serine/threonine protein kinase 5.11...”

Mmah_0582 isocitrate dehydrogenase (NADP) from Methanohalophilus mahii DSM 5219
30% identity, 92% coverage

• The genome sequence of Methanohalophilus mahii SLP(T) reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments
  Spring, Archaea (Vancouver, B.C.) 2010
  • “...the citric acid cycle using the enzymes citrate synthase (Mmah_0479), aconitase (Mmah_0478), and isocitrate dehydrogenase (Mmah_0582). It has to be considered that the citrate synthase gene of Mhp. mahii contains an amber stop codon at position 177 of the coding nucleotide sequence, so that it is...”

LOC18037111 isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial from Citrus x clementina
30% identity, 93% coverage

• Transcriptome analysis of Harumi tangor fruits: Insights into interstock-mediated fruit quality
  Liao, Frontiers in plant science 2022
  • “...pyruvate kinase (LOC18045215, LOC18050485), fructokinase-4 ( FRK4 , LOC18046804), and isocitrate dehydrogenase ( NAD-IDH , LOC18037111) were >1.2-fold higher in the HP4 group than in the HPP4 group. In contrast, the expression levels of genes encoding pyruvate kinase ( PK , LOC18046239), cytochrome P450 ( CYP82C4...”
  • “...DAF and downregulated in the HPP group at 180 DAF. The isocitrate dehydrogenase gene IDH-III (LOC18037111), fructokinase gene FRK4 (LOC18046804), alkaline/neutral invertase gene CINV2 (CICLE_v10003734mg, LOC18042730), hexokinase gene HXK1 (LOC18035909), and sucrase/ferredoxin-like gene (LOC18051223) were downregulated in the HPP group at 45, 90, and 180 DAF...”

EHS24_002540 NAD-dependent isocitrate dehydrogenase from Apiotrichum porosum
31% identity, 94% coverage

• Draft Genome Sequence of the Oleaginous Yeast Apiotrichum porosum (syn. Trichosporon porosum) DSM 27194
  Gorte, Journal of genomics 2019
  • “...SCO production 11 , 12 . These include putative AMP deaminase (EHS24_003651), isocitrate dehydrogenase (EHS24_007601, EHS24_002540 and EHS24_002733), malic enzyme (EHS24_008089), ATP citrate lyase (EHS24_004735), acetyl-CoA carboxylase (EHS24_004089) and fatty acid synthase (EHS24_002351, EHS24_002352). The genome also encodes multiple copies of glucose oxidase (EHS24_007400, EHS24_008706, EHS24_008979,...”

I1IYV8 Isopropylmalate dehydrogenase-like domain-containing protein from Brachypodium distachyon
32% identity, 93% coverage

• Proteomic and metabolic disturbances in lignin-modified Brachypodium distachyon
  Barros, The Plant cell 2022
  • “...up) with phospholipase A2 (I1GP43, down); and -ketoglutarate (42, up) with two isocitrate dehydrogenases (I1IB67, I1IYV8, down). In the phenylpropanoid pathway, the reduced concentrations of all three monolignols (J, K, L) and the identified lignans (28, 35, 82) in the BdPTAL1i lines was accompanied by downregulation...”

NP_849963 isocitrate dehydrogenase subunit 2 from Arabidopsis thaliana
31% identity, 90% coverage

• NAD-dependent isocitrate dehydrogenase mutants of Arabidopsis suggest the enzyme is not limiting for nitrogen assimilation.
  Lemaitre, Plant physiology 2007
  • GeneRIF: Leaf IDH activity reduced by 43% in mutant

PAAG_00856 isocitrate dehydrogenase subunit 1 from Paracoccidioides lutzii Pb01
30% identity, 93% coverage

• Interaction of Isocitrate Lyase with Proteins Involved in the Energetic Metabolism in Paracoccidioides lutzii
  Freitas, Journal of fungi (Basel, Switzerland) 2020
  • “...iron-sulfur subunit 12,727.08 PAAG_00417 succinyl-CoA ligase subunit alpha 7841.01 PAAG_01463 succinyl-CoA ligase subunit beta 9100.539 PAAG_00856 isocitrate dehydrogenase subunit 1 11,681.96 PAAG_07729 isocitrate dehydrogenase subunit 2 10,708.71 PAAG_08351 mitochondrial NADP-specific isocitrate dehydrogenase 13,966.9 PAAG_00053 malate dehydrogenase 10,102.86 PAAG_08449 malate dehydrogenase 8959.159 PAAG_05150 ATP-citrate synthase subunit 1...”
• Proteomic profile response of Paracoccidioides lutzii to the antifungal argentilactone
  Prado, Frontiers in microbiology 2015
  • “...cycle Malate dehydrogenase PAAG_00053 47991.24 0.795 Malate dehydrogenase PAAG_08449 7490.87 0.756 Isocitrate dehydrogenase subunit 1 PAAG_00856 1820.37 * Isocitrate dehydrogenase subunit 2 PAAG_07729 1604.29 * Succinate dehydrogenase flavoprotein subunit, mitochondrial PAAG_01725 1798.19 0.827 Oxidation of fatty acids Short-chain specific acyl-CoA dehydrogenase PAAG_05454 1028.15 * Transport Carbonic...”

I1IB67 Isopropylmalate dehydrogenase-like domain-containing protein from Brachypodium distachyon
31% identity, 93% coverage

• Proteomic and metabolic disturbances in lignin-modified Brachypodium distachyon
  Barros, The Plant cell 2022
  • “...(31, up) with phospholipase A2 (I1GP43, down); and -ketoglutarate (42, up) with two isocitrate dehydrogenases (I1IB67, I1IYV8, down). In the phenylpropanoid pathway, the reduced concentrations of all three monolignols (J, K, L) and the identified lignans (28, 35, 82) in the BdPTAL1i lines was accompanied by...”

CNA04610 isocitrate dehydrogenase from Cryptococcus neoformans var. neoformans JEC21
30% identity, 94% coverage

• Brain inositol is a novel stimulator for promoting Cryptococcus penetration of the blood-brain barrier
  Liu, PLoS pathogens 2013
  • “...CNAG_01539 Inositol-1-phosphate synthase (Ino1) 2.79 CNE01560 CNAG_02399 Glutathione reductase 2.72 CND00180 CNAG_00879 Glutamate dehydrogenase 2.63 CNA04610 CNAG_07363 Isocitrate dehydrogenase 2.59 CNL04840 CNAG_05138 Exo-beta-1,3-glucanase 2.54 CNC02410 CNAG_01737 Methyl sterol oxidase 2.54 CNB00990 CNAG_03596 2-Oxoglutarate_dehydrogenase_complex 2.53 CNE02710 CNAG_07639 Triacylglycerol lipase 2.50 Signal transduction CNA01180 CNAG_00130 Serine/threonine protein kinase...”
• Metabolic adaptation in Cryptococcus neoformans during early murine pulmonary infection
  Hu, Molecular microbiology 2008
  • “...1 55 6 3 1 CNG03490 XM_572038 malate dehydrogenase AACTTTGTTC 13 0 4 2 15 CNA04610 XM_566837 isocitrate dehydrogenase CATTTTGATT 8 0 0 0 2 CNF03780 XM_571672 malic enzyme TTGGCTCCCA 5 1 0 0 2 CNC01700 XM_569517 fumarase Glycolysis ACTCAGGTTG 1 65 19 17 3 CNB00300...”

MMP0539 3-isopropylmalate dehydrogenase from Methanococcus maripaludis S2
31% identity, 91% coverage

• Global responses of Methanococcus maripaludis to specific nutrient limitations and growth rate
  Hendrickson, Journal of bacteriology 2008
  • “...significant. In contrast, the mRNA levels for leuB (Mmp0539), which is specific for leucine biosynthesis, was not affected similarly. Somewhat larger increases...”
  • “...Amino acid biosynthesis ilvB (Mmp0650) ilvN (Mmp0651) leuB (Mmp0539) argH (Mmp0013) hisA (Mmp0417) hisG (Mmp0947) carB (Mmp1013) 0.45 0.63 0.22 0.22 2.1 0.48...”

Marky_1533 isocitrate/isopropylmalate dehydrogenase family protein from Marinithermus hydrothermalis DSM 14884
30% identity, 87% coverage

• Evolution of lysine biosynthesis in the phylum deinococcus-thermus
  Nishida, International journal of evolutionary biology 2012
  • “...Mesil_0441* Mesil_0442* Oceanithermus profundus Ocepr_1387 Ocepr_1797* Ocepr_1798* Ocepr_1796* Ocepr_1788* Ocepr_1784* Ocepr_1781* Ocepr_1780* Ocepr_1779* Marinithermus hydrothermalis Marky_1533 Marky_0665* Marky_0663* Marky_0666* Marky_0667* Marky_0668* Marky_0671* Marky_0672* Marky_0673* Deinococcus radiodurans DR_1674 DR_0794 DR_1413 DR_1420 DR_0963 DR_2194 DR_1614 DR_1610 DR_1238 Deinococcus geothermalis Dgeo_2084 Dgeo_1458 Dgeo_1416 Dgeo_1391 Dgeo_0678 Dgeo_0685 Dgeo_1151* Dgeo_1154* Dgeo_1156*...”

MMP0880 2-oxosuberate synthase, last step from Methanococcus maripaludis S2
28% identity, 88% coverage

• Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis
  Hendrickson, Journal of bacteriology 2004
  • “...Mmp0153), spontaneous hydration, and oxidative decarboxylation (AksF; Mmp0880) reactions are involved in the synthesis of 2-oxosuberate, an intermediate in...”

AO090003000008 No description from Aspergillus oryzae RIB40
30% identity, 93% coverage

• Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing
  Wang, Nucleic acids research 2010
  • “...For example, the key regulator genes of the TCA cycle, citrate synthase (AO090102000627), isocitrate dehydrogenase (AO090003000008, AO090005001404 and AO090012000629) and succinate dehydrogenase (AO090010000505, AO090020000415 and AO090020000596), were upregulated on SC ( Supplementary Table S10 ), as well as some important genes of oxidative phosphorylation (AO090001000657, AO090005000617,...”

Q4WNH3 isocitrate dehydrogenase (NAD(+)) from Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)
29% identity, 87% coverage

• The proteomic signature of Aspergillus fumigatus during early development
  Cagas, Molecular & cellular proteomics : MCP 2011
  • “...Q4WTX0 Q4WYW4 32 kDa 84 kDa 50 kDa 26 kDa 15 kDa Q4WNH3 Q4WRU9 Q4WAQ6 Q4WYK1 Q4WQR1 46 kDa 41 kDa Q4WHT0 Q4WEH4 122 kDa 90 kDa 41 kDa 24 kDa 62 kDa Q4X1E0...”

B7Z9J8 Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial from Homo sapiens
34% identity, 62% coverage

• Quantitative proteomic analysis for high-throughput screening of differential glycoproteins in hepatocellular carcinoma serum
  Gao, Cancer biology & medicine 2015
  • “...(Fragment) OS=Homo sapiens GN=TEX11 PE=4 SV=1 - [B1ALL0_HUMAN] 1.72 3 1 1 754 86.8 5.16 B7Z9J8 cDNA, FLJ78862, highly similar to Isocitrate dehydrogenase OS=Homo sapiens PE=2 SV=1 - [B7Z9J8_HUMAN] 6.61 6 1 1 257 28.1 5.66 B3KTT7 Pannexin 2, isoform CRA_a OS=Homo sapiens GN=PANX2 PE=2 SV=1...”

NCU00775 isocitrate dehydrogenase subunit 1 from Neurospora crassa OR74A
28% identity, 93% coverage

• Quantitative trait loci (QTL) underlying phenotypic variation in bioethanol-related processes in Neurospora crassa
  Waters, PloS one 2020
  • “...(FGSC2489/2223/4825), Region NCU00629 emp-3 6-phosphofructokinase 7765548 (G/G/T), Exon NCU00742 glp-1 glycerol-3-phosphate dehydrogenase 7361975 (C/T/C), Exon NCU00775 tca-6 isocitrate dehydrogenase subunit 1 7215729 (A/A/G), Exon NCU00801 cdt-1 MFS lactose permease 7123185 (G/A/A), Exon NCU00821 sut-15 sugar transporter-15 7056785 (A/A/G), Exon 7057292 (G/G/A), Exon 7057328 (A/A/G), Exon NCU00809...”

An18g06760 uncharacterized protein from Aspergillus niger
29% identity, 93% coverage

• Identification of novel citramalate biosynthesis pathways in Aspergillus niger
  Hossain, Fungal biology and biotechnology 2019
  • “...7.34 6.20 11.04 5 ANI_1_1802134 An15g07730 Aconitate hydratase Cyto 28.75 43.79 46.11 27.81 6 ANI_1_906164 An18g06760 Isocitrate dehydrogenase (NAD+) subunit 1 Mito 189.71 209.47 167.93 190.84 6 ANI_1_798074 An08g05580 Isocitrate dehydrogenase [NAD] subunit 2 Mito 165.29 175.80 165.81 151.75 6 ANI_1_3136024 An02g12430 Isocitrate dehydrogenase [NADP] Per...”
• Functional exploration of co-expression networks identifies a nexus for modulating protein and citric acid titres in Aspergillus niger submerged culture
  Cairns, Fungal biology and biotechnology 2019
  • “...Sec31p Tricarboxylic acid cycle (GO:0006099) kgdA An04g04750 Oxoglutarate dehydrogenase mdhA An07g02160 Mitochondrial malate dehydrogenase idh1 An18g06760 Isocitrate dehydrogenase idh2 An08g05580 Isocitrate dehydrogenase ico2 An09g03870 Aconitate hydratase citA An09g06680 Citrate synthase aclA An11g00530 Cytoplasmic ATP-citrate lyase kgd2 An11g11280 Dihydrolipoamide S-succinyl transferase fumR An12g07850 Fumarate hydratase aclB An11g00510...”
• The amyR-deletion strain of Aspergillus niger CICC2462 is a suitable host strain to express secreted protein with a low background
  Zhang, Microbial cell factories 2016
  • “...activity An08g05580 386.02 899.66 1.22 Isocitrate dehydrogenase activity An02g12770 389.46 891.41 1.19 Succinate dehydrogenase activity An18g06760 594 1299.36 1.13 Isocitrate dehydrogenase activity An14g04400 390.85 854.72 1.13 Succinate dehydrogenase activity Influence of the deletion of amyR on mycelium morphology Up-regulation of the oxidative phosphorylation and tricarboxylic acid...”
• Trancriptional landscape of Aspergillus niger at breaking of conidial dormancy revealed by RNA-sequencing
  Novodvorska, BMC genomics 2013
  • “...semialdehyde dehydrogenase 31.91 274.43 2.34 117.27 TCA cycle An08g05580 isocitrate dehydrogenase 2.71 10.85 69.17 6.37 An18g06760 isocitrate dehydrogenase 3.17 55.23 354.46 6.41 An04g04750 oxoglutarate dehydrogenase 2.23 22.9 109.76 4.79 An17g01670 succinyl-CoA synthetase 5.36 24.29 128.98 5.31 Metabolism of internal carbohydrates An01g09290 neutral trehalase ( A. nidulans...”
  • “...expression of tricarboxylic acid cycle (TCA cycle) genes. Genes coding for putative isocitrate dehydrogenases (An08g05580, An18g06760), -ketoglutarate dehydrogenase An04g04750) and succinyl-CoA synthetase (An17g01670) exhibited increased transcript levels at the breaking of dormancy. After the onset of germination, we detected increased transcript levels of genes encoding putative...”

Pyrde_1536 isocitrate/isopropylmalate dehydrogenase family protein from Pyrodictium delaneyi
30% identity, 82% coverage

• Microbe-Mineral Interaction and Novel Proteins for Iron Oxide Mineral Reduction in the Hyperthermophilic Crenarchaeon Pyrodictium delaneyi
  Kashyap, Applied and environmental microbiology 2021
  • “...lyase None ND d Citrate synthase Pyrde_1539 No 0 Aconitase Pyrde_0502-Pyrde_0503 No/Yes 0 Isocitrate dehydrogenase Pyrde_1536 Yes a c 0 2-oxoglutarate oxidoreductase Pyrde_1713-Pyrde_1714 Yes a b 277127 Succinyl-CoA synthetase Pyrde_0793-Pyrde_0794 No 39514 Fumarate reductase Pyrde_1917-Pyrde_1920 No/No/No/Yes a b 0 Fumarase Pyrde_1915-Pyrde_1916 Yes a c 0 Malate...”

Ocepr_1387 No description from Oceanithermus profundus 506, DSM 14977
28% identity, 93% coverage

• Evolution of lysine biosynthesis in the phylum deinococcus-thermus
  Nishida, International journal of evolutionary biology 2012
  • “...Mrub_2727* Mrub_2728* Meiothermus silvanus Mesil_2567 Mesil_1337 Mesil_0348 Mesil_0347 Mesil_0435* Mesil_0436* Mesil_0438* Mesil_0441* Mesil_0442* Oceanithermus profundus Ocepr_1387 Ocepr_1797* Ocepr_1798* Ocepr_1796* Ocepr_1788* Ocepr_1784* Ocepr_1781* Ocepr_1780* Ocepr_1779* Marinithermus hydrothermalis Marky_1533 Marky_0665* Marky_0663* Marky_0666* Marky_0667* Marky_0668* Marky_0671* Marky_0672* Marky_0673* Deinococcus radiodurans DR_1674 DR_0794 DR_1413 DR_1420 DR_0963 DR_2194 DR_1614 DR_1610 DR_1238...”

IDH1_SCHPO / O13696 Isocitrate dehydrogenase [NAD] subunit 1, mitochondrial; Isocitric dehydrogenase; NAD(+)-specific ICDH; EC 1.1.1.41 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
idh1 / RF|NP_594397.1 isocitrate dehydrogenase (NAD+) subunit 1 Idh1; EC 1.1.1.41 from Schizosaccharomyces pombe (see 3 papers)
SPAC11G7.03 isocitrate dehydrogenase (NAD+) subunit 1 Idh1 (PMID 10975257) from Schizosaccharomyces pombe
30% identity, 93% coverage

• function: Performs an essential role in the oxidative function of the citric acid cycle. Also binds RNA; specifically to the 5'-untranslated leaders of mitochondrial mRNAs.
  catalytic activity: D-threo-isocitrate + NAD(+) = 2-oxoglutarate + CO2 + NADH (RHEA:23632)
  cofactor: Mg(2+) Mn(2+) (Binds 1 Mg(2+) or Mn(2+) ion per subunit.)
  subunit: Octamer of two non-identical subunits IDH1 and IDH2.
• CharProtDB Source (per GeneDB): GeneDB_Spombe
• Key function for the CCAAT-binding factor Php4 to regulate gene expression in response to iron deficiency in fission yeast
  Mercier, Eukaryotic cell 2008
  • “...of subunits encoded by distinct genes: SPAC11G7.03 and SPBC902.05c for the NAD-dependent isocitrate dehydrogenase; SPBC3H7.03, SPBC776.15c, and SPAC1002.09c...”

CNAG_07851 isocitrate dehydrogenase, NAD-dependent from Cryptococcus neoformans var. grubii H99
31% identity, 84% coverage

• A PAS Protein Directs Metabolic Reprogramming during Cryptococcal Adaptation to Hypoxia
  Zhao, mBio 2021
  • “...key genes involved in the reductive branch of the TCA cycle, including the IDH1 ( CNAG_07851 ) and IDH2 ( CNAG_07363 ) homologs, were upregulated under hypoxia in Cryptococcus ( Fig.1C and Data Set S2 ). In addition, genes involved in the PPP ( CNAG_01984 ,...”
• Cryptococcus neoformans can form titan-like cells in vitro in response to multiple signals
  Trevijano-Contador, PLoS pathogens 2018
  • “...components of ketoglutarate deshydrogenase (CNAG_03674 and CNAG_03596), the two subunits of isocitrate dehydrogenase (CNAG_07363 and CNAG_07851), and CNAG_05653, encoding malate synthase. In addition, genes belonging to the oxidative segment of the pentose-phosphate shunt were also induced, such as glucose-6-phosphate dehydrogenase (CNAG_03245), 6-phosphogluconolactonase (CNAG_02133), and two isoforms...”
  • “...2-oxoglutarate deHase E2 component 0.6 2.0 2.4E-02 CNAG_07363 isocitrate deHase, NAD-dependent 1.0 3.4E-03 2.8 2.0E-03 CNAG_07851 isocitrate deHase, NAD-dependent 2.1 1.8E-09 2.7 5.7E-04 CNAG_05653 malate synthase A (MLS1) 1.8 2.4E-05 7.8 1.7E-11 Pentose-phosphate shunt (p-value : 5 . 3E-04) CNAG_03245 glucose-6-phosphate deHase 0.6 2.8 3.2E-04 CNAG_02133...”

AM1131 isocitrate dehydrogenase from Anaplasma marginale str. St. Maries
31% identity, 81% coverage

• Identification of Anaplasma marginale outer membrane protein antigens conserved between A. marginale sensu stricto strains and the live A. marginale subsp. centrale vaccine
  Agnes, Infection and immunity 2011
  • “...chain (SucC) AM254 elongation factor Tu (TufB) AM1131 isocitrate dehydrogenase (Icd) AM944 Hsp chaperonin (GroEL) AM1174 F1-ATP synthase alpha subunit (AtpA)...”
  • “...synthetase (SucC) AM254 elongation factor Tu (TufB) AM1131 isocitrate dehydrogenase (Icd) AM944 60-kD chaperonin (GroEL) AM1174 F1-ATP synthase alpha subunit...”

HCAG_04093 isocitrate dehydrogenase subunit 1, mitochondrial precursor from Histoplasma mississippiense (nom. inval.)
30% identity, 81% coverage

• Comparative Proteomic Analysis of Histoplasma capsulatum Yeast and Mycelium Reveals Differential Metabolic Shifts and Cell Wall Remodeling Processes in the Different Morphotypes
  Almeida, Frontiers in microbiology 2021
  • “...the TCA cycle were more abundant in the yeast form: alpha-ketoglutarate dehydrogenase (HCAG_01535), isocitrate dehydrogenase (HCAG_04093), succinate dehydrogenase (HCAG_06317), and succinyl-CoA ligase (HCAG_07697). In contrast, only two enzymes were predominant in mycelium: fumarate reductase (HCAG_03323) and isocitrate dehydrogenase (HCAG_04358). As for oxidative phosphorylation, proteins associated with...”

BBA_01606 isocitrate/isopropylmalate dehydrogenase from Beauveria bassiana ARSEF 2860
31% identity, 85% coverage

• Comprehensive Insights into the Remarkable Function and Regulatory Mechanism of FluG during Asexual Development in Beauveria bassiana
  Li, International journal of molecular sciences 2024
  • “...ssr3 36 BBA_01481 ubiquitin carrier protein 4 BBA_03721 alkaline phosphatase 37 BBA_06393 malate dehydrogenase 5 BBA_01606 isocitrate/isopropylmalate dehydrogenase 38 BBA_04259 carbon catabolite derepressing protein kinase 6 BBA_08294 biogenesis of lysosome-related organelles complex 1 subunit KXD1 39 BBA_09482 polynucleotide kinase 3 phosphatase 711 BBA_08577 ribosomal protein S7...”

PAS_chr4_0580 Subunit of mitochondrial NAD(+)-dependent isocitrate dehydrogenase from Komagataella phaffii GS115
30% identity, 93% coverage

• Improving Methanol Utilization by Reducing Alcohol Oxidase Activity and Adding Co-Substrate of Sodium Citrate in Pichia pastoris
  Liu, Journal of fungi (Basel, Switzerland) 2023
  • “...+ -specific isocitrate dehydrogenase), PAS_chr2-1_0120 (encoding Idh3, subunit of mitochondrial NAD + -dependent isocitrate dehydrogenase), PAS_chr4_0580 (encoding Idh3, subunit of mitochondrial NAD + -dependent isocitrate dehydrogenase), PAS_chr3_0831 (encoding LSC1, alpha subunit of succinyl-CoA ligase), PAS_chr4_0733 (encoding SdhA, flavoprotein subunit of succinate dehydrogenase), PAS_chr1-4_0487 (encoding SdhC, putative...”
• Transcriptome Analysis Unveils the Effects of Proline on Gene Expression in the Yeast Komagataella phaffii
  Rumyantsev, Microorganisms 2021
  • “...respiring filamentous fungi ACO2 orthologs are enzymatically inactive [ 46 ]. Expression of the KpIDH1 (PAS_chr4_0580) and KpIDH2 (PAS_chr2-1_0120) genes presumably encoding NAD(+)-dependent isocitrate dehydrogenase was higher in proline-containing media. Two of the genes, that presumably encode -ketoglutarate dehydrogenase complex, KpKGD1 (PAS_chr2-1_0089) and KpKGD2 (PAS_chr1-3_0094), also...”

Deima_1545 isocitrate/isopropylmalate dehydrogenase family protein from Deinococcus maricopensis DSM 21211
29% identity, 93% coverage

• Evolution of lysine biosynthesis in the phylum deinococcus-thermus
  Nishida, International journal of evolutionary biology 2012
  • “...Dgeo_1257 Deinococcus deserti Deide_09240 Deide_16910 Deide_17960 Deide_10430 Deide_10350 Deide_13430* Deide_13460* Deide_13470* Deide_13980 Deinococcus maricopensis Deima_0046 Deima_1545 Deima_2454 Deima_2593 Deima_1346* Deima_1349* Deima_1350* Deima_1353* Deima_1355* Deima_1358* Deinococcus proteolyticus Deipr_0213 Truepera radiovictrix Trad_2841 Trad_1401* Trad_1404* Trad_1399* Trad_1395* Trad_1392* Trad_1390* Trad_1389* Trad_1388* Enzyme 1, -aminoadipate aminotransferase. Enzyme 2, Homoisocitrate dehydrogenase....”

A8J6V1 Isopropylmalate dehydrogenase-like domain-containing protein from Chlamydomonas reinhardtii
31% identity, 84% coverage

• Quantitative Proteomics of Chromochloris zofingiensis Reveals the Key Proteins Involved in Cell Growth and Bioactive Compound Biosynthesis
  Qiu, Plants (Basel, Switzerland) 2022
  • “...up 7.06 10 6 IDH3 A8J9S7 Isocitrate dehydrogenase [NADP] 0.05 NS 5.90 10 1 IDH1 A8J6V1 Isocitrate dehydrogenase, NAD-dependent 0.66 down 5.74 10 5 MNEG_16102 A0A0D2LPD2 Phosphoenolpyruvate carboxylase 0.05 NS 5.09 10 1 CHLRE_03g171950v5 A0A2K3DX44 Phosphoenolpyruvate carboxylase 0.08 NS 3.91 10 1 MNEG_10533 A0A0D2MS98 Phosphopyruvate hydratase...”

EHS24_002733 isocitrate dehydrogenase (NAD(+)) idh1 from Apiotrichum porosum
29% identity, 92% coverage

• Draft Genome Sequence of the Oleaginous Yeast Apiotrichum porosum (syn. Trichosporon porosum) DSM 27194
  Gorte, Journal of genomics 2019
  • “...11 , 12 . These include putative AMP deaminase (EHS24_003651), isocitrate dehydrogenase (EHS24_007601, EHS24_002540 and EHS24_002733), malic enzyme (EHS24_008089), ATP citrate lyase (EHS24_004735), acetyl-CoA carboxylase (EHS24_004089) and fatty acid synthase (EHS24_002351, EHS24_002352). The genome also encodes multiple copies of glucose oxidase (EHS24_007400, EHS24_008706, EHS24_008979, EHS24_009251, EHS24_009561),...”

Deide_09240 putative 3-isopropylmalate dehydrogenase (Beta-IPM dehydrogenase) (IMDH) from Deinococcus deserti VCD115
30% identity, 94% coverage

• Evolution of lysine biosynthesis in the phylum deinococcus-thermus
  Nishida, International journal of evolutionary biology 2012
  • “...DR_1238 Deinococcus geothermalis Dgeo_2084 Dgeo_1458 Dgeo_1416 Dgeo_1391 Dgeo_0678 Dgeo_0685 Dgeo_1151* Dgeo_1154* Dgeo_1156* Dgeo_1257 Deinococcus deserti Deide_09240 Deide_16910 Deide_17960 Deide_10430 Deide_10350 Deide_13430* Deide_13460* Deide_13470* Deide_13980 Deinococcus maricopensis Deima_0046 Deima_1545 Deima_2454 Deima_2593 Deima_1346* Deima_1349* Deima_1350* Deima_1353* Deima_1355* Deima_1358* Deinococcus proteolyticus Deipr_0213 Truepera radiovictrix Trad_2841 Trad_1401* Trad_1404* Trad_1399* Trad_1395*...”

Q5A9D9 Homoisocitrate dehydrogenase from Candida albicans (strain SC5314 / ATCC MYA-2876)
30% identity, 85% coverage

• Delicate Metabolic Control and Coordinated Stress Response Critically Determine Antifungal Tolerance of Candida albicans Biofilm Persisters
  Li, Antimicrobial agents and chemotherapy 2015
  • “...Asparagine synthetasea Asparagine synthetasea P79023 P82610 Q5A9D9 Q5AIA2 Q5ALQ9 Q59P52 Q59YS9 Q5AHJ9 Q5AAM0 Q5AFI8 Q59WW5 Q59XR8 Q59SH9 Q59SE8...”

Dgeo_1458 3-isopropylmalate dehydrogenase from Deinococcus geothermalis DSM 11300
30% identity, 93% coverage

• Evolution of lysine biosynthesis in the phylum deinococcus-thermus
  Nishida, International journal of evolutionary biology 2012
  • “...Marky_0673* Deinococcus radiodurans DR_1674 DR_0794 DR_1413 DR_1420 DR_0963 DR_2194 DR_1614 DR_1610 DR_1238 Deinococcus geothermalis Dgeo_2084 Dgeo_1458 Dgeo_1416 Dgeo_1391 Dgeo_0678 Dgeo_0685 Dgeo_1151* Dgeo_1154* Dgeo_1156* Dgeo_1257 Deinococcus deserti Deide_09240 Deide_16910 Deide_17960 Deide_10430 Deide_10350 Deide_13430* Deide_13460* Deide_13470* Deide_13980 Deinococcus maricopensis Deima_0046 Deima_1545 Deima_2454 Deima_2593 Deima_1346* Deima_1349* Deima_1350* Deima_1353* Deima_1355*...”

LEU3_SULTO / P50455 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; Beta-IPM dehydrogenase; EC 1.1.1.85 from Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) (Sulfolobus tokodaii) (see paper)
P50455 3-isopropylmalate dehydrogenase (EC 1.1.1.85) from Sulfurisphaera tokodaii (see 3 papers)
29% identity, 87% coverage

• function: Catalyzes the oxidation of 3-carboxy-2-hydroxy-4- methylpentanoate (3-isopropylmalate) to 3-carboxy-4-methyl-2- oxopentanoate. The product decarboxylates to 4-methyl-2 oxopentanoate
  catalytic activity: (2R,3S)-3-isopropylmalate + NAD(+) = 4-methyl-2-oxopentanoate + CO2 + NADH (RHEA:32271)
  cofactor: Mg(2+) Mn(2+) (Binds 1 Mg(2+) or Mn(2+) ion per subunit.)
  subunit: Homotetramer.

hdh / BAD06515.1 homoisocitrate dehydrogenase, partial from Deinococcus radiodurans (see paper)
DR1674, DR_1674 isocitrate dehydrogenase, putative from Deinococcus radiodurans R1
29% identity, 93% coverage

• Evolution of lysine biosynthesis in the phylum deinococcus-thermus
  Nishida, International journal of evolutionary biology 2012
  • “...Ocepr_1780* Ocepr_1779* Marinithermus hydrothermalis Marky_1533 Marky_0665* Marky_0663* Marky_0666* Marky_0667* Marky_0668* Marky_0671* Marky_0672* Marky_0673* Deinococcus radiodurans DR_1674 DR_0794 DR_1413 DR_1420 DR_0963 DR_2194 DR_1614 DR_1610 DR_1238 Deinococcus geothermalis Dgeo_2084 Dgeo_1458 Dgeo_1416 Dgeo_1391 Dgeo_0678 Dgeo_0685 Dgeo_1151* Dgeo_1154* Dgeo_1156* Dgeo_1257 Deinococcus deserti Deide_09240 Deide_16910 Deide_17960 Deide_10430 Deide_10350 Deide_13430* Deide_13460* Deide_13470*...”
• Predicted highly expressed and putative alien genes of Deinococcus radiodurans and implications for resistance to ionizing radiation damage
  Karlin, Proceedings of the National Academy of Sciences of the United States of America 2001
  • “...1.36 1.29 1.05 DR1720 DR0828 DR1540 DR0325 DR1247 DR0287 DR2627 DR1248 DR1674 DR0757 DR0083 905 463 430 329 385 955 812 300 332 410 416 2.56 2.19 2.07 1.80 1.71...”
• Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics
  Makarova, Microbiology and molecular biology reviews : MMBR 2001
  • “...DR1614 (small subunit of 3-isopropylmalate dehydratase), DR1674 (isocitrate dehydrogenase), and DR2194 (glutaminyl transferase); the pathway also could include...”

T5A5Y2 isocitrate dehydrogenase (NAD(+)) from Ophiocordyceps sinensis (strain Co18 / CGMCC 3.14243)
28% identity, 93% coverage

• iTRAQ-based comparative proteome analyses of different growth stages revealing the regulatory role of reactive oxygen species in the fruiting body development of Ophiocordyceps sinensis
  Tong, PeerJ 2021
  • “...at the stage of ST, such as succinate-CoA ligase (ADP-forming) subunit (T5A666), isocitrate dehydrogenase subunit (T5A5Y2) and pyruvate dehydrogenase subunit (T4ZWD4). So high amounts of energy and carbohydrates might be needed for the pathogen-host interactions and hyphae growth at the stage of ST, as well as...”

IHV18_09900 3-isopropylmalate dehydrogenase from Bifidobacterium breve
32% identity, 93% coverage

• Bifidobacterium breve PRL2020: Antibiotic-Resistant Profile and Genomic Detection of Antibiotic Resistance Determinants
  Di, Microorganisms 2023
  • “...GcvH IHV18_09890 7958 9215 1 DUF2183 domain-containing protein IHV18_09895 9237 11,994 1 S9 family peptidase IHV18_09900 12,060 13,092 1 3-isopropylmalate dehydrogenase IHV18_09905 13,142 14,276 1 lipoateprotein ligase family protein IHV18_09910 14,428 15,148 1 Crp/Fnr family transcriptional regulator IHV18_09915 15,276 17,553 1 transglycosylase domain-containing protein IHV18_09920 17,697...”

BBMN68_984 3-isopropylmalate dehydrogenase from Bifidobacterium longum subsp. longum BBMN68
32% identity, 93% coverage

• Transcriptomic analysis of Bifidobacterium longum subsp. longum BBMN68 in response to oxidative shock
  Zuo, Scientific reports 2018
  • “...leucine and isoleucine biosynthesis 2-Isopropylmalate synthase leuA 1.35 1.13 BBMN68_1222 3-Isopropylmalate dehydrogenase leuB 1.55 1.42 BBMN68_984 3-Isopropylmalate/(R)-2-methylmalate dehydratase large subunit leuC 2.32 2.98 BBMN68_1521 3-Isopropylmalate/(R)-2-methylmalate dehydratase small subunit leuD 1.42 1.78 BBMN68_1522 Ketol-acid reductoisomerase ilvc1 NS 1.44 BBMN68_1262 Ketol-acid reductoisomerase ilvc2 1.55 1.28 BBMN68_1263 Branched-chain amino...”
• Mechanism analysis of acid tolerance response of bifidobacterium longum subsp. longum BBMN 68 by gene expression profile using RNA-sequencing
  Jin, PloS one 2012
  • “...acid aminotransferase [EC:2.6.1.42] BBMN68_1222 366.15 825.87 2.26 * E COG0119 leuA K01649, 2-isopropylmalate synthase [EC:2.3.3.13] BBMN68_984 237.25 1102.93 4.65 * E COG0473 leuB K00052, 3-isopropylmalate dehydrogenase [EC:1.1.1.85] BBMN68_1521 37.07 107.49 2.90 * E COG0065 leuC K01703, 3-isopropylmalate/(R)-2-methylmalate dehydratase large subunit [EC:4.2.1.33 4.2.1.35] BBMN68_1522 84.05 216.49 2.58...”

Mrub_2738 3-isopropylmalate dehydrogenase from Meiothermus ruber DSM 1279
31% identity, 83% coverage

• Evolution of lysine biosynthesis in the phylum deinococcus-thermus
  Nishida, International journal of evolutionary biology 2012
  • “...Thermus scotoductus TSC_c05810 TSC_c20650 TSC_c03550 TSC_c3520 TSC_c01940* TSC_c01930* TSC_c01920* TSC_c01890* TSC_c01880* TSC_c01850* Meiothermus ruber Mrub_0871 Mrub_2738 Mrub_0027 Mrub_2721* Mrub_2723* Mrub_2724* Mrub_2727* Mrub_2728* Meiothermus silvanus Mesil_2567 Mesil_1337 Mesil_0348 Mesil_0347 Mesil_0435* Mesil_0436* Mesil_0438* Mesil_0441* Mesil_0442* Oceanithermus profundus Ocepr_1387 Ocepr_1797* Ocepr_1798* Ocepr_1796* Ocepr_1788* Ocepr_1784* Ocepr_1781* Ocepr_1780* Ocepr_1779* Marinithermus hydrothermalis...”

NCU02954 homoisocitrate dehydrogenase from Neurospora crassa OR74A
31% identity, 83% coverage

• Effect of itaconic acid production on Neurospora crassa in consolidated bioprocessing of cellulose
  Zhao, Microbial cell factories 2023
  • “...NCU06558 in glycine degradation; NCU04118 and NCU08162 in aspartic acid metabolism; NCU04754 in valine metabolism; NCU02954 and NCU03118 in lysine synthesis; NCU01195 in glutamate metabolism (See Fig. 5 for details). These amino acids have lower energetic costs than methionine, tyrosine and tryptophan [ 14 , 15...”
• Use of 1H nuclear magnetic resonance to measure intracellular metabolite levels during growth and asexual sporulation in Neurospora crassa
  Kim, Eukaryotic cell 2011
  • “...1.2.1.31 Threonine synthesis Arginine synthesis NCU08898 NCU02954 NCU03010 1.5.1.10 Glutamate synthesis Arginine degradation Lysine synthesis NCU03748 NCU01632...”

Trad_2841 isocitrate/isopropylmalate dehydrogenase family protein from Truepera radiovictrix DSM 17093
28% identity, 92% coverage

• Evolution of lysine biosynthesis in the phylum deinococcus-thermus
  Nishida, International journal of evolutionary biology 2012
  • “...Deima_0046 Deima_1545 Deima_2454 Deima_2593 Deima_1346* Deima_1349* Deima_1350* Deima_1353* Deima_1355* Deima_1358* Deinococcus proteolyticus Deipr_0213 Truepera radiovictrix Trad_2841 Trad_1401* Trad_1404* Trad_1399* Trad_1395* Trad_1392* Trad_1390* Trad_1389* Trad_1388* Enzyme 1, -aminoadipate aminotransferase. Enzyme 2, Homoisocitrate dehydrogenase. Enzyme 3, LysW- - l -lysine aminotransferase. Enzyme 4, LysW- - l -lysine hydrolase....”

LYS12_YEAST / P40495 Homoisocitrate dehydrogenase, mitochondrial; HIcDH; EC 1.1.1.87 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 8 papers)
P40495 homoisocitrate dehydrogenase (EC 1.1.1.87) from Saccharomyces cerevisiae (see 2 papers)
NP_012172 homoisocitrate dehydrogenase from Saccharomyces cerevisiae S288C
YIL094C Homo-isocitrate dehydrogenase, an NAD-linked mitochondrial enzyme required for the fourth step in the biosynthesis of lysine, in which homo-isocitrate is oxidatively decarboxylated to alpha-ketoadipate from Saccharomyces cerevisiae
29% identity, 85% coverage

• function: Catalyzes the NAD(+)-dependent conversion of homoisocitrate to alpha-ketoadipate.
  catalytic activity: (2R,3S)-homoisocitrate + NAD(+) = 2-oxoadipate + CO2 + NADH (RHEA:11900)
  cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
• Evidence for an induced conformational change in the catalytic mechanism of homoisocitrate dehydrogenase for Saccharomyces cerevisiae: Characterization of the D271N mutant enzyme.
  Hsu, Archives of biochemistry and biophysics 2015
  • GeneRIF: This pH independence of the chemical reaction over the range 5.5-9.5 is consistent with the much slower conformational change that would effectively perturb the observed pK values for catalytic groups to lower and higher pH
• Site-directed mutagenesis as a probe of the acid-base catalytic mechanism of homoisocitrate dehydrogenase from Saccharomyces cerevisiae.
  Lin, Biochemistry 2009
  • GeneRIF: Data suggest that K206 of homoisocitrate dehydrogenase acts as a general base in the hydride transfer step of the wild-type enzyme but as a general acid in the Y150F mutant enzyme, replacing Y150 in the tautomerization reaction.
• Complete kinetic mechanism of homoisocitrate dehydrogenase from Saccharomyces cerevisiae.
  Lin, Biochemistry 2007
  • GeneRIF: kinetic mechanism in toward oxidative decarboxylation of isocitrate, based on initial velocity studies in absence & presence of dead-end inhibitors, suggests random addition of NAD & isocitrate with Mg2+ binding before isocitrate in rapid equilibrium
• Mitochondria, Peroxisomes and Beyond-How Dual Targeting Regulates Organelle Tethering
  Freitag, Contact (Thousand Oaks (Ventura County, Calif.)) 2024
  • “...Conserved component of the MICOS complex Pfanner et al., 2014; Barbot et al., 2015 LYS12 YIL094C NAD-linked homo-isocitrate dehydrogenase Zabriskie and Jackson, 2000 DPI8 YJL133C-A Putative mitochondrial protein of unknown function Stehlik et al., 2020 CTA1 YDR256C Peroxisomal catalase A Cohen et al., 1985; Hiltunen et...”
• Metabolic regulation of misfolded protein import into mitochondria
  Wang, eLife 2024
  • “...MRM2 Class 2 YER174C GRX4 Class 2 YER167W BCK2 Class 2 YMR221C FMP42 Class 2 YIL094C LYS12 Class 2 YGR254W ENO1 Class 2 YMR257C PET111 Class 2 YMR278W PRM15 Class 2 YMR291W TDA1 Class 2 YMR303C ADH2 Class 2 YNL303W Class 2 YNL302C RPS19B Class 2...”
• Heme, A Metabolic Sensor, Directly Regulates the Activity of the KDM4 Histone Demethylase Family and Their Interactions with Partner Proteins
  Konduri, Cells 2020
  • “...6320836 Increased recombination centers protein IRC5 YFR038W 42742173 Uncharacterized ATP-dependent helicase HELLS, SMARCAL1 + LYS12 YIL094C 6322097 Mitochondrial homoisocitrate dehydrogenase IDH3A + + LYS20 YDL182W 6320019 Homocitrate synthase isozyme HMGCL + LYS21 YDL131W 6320071 Mitochondrial homocitrate synthase HMGCL + MIG3 YER028C 6320866 Transcription corepressor EGR1, EGR2,...”
• Persistent DNA-break potential near telomeres increases initiation of meiotic recombination on short chromosomes
  Subramanian, Nature communications 2019
  • “...=8h are shown for ndt80 , and pch2 ndt80 . Interstitial hotspots ( YGR175C , YIL094C ) are shown in shades of magenta and hotspots in EARs ( YCR047C , YGR279C) are depicted in shades of orange. The data are averages of two independent biological replicates....”
  • “...ndt80 , and sir2 ndt80 mutants (see Fig. 4e ). Interstitial hotspots ( YGR175C , YIL094C ) are shown in shades of magenta and hotspots in EARs ( YCR047C , YGR279C) are depicted in shades of orange. The data are averages of two independent biological replicates....”
• Chromosome Synapsis Alleviates Mek1-Dependent Suppression of Meiotic DNA Repair
  Subramanian, PLoS biology 2016
  • “...). (D, E, F) Percentage of DSB fragments over total DNA at the ERG1 (D), YIL094c (E) and YGR279c hotspot locus (F) for the indicated genotypes, time points and treatments. (G) Rad51 (green) and Zip1 (red) immunofluorescence on spread chromosomes of RAD54-FRB ndt80 (H7121) cells. Scale...”
  • “...upon depletion [ 42 ]. A similar increase in DSBs was also observed at the YIL094c hotspot after Zip1 nuclear depletion ( Fig 5E and S6B Fig ). However, Zip1 nuclear depletion did not lead to significant DSB reappearance at the YGR279c or the YCR047c hotspot...”
• Comparative transcriptomic and proteomic profiling of industrial wine yeast strains
  Rossouw, Applied and environmental microbiology 2010
  • “...YLR432W YML056C YBR011C YCL018W YNL104C YFL018C YIR034C YIL094C YDL131W YDR234W YNR050C YKL029C YKL150W YKL085W YFR030W YLR303W YOL064C YJR010W YER091C MIR1...”
  • “...YHR208W YOR375C YDL022W YPR160W YJR016C YLR355C YCL018W YIL094C YDL131W YDR234W YNR050C YLR044C YGR240C YMR205C YMR105C YDR502C YLR058C YJL052W YGR192C YHR025W...”
• Mitochondrial Iba57p is required for Fe/S cluster formation on aconitase and activation of radical SAM enzymes
  Gelling, Molecular and cellular biology 2008
  • “...VPS54 YDR034C YDR234W YGL154C LYS14 LYS4 LYS5 YGR037C YIL094C YIR034C YJR104C YJR122W ACB1 LYS12 LYS1 SOD1 CAF17/IBA57 YLL027W YML022W YMR135W-A YOR140W ISA1...”
• Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level
  Jiménez, Genome biology 2003
  • “...E E7 MIT COG0059 YLR355C ILV5 ketol-acid reducto-isomerase - - - E E7 MIT COG0473 YIL094C LYS12 homoisocitrate dehydrogenase - - - E H7 - COG0722 YBR249C ARO4 2-dehydro-3-deoxyphosphoheptonate aldolase, tyrosine-inhibited - - - E H7 - COG0082 YGL148W ARO2 chorismate synthase - - - EH...”
• More

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Statistics

How It Works

PaperBLAST builds a database of protein sequences that are linked to scientific articles. These links come from automated text searches against the articles in EuropePMC and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot, BRENDA, CAZy (as made available by dbCAN), BioLiP, CharProtDB, MetaCyc, EcoCyc, TCDB, REBASE, the Fitness Browser, and a subset of the European Nucleotide Archive with the /experiment tag. Given this database and a protein sequence query, PaperBLAST uses protein-protein BLAST to find similar sequences with E < 0.001.

To build the database, we query EuropePMC with locus tags, with RefSeq protein identifiers, and with UniProt accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use queries of the form "locus_tag AND genus_name" to try to ensure that the paper is actually discussing that gene. Because EuropePMC indexes most recent biomedical papers, even if they are not open access, some of the links may be to papers that you cannot read or that our computers cannot read. We query each of these identifiers that appears in the open access part of EuropePMC, as well as every locus tag that appears in the 500 most-referenced genomes, so that a gene may appear in the PaperBLAST results even though none of the papers that mention it are open access. We also incorporate text-mined links from EuropePMC that link open access articles to UniProt or RefSeq identifiers. (This yields some additional links because EuropePMC uses different heuristics for their text mining than we do.)

For every article that mentions a locus tag, a RefSeq protein identifier, or a UniProt accession, we try to select one or two snippets of text that refer to the protein. If we cannot get access to the full text, we try to select a snippet from the abstract, but unfortunately, unique identifiers such as locus tags are rarely provided in abstracts.

PaperBLAST also incorporates manually-curated protein functions:

• Proteins from NCBI's RefSeq are included if a GeneRIF entry links the gene to an article in PubMed^®. GeneRIF also provides a short summary of the article's claim about the protein, which is shown instead of a snippet.
• Proteins from Swiss-Prot (the curated part of UniProt) are included if the curators identified experimental evidence for the protein's function (evidence code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that describe the protein's function are shown (with bold headings).
• Proteins from BRENDA, a curated database of enzymes, are included if they are linked to a paper in PubMed and their full sequence is known.
• Every protein from the non-redundant subset of BioLiP, a database of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself does not include descriptions of the proteins, those are taken from the Protein Data Bank. Descriptions from PDB rely on the original submitter of the structure and cannot be updated by others, so they may be less reliable. (For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every ligand is represented among a group of structures with similar sequences, but for PaperBLAST, we use the non-redundant set provided by BioLiP.)
• Every protein from EcoCyc, a curated database of the proteins in Escherichia coli K-12, is included, regardless of whether they are characterized or not.
• Proteins from the MetaCyc metabolic pathway database are included if they are linked to a paper in PubMed and their full sequence is known.
• Proteins from the Transport Classification Database (TCDB) are included if they have known substrate(s), have reference(s), and are not described as uncharacterized or putative. (Some of the references are not visible on the PaperBLAST web site.)
• Every protein from CharProtDB, a database of experimentally characterized protein annotations, is included.
• Proteins from the CAZy database of carbohydrate-active enzymes are included if they are associated with an Enzyme Classification number. Even though CAZy does not provide links from individual protein sequences to papers, these should all be experimentally-characterized proteins.
• Proteins from the REBASE database of restriction enzymes are included if they have known specificity.
• Every protein with an evidence-based reannotation (based on mutant phenotypes) in the Fitness Browser is included.
• Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators) with experimentally-determined DNA binding sites from the PRODORIC database of gene regulation in prokaryotes.
• Putative transcription factors from RegPrecise that have manually-curated predictions for their binding sites. These predictions are based on conserved putative regulatory sites across genomes that contain similar transcription factors, so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
• Coding sequence (CDS) features from the European Nucleotide Archive (ENA) are included if the /experiment tag is set (implying that there is experimental evidence for the annotation), the nucleotide entry links to paper(s) in PubMed, and the nucleotide entry is from the STD data class (implying that these are targeted annotated sequences, not from shotgun sequencing). Also, to filter out genes whose transcription or translation was detected, but whose function was not studied, nucleotide entries or papers with more than 25 such proteins are excluded. Descriptions from ENA rely on the original submitter of the sequence and cannot be updated by others, so they may be less reliable.

Except for GeneRIF and ENA, the curated entries include a short curated description of the protein's function. For entries from BioLiP, the protein's function may not be known beyond binding to the ligand. Many of these entries also link to articles in PubMed.

For more information see the PaperBLAST paper (mSystems 2017) or the code. You can download PaperBLAST's database here.

Changes to PaperBLAST since the paper was written:

• November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
• February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
• June 2022: incorporated some coding sequences from ENA with the /experiment tag.
• March 2022: incorporated BioLiP.
• April 2020: incorporated TCDB.
• April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
• February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
• January 2018: incorporated BRENDA.
• December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
• September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.

Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.

Secrets

PaperBLAST cannot provide snippets for many of the papers that are published in non-open-access journals. This limitation applies even if the paper is marked as "free" on the publisher's web site and is available in PubmedCentral or EuropePMC. If a journal that you publish in is marked as "secret," please consider publishing elsewhere.

Omissions from the PaperBLAST Database

Many important articles are missing from PaperBLAST, either because the article's full text is not in EuropePMC (as for many older articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an article that characterizes a protein's function but is missing from PaperBLAST, please notify the curators at UniProt or add an entry to GeneRIF. Entries in either of these databases will eventually be incorporated into PaperBLAST. Note that to add an entry to UniProt, you will need to find the UniProt identifier for the protein. If the protein is not already in UniProt, you can ask them to create an entry. To add an entry to GeneRIF, you will need an NCBI Gene identifier, but unfortunately many prokaryotic proteins in RefSeq do not have corresponding Gene identifers.

References

PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.

Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.

Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.

UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.

BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.

The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.

The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.

CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.

The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.

The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.

REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.

Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.