PaperBLAST
PaperBLAST Hits for CharProtDB::CH_005143 isocitrate dehydrogenase; EC 1.1.1.42 (Bacillus subtilis) (423 a.a., MAQGEKITVS...)
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>CharProtDB::CH_005143 isocitrate dehydrogenase; EC 1.1.1.42 (Bacillus subtilis)
MAQGEKITVSNGVLNVPNNPIIPFIEGDGTGPDIWNAASKVLEAAVEKAYKGEKKITWKE
VYAGEKAYNKTGEWLPAETLDVIREYFIAIKGPLTTPVGGGIRSLNVALRQELDLFVCLR
PVRYFTGVPSPVKRPEDTDMVIFRENTEDIYAGIEYAKGSEEVQKLISFLQNELNVNKIR
FPETSGIGIKPVSEEGTSRLVRAAIDYAIEHGRKSVTLVHKGNIMKFTEGAFKNWGYELA
EKEYGDKVFTWAQYDRIAEEQGKDAANKAQSEAEAAGKIIIKDSIADIFLQQILTRPNEF
DVVATMNLNGDYISDALAAQVGGIGIAPGANINYETGHAIFEATHGTAPKYAGLDKVNPS
SVILSGVLLLEHLGWNEAADLVIKSMEKTIASKVVTYDFARLMDGATEVKCSEFGEELIK
NMD
Running BLASTp...
Found 250 similar proteins in the literature:
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
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. - 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...”
- 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.
GYA98_RS12235 NADP-dependent isocitrate dehydrogenase from Bacillus velezensis
95% identity, 100% 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),...”
YP_092619 Icd from Bacillus licheniformis DSM 13
95% identity, 96% coverage
W8Y9G2 Isocitrate dehydrogenase [NADP] from Bacillus thuringiensis DB27
BC4593 Isocitrate dehydrogenase [NADP] from Bacillus cereus ATCC 14579
86% identity, 98% coverage
BAS4487 isocitrate dehydrogenase, NADP-dependent from Bacillus anthracis str. Sterne
86% identity, 97% coverage
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
81% identity, 99% 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...”
UH47_10560 NADP-dependent isocitrate dehydrogenase from Staphylococcus pseudintermedius
80% identity, 98% coverage
N007_05885 NADP-dependent isocitrate dehydrogenase from Alicyclobacillus acidoterrestris ATCC 49025
78% identity, 98% coverage
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)
80% identity, 99% coverage
SXYL_01173 NADP-dependent isocitrate dehydrogenase from Staphylococcus xylosus
79% identity, 99% coverage
SAS1622 isocitrate dehydrogenase from Staphylococcus aureus subsp. aureus MSSA476
79% identity, 99% 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...”
SAPIG1748 NADP-dependent isocitrate dehydrogenase from Staphylococcus aureus subsp. aureus ST398
79% identity, 99% 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...”
SACOL1741 isocitrate dehydrogenase, NADP-dependent from Staphylococcus aureus subsp. aureus COL
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
SAUSA300_1640 isocitrate dehydrogenase, NADP-dependent from Staphylococcus aureus subsp. aureus USA300_FPR3757
79% identity, 99% coverage
- 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....”
- 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...”
- 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...”
Q6GG12 Isocitrate dehydrogenase [NADP] from Staphylococcus aureus (strain MRSA252)
79% identity, 99% coverage
MXAN_3537 isocitrate dehydrogenase, NADP-dependent from Myxococcus xanthus DK 1622
69% identity, 97% coverage
Pcar_1038 isocitrate dehydrogenase, NADP-dependent from Pelobacter carbinolicus str. DSM 2380
66% identity, 90% coverage
Dgeo_1166 isocitrate/isopropylmalate dehydrogenase from Deinococcus geothermalis DSM 11300
68% identity, 99% coverage
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)
DR1540, DR_1540 isocitrate dehydrogenase from Deinococcus radiodurans R1
67% identity, 98% coverage
- 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...”
- 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...”
Ppro_0452 isocitrate dehydrogenase, NADP-dependent from Pelobacter propionicus DSM 2379
62% identity, 89% coverage
Q8X722 Isocitrate dehydrogenase [NADP] from Escherichia coli O157:H7
67% identity, 100% coverage
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
67% 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 (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)
- 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 <i>Pseudomonas aeruginosa</i>
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
- 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
- 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...”
SF1155 isocitrate dehydrogenase from Shigella flexneri 2a str. 301
UTI89_C1266 NADP Isocitrate dehydrogenase from Escherichia coli UTI89
S1238 isocitrate dehydrogenase from Shigella flexneri 2a str. 2457T
67% identity, 100% coverage
- 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%...”
- 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...”
- 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...”
Entcl_2658 NADP-dependent isocitrate dehydrogenase from [Enterobacter] lignolyticus SCF1
68% identity, 100% 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...”
A6T7K6 Isocitrate dehydrogenase [NADP] from Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
67% identity, 100% 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
66% identity, 100% coverage
STY1278 isocitrate dehydrogenase from Salmonella enterica subsp. enterica serovar Typhi str. CT18
67% identity, 99% coverage
SPC_2506 isocitrate dehydrogenase from Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
66% 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...”
STM1238 isocitrate dehydrogenase in e14 prophage, specific for NADP+ from Salmonella typhimurium LT2
66% identity, 99% coverage
JHW33_RS08805 NADP-dependent isocitrate dehydrogenase from Rahnella aceris
66% identity, 100% coverage
PMI0891 isocitrate dehydrogenase [NADP] from Proteus mirabilis HI4320
67% identity, 100% coverage
CtesDRAFT_PD1824 NADP-dependent isocitrate dehydrogenase from Comamonas testosteroni KF-1
66% identity, 100% 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...”
H16_A3056 NADP-dependent isocitrate dehydrogenase from Cupriavidus necator H16
H16_A3056 isocitrate dehydrogenase [NADP] from Ralstonia eutropha H16
65% identity, 99% coverage
Rmet_2895 NADP-dependent isocitrate dehydrogenase from Cupriavidus metallidurans CH34
Rmet_2895 isocitrate dehydrogenase, NADP-dependent from Ralstonia metallidurans CH34
65% identity, 99% 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...”
CBU_1200 isocitrate dehydrogenase from Coxiella burnetii RSA 493
66% identity, 98% 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...”
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)
66% 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. - 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...”
VAS14_05433 NADP-dependent isocitrate dehydrogenase from Photobacterium angustum S14
64% identity, 99% coverage
ZMO0544 isocitrate dehydrogenase, NADP-dependent from Zymomonas mobilis subsp. mobilis ZM4
61% identity, 99% 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...”
y1802 isocitrate dehydrogenase, specific for NADP+ from Yersinia pestis KIM
65% identity, 97% coverage
YPO1641 isocitrate dehydrogenase [NADP] from Yersinia pestis CO92
YPTB2427 isocitrate dehydrogenase [NADP] from Yersinia pseudotuberculosis IP 32953
65% identity, 100% coverage
Q3JV82 Isocitrate dehydrogenase [NADP] from Burkholderia pseudomallei (strain 1710b)
BURPS1710b_1108 isocitrate dehydrogenase, NADP-dependent from Burkholderia pseudomallei 1710b
BPSL0896 isocitrate dehydrogenase from Burkholderia pseudomallei K96243
65% identity, 99% coverage
- 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...”
- 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...”
- 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...”
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
65% identity, 99% coverage
BCAL2736 isocitrate dehydrogenase from Burkholderia cenocepacia J2315
65% identity, 99% 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...”
E2566_10015 NADP-dependent isocitrate dehydrogenase from Pectobacterium punjabense
65% identity, 99% coverage
RSc2490 PROBABLE ISOCITRATE DEHYDROGENASE [NADP] OXIDOREDUCTASE PROTEIN from Ralstonia solanacearum GMI1000
65% identity, 99% 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
65% identity, 99% coverage
RSUY_RS12515 NADP-dependent isocitrate dehydrogenase from Ralstonia solanacearum
64% identity, 99% coverage
EDI29_02475 NADP-dependent isocitrate dehydrogenase from Pectobacterium polonicum
65% identity, 99% coverage
BP2488 isocitrate dehydrogenase [NADP] from Bordetella pertussis Tohama I
64% identity, 99% 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...”
Q1XIQ8 isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) from Colwellia psychrerythraea (see paper)
64% identity, 99% coverage
jhp0023 ISOCITRATE DEHYDROGENASE from Helicobacter pylori J99
Q9ZN36 Isocitrate dehydrogenase [NADP] from Helicobacter pylori (strain J99 / ATCC 700824)
63% identity, 99% coverage
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)
Q9I0L5 Isocitrate dehydrogenase [NADP] from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
NP_251313 isocitrate dehydrogenase from Pseudomonas aeruginosa PAO1
PA14_30190 isocitrate dehydrogenase from Pseudomonas aeruginosa UCBPP-PA14
PA2623 isocitrate dehydrogenase from Pseudomonas aeruginosa PAO1
63% 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. - Acetylomics reveals an extensive acetylation diversity within <i>Pseudomonas aeruginosa</i>
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...”
- 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...”
- 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...”
- 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...”
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P56063 Isocitrate dehydrogenase [NADP] from Helicobacter pylori (strain ATCC 700392 / 26695)
HP0027 isocitrate dehydrogenase (icd) from Helicobacter pylori 26695
63% identity, 99% 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...”
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icd / B2ZP83 isocitrate dehydrogenase subunit (EC 1.1.1.42) from Helicobacter pylori (see 4 papers)
62% identity, 99% coverage
LT988_17130 NADP-dependent isocitrate dehydrogenase from Thiocapsa bogorovii
63% identity, 100% coverage
HPG27_RS00150 isocitrate dehydrogenase (NADP(+)) from Helicobacter pylori G27
62% identity, 99% coverage
V6E02_11500 NADP-dependent isocitrate dehydrogenase from Thiobacter sp. AK1
64% identity, 100% 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...”
Q8GAX0 isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) from Acidithiobacillus thiooxidans (see paper)
61% identity, 98% coverage
2d4vA / Q8GAX0 Crystal structure of NAD dependent isocitrate dehydrogenase from acidithiobacillus thiooxidans (see paper)
61% identity, 99% coverage
- Ligands: citrate anion; nicotinamide-adenine-dinucleotide (2d4vA)
T1E_0537 NADP-dependent isocitrate dehydrogenase from Pseudomonas putida DOT-T1E
62% identity, 99% coverage
PPUTLS46_011960 NADP-dependent isocitrate dehydrogenase from Pseudomonas putida LS46
62% identity, 99% coverage
PPUBIRD1_1803 NADP-dependent isocitrate dehydrogenase from Pseudomonas putida BIRD-1
62% identity, 99% coverage
Q5ZXB6 Isocitrate dehydrogenase [NADP] from Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)
61% identity, 100% coverage
ACIAD1190 isocitrate dehydrogenase from Acinetobacter sp. ADP1
62% identity, 96% coverage
PP4011 isocitrate dehydrogenase, NADP-dependent, prokaryotic-type from Pseudomonas putida KT2440
PP_4011 NADP-dependent isocitrate dehydrogenase from Pseudomonas putida KT2440
61% identity, 99% 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...”
lpp0878 isocitrate dehydrogenase from Legionella pneumophila str. Paris
61% 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,...”
6c0eA / Q5ZXB6 Crystal structure of isocitrate dehydrogenase from legionella pneumophila with bound NADPH with an alpha-ketoglutarate adduct
61% 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)
ABO_1282 isocitrate dehydrogenase (NADP-dependent) from Alcanivorax borkumensis SK2
62% identity, 100% coverage
AFE_RS02000 NADP-dependent isocitrate dehydrogenase from Acidithiobacillus ferrooxidans ATCC 23270
61% identity, 98% coverage
SGO_1611 Isocitrate dehydrogenase from Streptococcus gordonii str. Challis substr. CH1
60% identity, 99% 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...”
E9B494 Isocitrate dehydrogenase [NADP] from Leishmania mexicana (strain MHOM/GT/2001/U1103)
58% identity, 99% coverage
PFLU3808 isocitrate dehydrogenase from Pseudomonas fluorescens SBW25
60% 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...”
MS2370 Icd protein from Mannheimia succiniciproducens MBEL55E
MS2370 NADP-dependent isocitrate dehydrogenase from [Mannheimia] succiniciproducens MBEL55E
61% identity, 100% coverage
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)
61% identity, 99% coverage
Q59940 Isocitrate dehydrogenase [NADP] from Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
59% identity, 98% coverage
SSU1040 isocitrate dehydrogenase [NADP] from Streptococcus suis P1/7
59% identity, 99% coverage
Q1GZD1 isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) from Methylobacillus flagellatus (see paper)
61% identity, 99% coverage
IDH1_PSYS3 / A0A5A4WIX0 Isocitrate dehydrogenase [NADP] 1; IDH 1; EC 1.1.1.42 from Psychrobacter sp. (strain 13A) (see paper)
62% identity, 99% 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.
BP951000_0369 NADP-dependent isocitrate dehydrogenase from Brachyspira pilosicoli 95/1000
60% identity, 99% 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...”
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...”
LAF_0939 NADP-dependent isocitrate dehydrogenase from Limosilactobacillus fermentum IFO 3956
LAF_0939 isocitrate dehydrogenase from Lactobacillus fermentum IFO 3956
56% identity, 99% coverage
T303_07275 NADP-dependent isocitrate dehydrogenase from Streptococcus thermophilus ASCC 1275
60% 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...”
A1S_2475 isocitrate dehydrogenase from Acinetobacter baumannii ATCC 17978
63% identity, 91% coverage
llmg_0637 isocitrate dehydrogenase from Lactococcus lactis subsp. cremoris MG1363
58% identity, 98% 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...”
SRU_1973 isocitrate dehydrogenase, NADP-dependent from Salinibacter ruber DSM 13855
55% identity, 99% coverage
DOP62_07935 NADP-dependent isocitrate dehydrogenase from Synechococcus elongatus PCC 11801
53% identity, 89% coverage
Q31MH0 Isocitrate dehydrogenase [NADP] from Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)
Synpcc7942_1719 isocitrate dehydrogenase, NADP-dependent from Synechococcus elongatus PCC 7942
53% identity, 89% 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 - “...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...”
- 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...”
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
52% identity, 89% 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...”
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
56% identity, 99% 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)
- 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),...”
- 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...”
SYNW0166 Isocitrate dehydrogenase from Synechococcus sp. WH 8102
52% identity, 89% 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...”
A8YGS2 isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) from Microcystis aeruginosa (see paper)
51% identity, 88% coverage
slr1289 isocitrate dehydrogenase (NADP+) from Synechocystis sp. PCC 6803
52% 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
cce_3202 isocitrate dehydrogenase (NADP+) from Cyanothece sp. ATCC 51142
50% identity, 85% 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...”
cce_3202 NADP-dependent isocitrate dehydrogenase from Crocosphaera subtropica ATCC 51142
50% identity, 88% coverage
PMT1935 Isocitrate dehydrogenase from Prochlorococcus marinus str. MIT 9313
50% identity, 89% coverage
sync_0214 isocitrate dehydrogenase, NADP-dependent from Synechococcus sp. CC9311
53% identity, 88% coverage
Q9HLV8 isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) from Thermoplasma acidophilum (see paper)
54% identity, 97% coverage
GAH_01703 isocitrate dehydrogenase (NADP(+)) from Geoglobus ahangari
55% 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...”
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
53% 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. - 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)
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)
51% 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.
Q7V9S5 Isocitrate dehydrogenase [NADP] from Prochlorococcus marinus (strain SARG / CCMP1375 / SS120)
Pro1752 Isocitrate dehydrogenases from Prochlorococcus marinus str. SS120
50% identity, 88% coverage
Dret_0439 Isocitrate dehydrogenase (NADP(+)) from Desulfohalobium retbaense DSM 5692
52% identity, 95% 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...”
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, 100% coverage
Kole_1227 Isocitrate dehydrogenase (NADP(+)) from Thermotogales bacterium TBF 19.5.1
Kole_1227 isocitrate dehydrogenase (NADP(+)) from Kosmotoga olearia TBF 19.5.1
52% identity, 100% coverage
PMM1596 Isocitrate dehydrogenase from Prochlorococcus marinus sp. MED4
49% identity, 89% coverage
Q72EU1 isocitrate dehydrogenase (NADP(+)) from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)
53% identity, 93% coverage
Q9HNZ7 isocitrate dehydrogenase (NADP(+)) from Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)
52% identity, 97% coverage
ST2166 409aa long hypothetical NADP-dependent isocitrate dehydrogenase from Sulfolobus tokodaii str. 7
WP_010980246 NADP-dependent isocitrate dehydrogenase from Sulfurisphaera tokodaii str. 7
50% identity, 99% 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.
Micr_00902 NADP-dependent isocitrate dehydrogenase from Candidatus Micrarchaeum sp.
49% identity, 98% coverage
2e5mA / Q96YK6 Crystal structure of isocitrate dehydrogenase from sulfolobus tokodaii strain 7 (see paper)
49% identity, 99% coverage
- Ligand: nadp nicotinamide-adenine-dinucleotide phosphate (2e5mA)
Q4J6C9 isocitrate-homoisocitrate dehydrogenase (EC 1.1.1.286) from Sulfolobus acidocaldarius (see paper)
Saci_2375 isocitrate dehydrogenase from Sulfolobus acidocaldarius DSM 639
48% identity, 99% 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...”
Q9YE81 isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) from Aeropyrum pernix (see 4 papers)
48% identity, 97% coverage
1tyoA / Q9YE81 Isocitrate dehydrogenase from the hyperthermophile aeropyrum pernix in complex with etheno-NADP (see paper)
48% identity, 98% coverage
- Ligand: etheno-nadp (1tyoA)
SSO2182 Isocitrate dehydrogenase, probable (idh) from Sulfolobus solfataricus P2
47% identity, 99% coverage
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, 97% coverage
Q8U488 isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) from Pyrococcus furiosus (see 2 papers)
PF0202 isocitrate dehydrogenase from Pyrococcus furiosus DSM 3638
49% identity, 100% coverage
Tneu_0698 isocitrate dehydrogenase, NADP-dependent from Thermoproteus neutrophilus V24Sta
46% identity, 94% coverage
O67480 Isocitrate dehydrogenase [NADP] from Aquifex aeolicus (strain VF5)
aq_1512 isocitrate dehydrogenase from Aquifex aeolicus VF5
46% identity, 96% coverage
icd / Q76LM6 oxalosuccinate reductase subunit from Hydrogenobacter thermophilus (see 3 papers)
45% identity, 91% coverage
DhcVS_392, GY50_0375 isocitrate/isopropylmalate dehydrogenase family protein from Dehalococcoides mccartyi VS
42% identity, 95% 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...”
DehalGT_0391 Isocitrate dehydrogenase (NAD(+)) from Dehalococcoides sp. GT
cbdbA408 isocitrate/isopropylmalate dehydrogenase family protein from Dehalococcoides mccartyi CBDB1
42% identity, 95% 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...”
- 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...”
DET0450 isocitrate dehydrogenase, putative from Dehalococcoides ethenogenes 195
41% identity, 95% 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...”
dcmb_461 isocitrate/isopropylmalate dehydrogenase family protein from Dehalococcoides mccartyi DCMB5
41% identity, 95% 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...”
btf_415 isocitrate/isopropylmalate dehydrogenase family protein from Dehalococcoides mccartyi BTF08
41% identity, 95% 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...”
Mal48_24210 isocitrate/isopropylmalate dehydrogenase family protein from Thalassoglobus polymorphus
41% identity, 95% coverage
Mal4_26830 isocitrate/isopropylmalate dehydrogenase family protein from Maioricimonas rarisocia
40% identity, 95% coverage
ELEN_RS11715 isocitrate/isopropylmalate dehydrogenase family protein from Eggerthella lenta DSM 2243
40% identity, 94% coverage
Pan258_54730 isocitrate/isopropylmalate dehydrogenase family protein from Symmachiella dynata
39% identity, 95% coverage
CA54_25060 isocitrate/isopropylmalate dehydrogenase family protein from Symmachiella macrocystis
39% identity, 95% coverage
Mal52_56040 isocitrate/isopropylmalate dehydrogenase family protein from Symmachiella dynata
39% identity, 95% coverage
Csac_0751 Isocitrate dehydrogenase (NAD(+)) from Caldicellulosiruptor saccharolyticus DSM 8903
38% identity, 95% coverage
Clocel_2469 isocitrate/isopropylmalate dehydrogenase family protein from Clostridium cellulovorans 743B
38% identity, 95% 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 ;...”
CAC0972 Isocitrate dehydrogenase from Clostridium acetobutylicum ATCC 824
CA_C0972 isocitrate dehydrogenase (NAD(+)) from Clostridium acetobutylicum ATCC 824
37% identity, 96% 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...”
CAETHG_2753 isocitrate/isopropylmalate dehydrogenase family protein from Clostridium autoethanogenum DSM 10061
35% identity, 87% 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...”
CLJU_c06630 isocitrate/isopropylmalate dehydrogenase family protein from Clostridium ljungdahlii DSM 13528
34% identity, 87% coverage
6lkyA / Q602J2 Crystal structure of isocitrate dehydrogenase from methylococcus capsulatus
38% identity, 90% coverage
- Ligand: nicotinamide-adenine-dinucleotide (6lkyA)
Q18A33 Isocitrate dehydrogenase NAD-dependent from Clostridioides difficile (strain 630)
CD0834 putative isocitrate/3-isopropylmalate dehydrogenase from Clostridium difficile 630
37% identity, 94% coverage
GOX1336 Isocitrate dehydrogenase [NADP] from Gluconobacter oxydans 621H
34% identity, 87% 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...”
TTC1172 No description from Thermus thermophilus HB27
35% identity, 81% 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...”
2d1cA / P33197 Crystal structure of tt0538 protein from thermus thermophilus hb8
35% identity, 81% coverage
- Ligand: nadp nicotinamide-adenine-dinucleotide phosphate (2d1cA)
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
35% identity, 81% 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...”
ABO_0296 isocitrate dehydrogenase from Alcanivorax borkumensis SK2
33% identity, 96% coverage
APA386B_2558 isocitrate/isopropylmalate dehydrogenase family protein from Acetobacter pasteurianus 386B
34% identity, 88% coverage
XF2596 isocitrate dehydrogenase from Xylella fastidiosa 9a5c
WP_010895014 isocitrate dehydrogenase from Xylella fastidiosa 9a5c
34% identity, 88% coverage
6m3sB / A0A0H2XBX7 Dimeric isocitrate dehydrogenase from xanthomonas campestris pv. Campestris 8004
35% identity, 88% coverage
- Ligands: nicotinamide-adenine-dinucleotide; isocitrate calcium complex (6m3sB)
XAC1046 isocitrate dehydrogenase from Xanthomonas axonopodis pv. citri str. 306
XAUB_41080 isocitrate dehydrogenase from Xanthomonas citri pv. aurantifolii str. ICPB 11122
35% identity, 88% coverage
SO1538 isocitrate dehydrogenase, NAD-dependent from Shewanella oneidensis MR-1
34% identity, 87% 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...”
AL01_06250 isocitrate/isopropylmalate dehydrogenase family protein from Bombella intestini
33% identity, 95% 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,...”
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, 86% 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. - 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...”
- 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
- 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
CG32026 uncharacterized protein from Drosophila melanogaster
32% identity, 56% 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...”
Q9VWH4 Probable isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial from Drosophila melanogaster
32% identity, 95% coverage
NP_728257 isocitrate dehydrogenase 3a, isoform C from Drosophila melanogaster
32% identity, 95% coverage
P29696 3-isopropylmalate dehydrogenase, chloroplastic from Solanum tuberosum
32% identity, 87% coverage
Q55BI2 Isocitrate dehydrogenase [NAD] regulatory subunit A, mitochondrial from Dictyostelium discoideum
31% identity, 95% 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, 92% 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...”
Rfer_2411 Isocitrate dehydrogenase (NAD+) from Rhodoferax ferrireducens DSM 15236
33% identity, 91% coverage
M1CHE3 3-isopropylmalate dehydrogenase, chloroplastic from Solanum tuberosum
32% identity, 86% coverage
B6TJM1 3-isopropylmalate dehydrogenase from Zea mays
31% identity, 87% coverage
Rfer_2380 Isocitrate dehydrogenase (NAD+) from Rhodoferax ferrireducens DSM 15236
34% identity, 89% coverage
LOC103934973 isocitrate dehydrogenase [NAD] catalytic subunit 5, mitochondrial from Pyrus x bretschneideri
31% identity, 90% coverage
TERG_07814 isocitrate dehydrogenase, NAD-dependent from Trichophyton rubrum CBS 118892
31% identity, 99% 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:...”
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)
33% identity, 81% coverage
Afu1g12800 isocitrate dehydrogenase, NAD-dependent from Aspergillus fumigatus Af293
32% identity, 95% 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...”
PAAG_07729 isocitrate dehydrogenase subunit 2 from Paracoccidioides lutzii Pb01
32% identity, 87% 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...”
PADG_02805 isocitrate dehydrogenase [NAD] subunit 2, mitochondrial from Paracoccidioides brasiliensis Pb18
C1G6K0 isocitrate dehydrogenase (NAD(+)) from Paracoccidioides brasiliensis (strain Pb18)
32% identity, 87% 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...”
Q28480 Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (Fragment) from Macaca fascicularis
30% identity, 95% coverage
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)
30% identity, 95% 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...”
An08g05580 uncharacterized protein from Aspergillus niger
30% identity, 96% 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...”
U3I2P1 Isocitrate dehydrogenase [NAD] subunit, mitochondrial from Anas platyrhynchos platyrhynchos
30% identity, 95% coverage
G3H0B5 Isocitrate dehydrogenase [NAD] subunit, mitochondrial from Cricetulus griseus
30% identity, 95% coverage
6kdeA / P50213 Crystal structure of the alpha beta heterodimer of human idh3 in complex with ca(2+) (see paper)
30% identity, 95% coverage
- Ligand: calcium ion (6kdeA)
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)
30% identity, 95% 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...”
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
35% identity, 89% 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...”
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
30% identity, 95% 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). - 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...”
- 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...”
- Sirt3 regulates adipogenesis and adipokine secretion via its enzymatic activity.
Ma, Pharmacology research & perspectives 2020 - “...Cytochrome bc1 complex subunit 6 EHCEQLEKCVK 1.1 K40 Q9JK81 UPF0160 protein MYG1 GGCPWKEHLYHLESELSPK 1.1 K272 Q9D6R2 Isocitrate dehydrogenase [NAD] subunit alpha IEAACFATIKDGK 1.1 K339 Q61425 Hydroxyacylcoenzyme A dehydrogenase TFESLVDFCKTLGK 1.1 K202 John Wiley & Sons, Ltd 4 DISCUSSION In this study, we demonstrated the novel important...”
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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)
30% identity, 95% 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 *...”
- 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...”
- 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...”
- 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...”
- 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...”
- Quantitative Proteomic Analysis in Alveolar Type II Cells Reveals the Different Capacities of RAS and TGF-β to Induce Epithelial-Mesenchymal Transition.
Zhou, Frontiers in molecular biosciences 2021 - “...Q9NQW6 Hallmark oxidative phosphorylation 2.510 DLST, ETFB, IDH3A, NDUFV2, PMPCA, TOMM22, GRPEL1 7/200 P36957, P38117, P50213, P19404, Q10713, Q9NS69, Q9HAV7 Hallmark G2M checkpoint 1.897 DR1, KPNB1, MARCKS, MCM5, NUMA1, SYNCRIP 6/200 Q01658, Q14974, P29966, P33992, Q14980, O60506 Hallmark DNA repair 1.791 PNP, POLR2H, EDF1, ADRM1, AK3...”
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G1TA59 Isocitrate dehydrogenase [NAD] subunit, mitochondrial from Oryctolagus cuniculus
30% identity, 88% 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...”
D2VQ70 Isocitrate dehydrogenase from Naegleria gruberi
32% identity, 94% coverage
Q53GF8 Isocitrate dehydrogenase [NAD] subunit, mitochondrial (Fragment) from Homo sapiens
30% identity, 95% coverage
AO090012000629 No description from Aspergillus oryzae RIB40
31% identity, 95% 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...”
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
31% identity, 95% 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...”
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F1LNF7 Isocitrate dehydrogenase [NAD] subunit, mitochondrial from Rattus norvegicus
30% identity, 95% 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...”
NP_446090 isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor from Rattus norvegicus
30% identity, 95% coverage
FAD_1632 isocitrate/isopropylmalate family dehydrogenase from Ferroplasma acidiphilum
28% identity, 99% coverage
- Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum YT
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...”
A0A0D1E633 isocitrate dehydrogenase (NAD(+)) from Ustilago maydis (strain 521 / FGSC 9021)
31% identity, 89% coverage
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
31% identity, 87% 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.
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, 90% 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.
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, 90% coverage
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)
29% identity, 95% 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 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...”
- 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...”
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LOC107804365 isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial-like from Nicotiana tabacum
32% identity, 89% 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...”
Q6CA33 isocitrate dehydrogenase (NAD(+)) from Yarrowia lipolytica (strain CLIB 122 / E 150)
32% identity, 95% 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...”
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, 89% coverage
- function: Performs an essential role in the oxidative function of the citric acid cycle.
subunit: Heterooligomer of catalytic and regulatory subunits - 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...”
- 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...”
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- 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...”
MMP0880 2-oxosuberate synthase, last step from Methanococcus maripaludis S2
29% identity, 90% coverage
Pyrde_1536 isocitrate/isopropylmalate dehydrogenase family protein from Pyrodictium delaneyi
33% identity, 92% coverage
M1BEG6 NAD-dependent isocitrate dehydrogenase from Solanum tuberosum
31% identity, 95% coverage
PF0940 3-isopropylmalate dehydrogenase 2 from Pyrococcus furiosus DSM 3638
34% identity, 95% coverage
LOC112172665 isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial from Rosa chinensis
31% identity, 88% 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)...”
3blwF / P28241 Yeast isocitrate dehydrogenase with citrate and amp bound in the regulatory subunits (see paper)
30% identity, 95% coverage
- Ligand: citrate anion (3blwF)
NP_001234366 isocitrate dehydrogenase [NAD] regulatory subunit 1 from Solanum lycopersicum
30% identity, 95% coverage
LOC18035427 isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial from Citrus x clementina
30% identity, 95% 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...”
AM1131 isocitrate dehydrogenase from Anaplasma marginale str. St. Maries
31% identity, 81% coverage
RHTO_01289 isocitrate dehydrogenase (NAD+) from Rhodotorula toruloides NP11
31% identity, 95% 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....”
Marky_1533 isocitrate/isopropylmalate dehydrogenase family protein from Marinithermus hydrothermalis DSM 14884
32% identity, 89% 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*...”
Q6ZI55 NAD-dependent isocitrate dehydrogenase c2 from Oryza sativa subsp. japonica
31% identity, 87% 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, 87% 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
32% identity, 90% 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...”
EHS24_002540 NAD-dependent isocitrate dehydrogenase from Apiotrichum porosum
32% identity, 90% 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,...”
Sb04g024840 No description from Sorghum bicolor
31% identity, 87% coverage
EHS24_002733 isocitrate dehydrogenase (NAD(+)) idh1 from Apiotrichum porosum
30% identity, 87% 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),...”
Mrub_2738 3-isopropylmalate dehydrogenase from Meiothermus ruber DSM 1279
31% identity, 89% 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...”
G1APK2 isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) from Rhodotorula toruloides (see paper)
31% identity, 95% coverage
NP_849963 isocitrate dehydrogenase subunit 2 from Arabidopsis thaliana
32% identity, 87% coverage
CNA04610 isocitrate dehydrogenase from Cryptococcus neoformans var. neoformans JEC21
31% identity, 90% 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...”
MCP_0437 isocitrate/isopropylmalate dehydrogenase family protein from Methanocella paludicola SANAE
31% identity, 95% coverage
PAAG_00856 isocitrate dehydrogenase subunit 1 from Paracoccidioides lutzii Pb01
29% identity, 95% 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...”
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)
28% identity, 94% 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.)
MJ1596 3-isopropylmalate dehydrogenase 2 (leuB2) from Methanocaldococcus jannaschii DSM 2661
28% identity, 94% coverage
G1APK3 isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) from Rhodotorula toruloides (see paper)
30% identity, 95% coverage
I1IYV8 Isopropylmalate dehydrogenase-like domain-containing protein from Brachypodium distachyon
29% identity, 95% 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...”
I1IB67 Isopropylmalate dehydrogenase-like domain-containing protein from Brachypodium distachyon
30% identity, 87% 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...”
RHTO_01290 isocitrate dehydrogenase (NAD+) from Rhodotorula toruloides NP11
30% identity, 95% coverage
AO090003000008 No description from Aspergillus oryzae RIB40
29% identity, 90% 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,...”
LOC18037111 isocitrate dehydrogenase [NAD] regulatory subunit 1, mitochondrial from Citrus x clementina
30% identity, 89% 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...”
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)
NP_195290 isocitrate dehydrogenase III from Arabidopsis thaliana
AT4G35650 isocitrate dehydrogenase, putative / NAD+ isocitrate dehydrogenase, putative from Arabidopsis thaliana
30% identity, 87% 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). - 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...”
- 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...”
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Q4WNH3 isocitrate dehydrogenase (NAD(+)) from Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)
28% identity, 85% coverage
An18g06760 uncharacterized protein from Aspergillus niger
28% identity, 90% 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...”
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)
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
NP_012172 homoisocitrate dehydrogenase from Saccharomyces cerevisiae S288C
31% identity, 87% 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.) - 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...”
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- 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
MA4265 isocitrate/isopropylmalate dehydrogenase family protein from Methanosarcina acetivorans C2A
30% identity, 94% 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...”
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, 90% 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...”
Ocepr_1387 No description from Oceanithermus profundus 506, DSM 14977
30% identity, 89% 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...”
3asjA / Q5SIJ1 Crystal structure of homoisocitrate dehydrogenase in complex with a designed inhibitor (see paper)
31% identity, 89% 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
31% identity, 89% 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...”
BBA_01606 isocitrate/isopropylmalate dehydrogenase from Beauveria bassiana ARSEF 2860
31% identity, 85% coverage
Q5A9D9 Homoisocitrate dehydrogenase from Candida albicans (strain SC5314 / ATCC MYA-2876)
31% identity, 89% coverage
MMP0539 3-isopropylmalate dehydrogenase from Methanococcus maripaludis S2
29% identity, 95% coverage
NCU00775 isocitrate dehydrogenase subunit 1 from Neurospora crassa OR74A
27% identity, 95% coverage
ecm3 / Q0X0C1 (2S,3R)-2-[(2-aminophenyl)amino]-3-carboxy-3-hydroxypropanoate dehydrogenase from Streptomyces lasalocidi (see 2 papers)
33% identity, 84% coverage
PAS_chr4_0580 Subunit of mitochondrial NAD(+)-dependent isocitrate dehydrogenase from Komagataella phaffii GS115
30% identity, 95% 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...”
3blvC / P28834 Yeast isocitrate dehydrogenase with citrate bound in the regulatory subunits (see paper)
29% identity, 95% coverage
- Ligand: citrate anion (3blvC)
EHI_143560 tartrate dehydrogenase, putative from Entamoeba histolytica HM-1:IMSS
29% identity, 94% coverage
TSC_c20650 homoisocitrate dehydrogenase from Thermus scotoductus SA-01
31% identity, 87% 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...”
HCAG_04093 isocitrate dehydrogenase subunit 1, mitochondrial precursor from Histoplasma mississippiense (nom. inval.)
30% identity, 83% coverage
CNAG_07851 isocitrate dehydrogenase, NAD-dependent from Cryptococcus neoformans var. grubii H99
29% identity, 85% 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...”
cg1453 3-isopropylmalate dehydrogenase from Corynebacterium glutamicum ATCC 13032
30% identity, 95% coverage
- Discovery of novel amino acid production traits by evolution of synthetic co-cultures
Zuchowski, Microbial cell factories 2023 - “...+ ) WT with an in-frame deletion of leuA (cg0303), leuC (cg1487), leuD (cg1488), leuB (cg1453), with point mutations ArgB A26V M31V (Cg1582) and eyfp under control of P tac integrated into the IGR between cg1121 and cg1122 This work CoNoS evolution Adaptive laboratory evolution (ALE)was...”
- The IclR-type transcriptional repressor LtbR regulates the expression of leucine and tryptophan biosynthesis genes in the amino acid producer Corynebacterium glutamicum
Brune, Journal of bacteriology 2007 - “...of California, Berkeley cg1488 cg1487 cg1413 cg1412 cg1658 cg1453 cg1411 cg1129 cg2893 cg1410 cg2391 cg3359 cg2894 cg1612 cg3362 cg2565 cg3361 cg1419 cg2610...”
- “...11, 2017 by University of California, Berkeley cg1487 cg1453 cg3359 cg1617 cg2391 cg1412 cg2545 12-bp sequence 2727 2728 BRUNE ET AL. J. BACTERIOL. examined...”
- The alternative sigma factor SigB of Corynebacterium glutamicum modulates global gene expression during transition from exponential growth to stationary phase
Larisch, BMC genomics 2007 - “...trypsine-like serine protease 1.29 cg2418 ilvE branched-chain amino acid aminotransferase 1.48 cg2884 dipeptide/tripeptide permease 1.21 cg1453 leuB 3-isopropylmalate dehydrogenase -1.04 cg2588 proB glutamate 5-kinase protein -1.43 CARBON METABOLISM AND TRANSPORT cg1479 glgP1 glycogen phosphorylase 1.17 cg2796 MmgE/PrpD family protein 1.19 cg0699 guaB2 inositol-monophosphate dehydrogenase, CBS domain...”
IHV18_09900 3-isopropylmalate dehydrogenase from Bifidobacterium breve
31% identity, 87% 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...”
Mmah_0582 isocitrate dehydrogenase (NADP) from Methanohalophilus mahii DSM 5219
30% identity, 89% coverage
IDH1 / P28834 isocitrate dehydrogenase [NAD] α subunit (EC 1.1.1.286) from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (see paper)
IDH1_YEAST / P28834 Isocitrate dehydrogenase [NAD] subunit 1, mitochondrial; Isocitric dehydrogenase; NAD(+)-specific ICDH; EC 1.1.1.41 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see paper)
P28834 isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) from Saccharomyces cerevisiae (see paper)
YNL037C Idh1p from Saccharomyces cerevisiae
NP_014361 isocitrate dehydrogenase (NAD(+)) IDH1 from Saccharomyces cerevisiae S288C
29% identity, 95% 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 - Data integration uncovers the metabolic bases of phenotypic variation in yeast
Petrizzelli, PLoS computational biology 2021 - “...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 YOR142W )...”
- Central Metabolism in Mammals and Plants as a Hub for Controlling Cell Fate
Selinski, Antioxidants & redox signaling 2021 - “...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 (EC 1.1.1.41) NAD-IDH5 AT5G03290 (EC 1.1.1.41) NAD-IDH6 AT3G09810 (EC 1.1.1.41) Malate dehydrogenase...”
- A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models
Reimers, Metabolites 2017 - “...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 setting up...”
- “...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 32...”
- The replicative lifespan-extending deletion of SGF73 results in altered ribosomal gene expression in yeast
Mason, Aging cell 2017 - “...321984 1733.550049 295 YDL075W RPL31A Ribosomal 60S subunit protein L31A chrXIV 559344 559470 1728.550049 405 YNL037C IDH1 Isocitrate dehydrogenase [NAD(+)] chrXV 253915 254041 1710.600098 319 YOL039W RPP2A Ribosomal protein P2A chrIX 257361 257495 1688.699951 365 YIL052C RPL34B Ribosomal 60S subunit protein L34B chrXIII 124367 124483 1627.349976...”
- Transcriptional profiling reveals molecular basis and novel genetic targets for improved resistance to multiple fermentation inhibitors in Saccharomyces cerevisiae
Chen, Biotechnology for biofuels 2016 - “...process (GO:0006520) YBR006W, YCL018W, 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,...”
- Adjustment of trehalose metabolism in wine Saccharomyces cerevisiae strains to modify ethanol yields
Rossouw, Applied and environmental microbiology 2013 - “...KGD2 LSC1 LSC2 YNR001c YCR005c YPR001w YLR304c YJL200C YNL037c YOR136w YIL125w YDR148c YOR142w YGR244c Y15376 Y13485 Y12828 Y15212 Y17022 Y15362 Y12392 Y12284...”
- High-throughput genetic and gene expression analysis of the RNAPII-CTD reveals unexpected connections to SRB10/CDK8
Aristizabal, PLoS genetics 2013 - “...occupancy differences were observed in the rpb1-CTD11 mutant at genes identified to have significantly increased (YNL037C - top) or decreased (YDR033W - bottom) mRNA levels. Light gray boxes depict ORFs and dark gray boxes depict ARSs. (B) Average gene profile of Rpb3 in genes with increased...”
- Pattern-driven neighborhood search for biclustering of microarray data
Ayadi, BMC bioinformatics 2012 - “...3.46e-15) For the bicluster labeled id9 PDNS (Table 1 ), the genes YCR005C, YHR037W, YLR304C, YNL037C, YNR001C and YOR136W are together involved in the glutamate biosynthetic process. Each GO term is associated with a tuple, for example glutamate biosynthetic process (10.2%, 8.62e-08) indicates the cluster frequency...”
- More
- Single arginine mutation in two yeast isocitrate dehydrogenases: biochemical characterization and functional implication.
Song, PloS one 2014 - GeneRIF: Kinetic analysis showed that ScIDH1 R148H and YlIDH R141H displayed 5.2-fold and 3.3-fold higher affinities, respectively, for alpha-KG than the HcIDH R132H mutant
- 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.
- 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
- Physiological consequences of loss of allosteric activation of yeast NAD+-specific isocitrate dehydrogenase.
Hu, The Journal of biological chemistry 2006 (PubMed)- GeneRIF: allosteric activation of IDH has an important physiological role during changes in environmental conditions
- 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 - “...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 29 31...”
- Identification of in vivo substrates of the yeast mitochondrial chaperonins reveals overlapping but non-identical requirement for hsp60 and hsp10
Dubaquié, The EMBO journal 1998 - “...ketol-acid reductoisomerase P06168 isocitrate dehydrogenase P28834 aconitase homolog P39533 aconitase P19414 malate dehydrogenase P17505 rhodanese homolog...”
BBMN68_984 3-isopropylmalate dehydrogenase from Bifidobacterium longum subsp. longum BBMN68
31% identity, 87% coverage
MSMEG_2379 3-isopropylmalate dehydrogenase from Mycobacterium smegmatis str. MC2 155
32% identity, 89% coverage
- Mycobacterium smegmatis NucS-promoted DNA mismatch repair involves limited resection by a 5'-3' exonuclease and is independent of homologous recombination and NHEJ
Rivera-Flores, Nucleic acids research 2024 - “...(defective hyg gene) inserted radA gene by ORBIT Kan R Zeo R This study KM229 MSMEG_2379 ( leuB frameshift) Two bp deletion in the leuB arginine-101 codon; pKM461; pKM585 Kan R Strep R This study KM230 MSMEG_2379 ( leuB frameshift) One bp deletion in the leuB...”
- “...insertion in the leuB arginine-101 codon; pKM461; pKM585 Kan R Strep R This study KM239 MSMEG_2379 ( leuB frameshift) Two bp deletion in the leuB arginine-101 codon; pKM461; cured ofpKM585 Kan R This study KM321 NucS-Y12A Binding site mutant of M. smegmatis NucS none This study...”
- Protein Composition of Mycobacterium smegmatis Differs Significantly Between Active Cells and Dormant Cells With Ovoid Morphology
Trutneva, Frontiers in microbiology 2018 - “...contain unique enzymes responsible for porphyrin synthesis (MSMEG_0953, MSMEG_0956, and MSMEG_2780), leucine synthesis (MSMEG_6271 and MSMEG_2379) and arginine synthesis (MSMEG_3769, MSMEG_3770, MSMEG_3773, and MSMEG_3774). Dormant cells evidently accumulate storage materials: we found several enzymes responsible for the synthesis and accumulation of glycogen (MSMEG_4918), trehalose (MSMEG_6514 and...”
- ORBIT: a New Paradigm for Genetic Engineering of Mycobacterial Chromosomes
Murphy, mBio 2018 - “...M. smegmatis modifications Gene Designation Function No. of correct recombinants/total no. tested Flag-Das4 tags leuB MSMEG_2379 3-Isopropylmalate dehydrogenase 2/4 recA MSMEG_2723 Recombinase 4/4 divIVA MSMEG_4217 DivIVA protein 3/4 dnaN MSMEG_0001 DNA polymerase III, beta subunit 2/2 dinB MSMEG_3172 DNA gyrase 2/2 dnaK MSMEG_0709 Chaperone (heat shock)...”
B7Z9J8 Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial from Homo sapiens
30% identity, 75% coverage
VDAG_01116 homoisocitrate dehydrogenase from Verticillium dahliae VdLs.17
30% identity, 83% coverage
- Transcriptome Analysis Reveals That C17 Mycosubtilin Antagonizes Verticillium dahliae by Interfering with Multiple Functional Pathways of Fungi
Zhang, Biology 2023 - “...external NADH-ubiquinone oxidoreductase; VDAG_02096, succinate dehydrogenase flavoprotein; VDAG_00910, cytochrome c), TCA cycles (VDAG_01642, pyruvate dehydrogenase; VDAG_01116, isocitrate dehydrogenase; VDAG_02096, dehydrogenase flavoprotein), fatty acid oxidative metabolism (VDAG_03968, l long-chain specific acyl-CoA dehydrogenase; VDAG_09867 and VDAG_03899, acyl-CoA dehydrogenase; VDAG_08517, 3-hydroxybutyryl-CoA dehydrogenase), and biofilm lipid formation (C-5 sterol desaturase...”
- “...hub of metabolism of the three major nutrients in the body. Isocitrate dehydrogenase encoded by VDAG_01116 is the rate-limiting step of the TCA cycle, and its downregulation seriously affects the energy supply and material metabolism of the body. These results suggested that C17 mycosubtilin may disrupt...”
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 789,361 different protein sequences to 1,256,019 scientific articles. Searches against EuropePMC were last performed on January 10 2025.
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.
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.
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.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory