PaperBLAST
PaperBLAST Hits for BRENDA::Q9Z4X8 4-hydroxymandelate oxidase (EC 1.1.3.46) (Streptomyces coelicolor) (377 a.a., MREPLTLDDF...)
Show query sequence
>BRENDA::Q9Z4X8 4-hydroxymandelate oxidase (EC 1.1.3.46) (Streptomyces coelicolor)
MREPLTLDDFARLARGQLPAATWDFIAGGAGRERTLAANEAVFGAVRLRPRALPGIEEPD
TSVEVLGSRWPAPVGIAPVAYHGLAHPDGEPATAAAAGALGLPLVVSTFAGRSLEEVARA
ASAPLWLQLYCFRDHETTLGLARRARDSGYQALVLTVDTPFTGRRLRDLRNGFAVPAHIT
PANLTGTAAAGSATPGAHSRLAFDRRLDWSFVARLGAASGLPVLAKGVLTAPDAEAAVAA
GVAGIVVSNHGGRQLDGAPATLEALPEVVSAVRGRCPVLLDGGVRTGADVLAALALGARA
VLVGRPALYALAVGGASGVRRMLTLLTEDFADTMVLTGHAATGTIGPDTLAPPHHAPPHH
GPPTAPRPAPHRDRSHG
Running BLASTp...
Found 225 similar proteins in the literature:
Q9Z4X8 4-hydroxymandelate oxidase (EC 1.1.3.46) from Streptomyces coelicolor (see paper)
SCO3228 glycolate oxidase from Streptomyces coelicolor A3(2)
100% identity, 100% coverage
5zzqA / O52792 The crystal structure of mandelate oxidase with (s)-4-hydroxymandelic acid (see paper)
48% identity, 90% coverage
- Ligands: flavin mononucleotide; (2s)-hydroxy(4-hydroxyphenyl)ethanoic acid (5zzqA)
HMO_AMYOR / O52792 4-hydroxymandelate oxidase; EC 1.1.3.46 from Amycolatopsis orientalis (Nocardia orientalis) (see 3 papers)
O52792 4-hydroxymandelate oxidase (EC 1.1.3.46) from Amycolatopsis orientalis (see 2 papers)
48% identity, 90% coverage
- function: Catalyzes the oxidation of p-hydroxymandelate to p- hydroxybenzoylformate in the biosynthesis of L-(4-hydroxyphenyl)glycine and L-(3,5-dihydroxyphenyl)glycine, 2 non-proteinogenic amino acids occurring in the vancomycin group of antibiotics.
catalytic activity: (S)-4-hydroxymandelate + O2 = 4-hydroxyphenylglyoxylate + H2O2 (RHEA:41227)
cofactor: FMN - Flavin Mononucleotide-Dependent l-Lactate Dehydrogenases: Expanding the Toolbox of Enzymes for l-Lactate Biosensors
Tsvik, ACS omega 2022 - “...P00175; MDH from Pseudomonas putida P20932; HAO from Rattus norvegicus Q07523; HMO from Amycolatopsis orientalis O52792; and mLDH from Pseudomonas stutzeri ADL63037) were used as queries for individual database searches on NCBI and UniProt using blastp and phmmer 56 with maximum E -values of 1 10...”
- Biosynthesis of L-p-hydroxyphenylglycine, a non-proteinogenic amino acid constituent of peptide antibiotics
Hubbard, Chemistry & biology 2000 (PubMed)- “...(ORF21: [PCZA361.1, O52791, CAA11761]; ORF22: [PCZA361.2, O52792, CAA11762]; ORF17: [PCZA361.25, O52815, CAA11790]), of the chloroeremomycin biosynthetic gene...”
AT4G18360 (S)-2-hydroxy-acid oxidase, peroxisomal, putative / glycolate oxidase, putative / short chain alpha-hydroxy acid oxidase, putative from Arabidopsis thaliana
NP_193570 Aldolase-type TIM barrel family protein from Arabidopsis thaliana
O49506 Glycolate oxidase 3 from Arabidopsis thaliana
45% identity, 89% coverage
- Identification of Clubroot (Plasmodiophora brassicae) Resistance Loci in Chinese Cabbage (Brassica rapa ssp. pekinensis) with Recessive Character
Zhang, Genes 2024 - “...and 20 dpi in Bap246 ( Figure 7 ). Among them, Bra013299 is homologous to AT4G18360 in Arabidopsis, which is annotated as the defense response signaling pathway. Bra013336 is homologous to AT4G18640 in Arabidopsis and is associated with the leucine-rich repeat N-terminal domain. Bra013341 is homologous...”
- Identification and characterization of Glycolate oxidase gene family in garden lettuce (Lactuca sativa cv. 'Salinas') and its response under various biotic, abiotic, and developmental stresses
Mariyam,, Scientific reports 2023 - “...LsHAOX2 Arabidopsis Ortholog Gene ID AtGOX1, AtGLO1 AtGOX3, AtGLO5 AtHAOX1, AtGOX4, AtGLO4 Accession no AT3G14420 AT4G18360 AT3G14130 % Homology 90.51 89.97 85.08 75.99 74.01 Functions Regulating signal transduction pathway through ROS during nonhost resistance Metabolize l-lactate to pyruvate at low intracellular concentrations Encoding medium and long...”
- “...were retrieved from TAIR at Phytozome v13, which consisted of three AtGOX (AT3G14420, AT3G14415 and AT4G18360), and two AtHAOX (AT3G14130 and AT3G14150) genes. These sequences were then used to BLAST-P (Protein- basic local alignment search tool) search in Lactuca sativa v8 ( Lactuca sativa cv. Salinas...”
- Photorespiration: regulation and new insights on the potential role of persulfidation
Aroca, Journal of experimental botany 2023 - “...(7) , N (11) AT3G14150 Q24JJ8 GLO3 Peroxisomal ( S )-2-hydroxyacid oxidase GLO3 P (3) AT4G18360 O49506 GLO5 Glycolate oxidase 3 (GOX 3) P (3) AT2G41220 Q9T0P4 GLU2 Ferredoxin-dependent glutamate synthase 2, (Fd-GOGAT 2) P (2,3,4) , S (6,7) AT3G25530 Q9LSV0 GLYR1 Glyoxylate/succinic semialdehyde reductase 1...”
- Identification of QTNs, QTN-by-environment interactions and genes for yield-related traits in rice using 3VmrMLM
Zhang, Frontiers in plant science 2022 - “...AT3G54050 high cyclic electron flow 1 PF LOC_Os04g33190 id4006172 AT5G36880 acetyl-CoA synthetase AUS_QE/FTAB/FTF LOC_Os04g53210 id4010914/id4010930/id4010984 AT4G18360 Aldolase-type TIM barrel family protein FT_Q LOC_Os05g35580 id5008977 AT2G16570/AT4G34740 GLN phosphoribosyl pyrophosphate amidotransferase 1/GLN phosphoribosyl pyrophosphate amidotransferase 2 PL/PH LOC_Os06g01630 id6000302 AT1G54220/AT3G13930 Dihydrolipoamide acetyltransferase, long form protein FTAB/FT_Q LOC_Os06g07120 id6002745/id6002690...”
- Enzymatic Properties of Recombinant Phospho-Mimetic Photorespiratory Glycolate Oxidases from Arabidopsis thaliana and Zea mays
Jossier, Plants (Basel, Switzerland) 2019 - “...[ 6 ]. In Arabidopsis , there are five GOX-related genes: At3g14420 , At3g14415 , At4g18360 , At3g14130 and At3g14150 (encoding At GOX1, At GOX2, At GOX3, At HAOX1 and At HAOX2, respectively). According to transcriptomic analyses, At3g14415 ( AtGOX2 ) and At3g14420 ( AtGOX1 )...”
- Multilevel Regulation of Peroxisomal Proteome by Post-Translational Modifications
Sandalio, International journal of molecular sciences 2019 - “...ntyr AT3G14420 Aldolase-type TIM barrel family protein/ glycolate oxidase ac; na; ng; nt; ph; ntyr AT4G18360 Aldolase-type TIM barrel family protein/ glycolate oxidase 3 ac; na; ph AT4G39660 alanine:glyoxylate aminotransferase 2 ac AT1G23310 glutamate:glyoxylate aminotransferase ac; na; no; nt; ph; ro; ub; ps GLUCONEO/GLYOXYLATE CYCLE AT1G54340...”
- Time-resolved interaction proteomics of the GIGANTEA protein under diurnal cycles in Arabidopsis
Krahmer, FEBS letters 2019 - “...2.4E04 0.0026 33 n n.d. AT1G14510 AL7 1 4.7E05 8.7E04 18 n n.d. AT3G14420.1 ; AT4G18360 Aldolasetype TIM barrel 1 0.0089 0.031 17 n n.d. AT1G26790 CDF6 1 0.0010 0.0068 15 n n.d. AT3G13470 TCP1/cpn60 chaperonin 1 0.018 0.048 15 n 4/0 AT1G70290 TPS8 1 5.4E04...”
- The Mutation of Glu at Amino Acid 3838 of AtMDN1 Provokes Pleiotropic Developmental Phenotypes in Arabidopsis
Li, Scientific reports 2016 - “...data libraries under the following accession numbers: MDN1 , AT1G67120; PCAP2 , AT5G44610; GOX3 , AT4G18360; FER2 , AT3G11050; PER1 , AT1G48130; RAD50 , AT2G31970; EM6 , AT2G40170; CRC , AT1G69180; SMC3 , AT2G27170; TOP2 , AT5G10540; GRF5 , AT3G13960; ELIP2 , AT4G14690; PAP85 , AT3G22640....”
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- GLYCOLATE OXIDASE3, a Glycolate Oxidase Homolog of Yeast l-Lactate Cytochrome c Oxidoreductase, Supports l-Lactate Oxidation in Roots of Arabidopsis.
Engqvist, Plant physiology 2015 - GeneRIF: GOX3(At4g18360) is the enzyme that metabolizes l-lactate to pyruvate.GOX3 is predominantly present in roots and mature to aging leaves but is largely absent from young photosynthetic leaves.[
- Photorespiration: regulation and new insights on the potential role of persulfidation
Aroca, Journal of experimental botany 2023 - “..., N (11) AT3G14150 Q24JJ8 GLO3 Peroxisomal ( S )-2-hydroxyacid oxidase GLO3 P (3) AT4G18360 O49506 GLO5 Glycolate oxidase 3 (GOX 3) P (3) AT2G41220 Q9T0P4 GLU2 Ferredoxin-dependent glutamate synthase 2, (Fd-GOGAT 2) P (2,3,4) , S (6,7) AT3G25530 Q9LSV0 GLYR1 Glyoxylate/succinic semialdehyde reductase 1 P...”
6a08A / O52792 The crystal structure of mandelate oxidase with benzoyl-formic acid (see paper)
47% identity, 90% coverage
- Ligands: magnesium ion; flavin mononucleotide; benzoyl-formic acid (6a08A)
HAOX2_ARATH / Q24JJ8 Peroxisomal (S)-2-hydroxyacid oxidase GLO3; Glycolate oxidase 3; AtGLO3; GOX 3; Short chain alpha-hydroxy acid oxidase GLO3; lHAOX2; EC 1.1.3.15 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
Q24JJ8 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Arabidopsis thaliana (see paper)
AT3G14150 (S)-2-hydroxy-acid oxidase, peroxisomal, putative / glycolate oxidase, putative / short chain alpha-hydroxy acid oxidase, putative from Arabidopsis thaliana
45% identity, 90% coverage
- function: Oxidase that catalyzes the oxidation of a broad range of 2- hydroxyacids to the corresponding 2-oxoacids, with a reduction of O2 to H2O2. Displays the highest activity with leucic acid (2-hydroxy-4- methylpentanoate) and has intermediate activity with 2-hydroxyhexanoate and 2-hydroxyoctanote. Shows lower activity with 2-hydroxydodecanoate, valic acid, and isoleucic acid and extremely low activity with glycolate and L-lactate. Cannot use 2-hydroxyhexadecanoate or D-lactate as substrates. May be involved in the conversion or degradation of 2- hydroxyacids produced during the metabolism of fatty acids or amino acids.
catalytic activity: a (2S)-2-hydroxycarboxylate + O2 = a 2-oxocarboxylate + H2O2 (RHEA:16789)
catalytic activity: 2-hydroxy-4-methylpentanoate + O2 = 4-methyl-2-oxopentanoate + H2O2 (RHEA:69380)
catalytic activity: 2-hydroxyhexanoate + O2 = 2-oxohexanoate + H2O2 (RHEA:69372)
catalytic activity: 2-hydroxyoctanoate + O2 = 2-oxooctanoate + H2O2 (RHEA:67940)
cofactor: FMN
subunit: Homotetramer. - Photorespiration: regulation and new insights on the potential role of persulfidation
Aroca, Journal of experimental botany 2023 - “...Q9S7E9 GGAT2 Glutamateglyoxylate aminotransferase 2 (GGT2) P (2,3) , S (7) , N (11) AT3G14150 Q24JJ8 GLO3 Peroxisomal ( S )-2-hydroxyacid oxidase GLO3 P (3) AT4G18360 O49506 GLO5 Glycolate oxidase 3 (GOX 3) P (3) AT2G41220 Q9T0P4 GLU2 Ferredoxin-dependent glutamate synthase 2, (Fd-GOGAT 2) P (2,3,4)...”
- RNA-Sequencing of Heterorhabditis nematodes to identify factors involved in symbiosis with Photorhabdus bacteria.
Bhat, BMC genomics 2022 - “...(P45896) 66. gst-5 (Q09596) 27. daf-7 (P92172) 67. gstk-1 (Q09652) 28. SMAD3 (P84022) 68. GLO-3 (Q24JJ8) Transcription factors Transmembrane transporters 29. daf-16 (O16850) 69. pgp-1 (P34712) 30. elt-2 (Q10655) 70. pgp-3 (P34713) 31. pnr (P52168) 71. SLC17A5 (Q9NRA2) 32. fos-1 (G5ECG2) 72. aqp-10 (Q09369) 33. TFEB...”
- The photo-inhibition of camphor leaves (Cinnamomum camphora L.) by NaCl stress based on physiological, chloroplast structure and comparative proteomic analysis
Yue, PeerJ 2020 - “...1401 gi743939144 PREDICTED: uncharacterized protein LOC105117914 Q8RXS1 PNSB4 0.36 0.01 1473 gi743899657 PREDICTED: nitronate monooxygenase Q24JJ8 GLO3 10.33 7.96 1534 gi743928583 PREDICTED: NAD(P)H-quinone oxidoreductase subunit N, organellar chromatophore Q9LVM2 ndhN 0.34 0.14 413 gi566151722 hypothetical protein POPTR_0001s29700g Q9LMU1 EGY3 0.33 0.21 223 gi566187985 hypothetical protein POPTR_0009s14500g...”
- Identification and characterization of Glycolate oxidase gene family in garden lettuce (Lactuca sativa cv. 'Salinas') and its response under various biotic, abiotic, and developmental stresses
Mariyam,, Scientific reports 2023 - “...v13, which consisted of three AtGOX (AT3G14420, AT3G14415 and AT4G18360), and two AtHAOX (AT3G14130 and AT3G14150) genes. These sequences were then used to BLAST-P (Protein- basic local alignment search tool) search in Lactuca sativa v8 ( Lactuca sativa cv. Salinas ) proteome database at Phytozome v13...”
- Photorespiration: regulation and new insights on the potential role of persulfidation
Aroca, Journal of experimental botany 2023 - “...AT1G70580 Q9S7E9 GGAT2 Glutamateglyoxylate aminotransferase 2 (GGT2) P (2,3) , S (7) , N (11) AT3G14150 Q24JJ8 GLO3 Peroxisomal ( S )-2-hydroxyacid oxidase GLO3 P (3) AT4G18360 O49506 GLO5 Glycolate oxidase 3 (GOX 3) P (3) AT2G41220 Q9T0P4 GLU2 Ferredoxin-dependent glutamate synthase 2, (Fd-GOGAT 2) P...”
- Enzymatic Properties of Recombinant Phospho-Mimetic Photorespiratory Glycolate Oxidases from Arabidopsis thaliana and Zea mays
Jossier, Plants (Basel, Switzerland) 2019 - “...Arabidopsis , there are five GOX-related genes: At3g14420 , At3g14415 , At4g18360 , At3g14130 and At3g14150 (encoding At GOX1, At GOX2, At GOX3, At HAOX1 and At HAOX2, respectively). According to transcriptomic analyses, At3g14415 ( AtGOX2 ) and At3g14420 ( AtGOX1 ) are highly expressed in...”
- Quantitative Proteomics Reveals a Role for SERINE/ARGININE-Rich 45 in Regulating RNA Metabolism and Modulating Transcriptional Suppression via the ASAP Complex in Arabidopsis thaliana
Chen, Frontiers in plant science 2019 - “...0.459 0.543 AT2G22400 ATTRM4B, TRM4B 0.352 0.498 AT2G27880 AGO5, ARGONAUTE 5, ATAGO5 0.344 0.437 SAR AT3G14150 Peroxisomal (S)-2-hydroxy-acid oxidase GLO3 0.416 0.591 SAS AT3G42850 ARA2, ARABINOKINASE 2 0.456 0.611 SAR AT4G38350 Patched family protein 0.468 0.332 SAR AT4G39460 S-adenosylmethionine carrier 1, chloroplastic/mitochondrial;SAMC1 0.470 0.461 AT5G13380 Auxin-responsive...”
- Multilevel Regulation of Peroxisomal Proteome by Post-Translational Modifications
Sandalio, International journal of molecular sciences 2019 - “...no; nt; ph; ps; ntyr AT3G14130 Aldolase-type TIM barrel family protein/ glycolate oxidase ac; na AT3G14150 Aldolase-type TIM barrel family protein/ glycolate oxidase na AT3G14415 Aldolase-type TIM barrel family protein/ glycolate oxidase ac; na; ng; nt; ph; ntyr AT3G14420 Aldolase-type TIM barrel family protein/ glycolate oxidase...”
- Arabidopsis ABI5 plays a role in regulating ROS homeostasis by activating CATALASE 1 transcription in seed germination
Bi, Plant molecular biology 2017 - “...AT3G09940 AT2G36470 AT2G26400 AT1G32060 AT1G59870 AT1G77120 AT1G74710 AT4G33070 AT1G02220 AT1G20020 AT5G20480 AT2G28200 AT5G66570 AT5G21090 AT3G28930 AT3G14150 AT5G60360 AT2G44490 AT1G68520 AT1G54410 AT1G66880 AT1G18570 AT1G66200 REGULATION_OF_HYDROGEN_PEROXIDE_METABOLIC_PROCESS(187) GO:0010310 regulation of hydrogen peroxide metabolic process, GOslim:biological_process 25 Down-regulation AT1G80840 AT1G59870 AT3G28930 AT1G32060 AT2G44490 AT5G24530 AT1G20020 AT4G33560 AT5G20480 AT1G18570 AT5G09660 AT5G66570...”
- Developmental genetic mechanisms of C4 syndrome based on transcriptome analysis of C3 cotyledons and C4 assimilating shoots in Haloxylon ammodendron
Li, PloS one 2015 - “...At3g14415 330.80 1326.77 -2.00 AtGOX3 At4g18360 151.29 679.40 -2.17 AtHAOX1 At3g14130 8.32 12.51 -0.59 AtHAOX2 At3g14150 9.20 16.56 -0.85 Ser:glyoxylate aminotransferase AtAGT1 At2g13360 362.28 2052.76 -2.50 Glu:glyoxylate aminotransferase AtGGT1 At1g23310 670.03 1607.05 -1.26 AtGGT2 At1g70580 527.48 1194.60 -1.18 Gly decarboxylase P-protein AtGLDP1 At4g33010 503.01 1461.69 -1.54...”
- 2-Hydroxy Acids in Plant Metabolism
Maurino, The arabidopsis book 2015 - “...family, GOX3 (At4g18360), lHAOX1 (At3g14130), and lHAOX2 (At3g14150), are involved in non-photosynthetic functions (Esser et al., 2014; Engqvist et al., 2015)....”
- More
HAOX1_HUMAN / Q9UJM8 2-Hydroxyacid oxidase 1; HAOX1; Glycolate oxidase; GO; GOX; Glyoxylate oxidase; EC 1.1.3.15; EC 1.2.3.5 from Homo sapiens (Human) (see 4 papers)
Q9UJM8 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Homo sapiens (see 2 papers)
NP_060015 2-Hydroxyacid oxidase 1 from Homo sapiens
43% identity, 90% coverage
- function: Broad substrate specificity (S)-2-hydroxy-acid oxidase that preferentially oxidizes glycolate (PubMed:10777549, PubMed:10978532, PubMed:17669354, PubMed:18215067). The glyoxylate produced by the oxidation of glycolate can then be utilized by alanine-glyoxylate aminotransferase for the peroxisomal synthesis of glycine; this pathway appears to be an important step for the detoxification of glyoxylate which, if allowed to accumulate, may be metabolized to oxalate with formation of kidney stones (PubMed:10978532, PubMed:17669354). Can also catalyze the oxidation of glyoxylate, and long chain hydroxyacids such as 2-hydroxyhexadecanoate and 2-hydroxyoctanoate, albeit with much lower catalytic efficiency (PubMed:10777549, PubMed:17669354, PubMed:18215067). Active in vitro with the artificial electron acceptor 2,6-dichlorophenolindophenol (DCIP), but O2 is believed to be the physiological electron acceptor, leading to the production of H2O2 (PubMed:10777549, PubMed:10978532, PubMed:17669354, PubMed:18215067). Is not active on L-lactate and 2-hydroxybutanoate (PubMed:10777549).
catalytic activity: a (2S)-2-hydroxycarboxylate + O2 = a 2-oxocarboxylate + H2O2 (RHEA:16789)
catalytic activity: glycolate + O2 = glyoxylate + H2O2 (RHEA:25311)
catalytic activity: glyoxylate + H2O + O2 = H(+) + H2O2 + oxalate (RHEA:14837)
catalytic activity: 2-hydroxyhexadecanoate + O2 = 2-oxohexadecanoate + H2O2 (RHEA:67944)
catalytic activity: 2-hydroxyoctanoate + O2 = 2-oxooctanoate + H2O2 (RHEA:67940)
cofactor: FMN
subunit: Homotetramer. - Early prediction of spontaneous preterm birth before 34 gestational weeks based on a combination of inflammation-associated plasma proteins.
Svenvik, Frontiers in immunology 2024 - “...10.66 (10.48-10.82) 10.48 (10.28-10.63) 0.001 CDCP1 Q9H5V8 1 0% 2.37 (2.04-2.64) 2.20 (1.96-2.44) 0.039 HAOX1 Q9UJM8 2 1% 4.77 (4.04-6.28) 4.19 (3.66-5.08) 0.035 HGF P14210 1 0% 8.37 (8.10-8.59) 8.20 (8.02-8.36) 0.011 0.065 LOX-1 P78380 2 1% 7.57 (7.18-7.73) 7.24 (6.97-7.53) 0.035 M-CSF P09603 1 0%...”
- “...8.98 (8.58-9.14) 8.65 (8.42-8.87) 0.005 Gal-9 O00182 2 1% 7.56 (7.38-7.86) 7.43 (7.32-7.57) 0.017 HAOX1 Q9UJM8 2 1% 6.23 (4.53-6.94) 5.13 (4.58-5.96) 0.041 HGF P14210 1 0% 8.63 (8.38-8.84) 8.42 (8.15-8.63) 0.023 IL-10 P22301 1 0% 3.59 (3.45-3.93) 3.42 (3.17-3.57) 0.001 0.096 IL-10RB Q08334 1 0%...”
- Cardiovascular disease-linked plasma proteins are mainly associated with lung volume.
Rydell, ERJ open research 2023 - “...responder 2 RARRES2 Q99969 1.96 (2.701.22) 1.210 5 0.84 (1.810.13) 0.09 Hydroxyacid oxidase 1 HAOX1 Q9UJM8 1.41 (2.080.73) 0.001 0.71 (1.650.23) 0.14 C-C motif chemokine 16 CCL16 O15467 1.46 (2.160.76) 0.001 0.68 (1.600.24) 0.15 Insulin-like growth factor-binding protein 1 IGFBP1 P08833 1.53 (0.752.30) 0.0027 0.76 (0.321.83)...”
- “...2 RARRES2 Q99969 1.96 (2.701.22) 1.210 5 2.07 (2.881.26) 4.410 5 Hydroxyacid oxidase 1 HAOX1 Q9UJM8 1.41 (2.080.73) 0.001 1.33 (2.110.55) 0.015 C-C motif chemokine 16 CCL16 O15467 1.46 (2.160.76) 0.001 1.31 (2.090.53) 0.02 Insulin-like growth factor-binding protein 1 IGFBP1 P08833 1.53 (0.752.30) 0.0027 1.59 (0.722.47)...”
- Flavin Mononucleotide-Dependent l-Lactate Dehydrogenases: Expanding the Toolbox of Enzymes for l-Lactate Biosensors
Tsvik, ACS omega 2022 - “...7120 Q8Z0C8, and Chlamydomonas reinhardtii F8WQN2; LMO from Mycolicibacterium smegmatis P21795; GLO from Homo sapiens Q9UJM8, Spinacia oleracea P05414, and Cyanidioschyzon merolae M1VAT1; FCB2 from Saccharomyces cerevisiae P00175; MDH from Pseudomonas putida P20932; HAO from Rattus norvegicus Q07523; HMO from Amycolatopsis orientalis O52792; and mLDH from...”
- ATRPred: A machine learning based tool for clinical decision making of anti-TNF treatment in rheumatoid arthritis patients.
Prasad, PLoS computational biology 2022 - “...- - - - 0.17 0.116 KRT19 P08727 3880 Keratin 19 IMMUNE 0.13 -2.126 HAOX1/HAO1 Q9UJM8 54363 Hydroxyacid oxidase 1 CVD II 0.13 -2.068 CXCL1 P09341 2919 C-X-C motif chemokine ligand 1 CVD II + INFLAM 0.10 0.421 RARRES2 Q99969 5919 Retinoic acid receptor responder 2...”
- Uncovering the anticancer mechanism of Compound Kushen Injection against HCC by integrating quantitative analysis, network analysis and experimental validation.
Gao, Scientific reports 2018 - “...1 precursor validated 5.02 0.05416 0.3813 P16070 CD44 CD44 antigen precursor validated 5.04 0.00918 0.3886 Q9UJM8 HAO1 hydroxyacid oxidase (glycolate oxidase) 1 predicted 5.12 0.01655 0.4330 P00915 CA1 Carbonic anhydrase 1 predicted 5.59 0.05388 0.4817 P01008 SERPINC1 serpin peptidase inhibitor, clade C (antithrombin), member 1 predicted...”
- Glycolate Oxidase Is a Safe and Efficient Target for Substrate Reduction Therapy in a Mouse Model of Primary Hyperoxaluria Type I.
Martin-Higueras, Molecular therapy : the journal of the American Society of Gene Therapy 2016 - iTRAQ-based proteomic analysis of hepatic tissues from patients with hepatitis B virus-induced acute-on-chronic liver failure
Peng, Experimental and therapeutic medicine 2015 - “...polypeptide B7, isoform CRA_b Unclassified 60 Unclassified Unclassified Unclassified Downregulation (3.031) 2 Hydroxyacid oxidase 1 Q9UJM8 41 Fatty acid -oxidation Oxidoreductase Protease Downregulation (2.000) 3 Membrane-associated progesterone receptor component 1 O00264 22 Unclassified Receptor Receptor Downregulation (2.000) 4 Enyol-CoA: hydratase/3-hydroxyacyl-CoA dehydrogenase Unclassified 79 Unclassified Unclassified Unclassified...”
- The cysteine proteome.
Go, Free radical biology & medicine 2015 - “...ALR GFER P55789 C, M, S H 2 O 2 Hydroxyacid oxidase 1 HAOX1 HAO1 Q9UJM8 Px H 2 O 2 Hydroxyacid oxidase 2 HAOX2 HAO2 Q9NYQ3 Px H 2 O 2 Membrane primary amine oxidase AOC3 AOC3 Q16853 PM H 2 O 2 Peroxisomal N(1)-acetyl-spermine/spermidine...”
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- Glycolate oxidase-1 gene variants influence the risk of hyperoxaluria and renal stone development.
Patel, World journal of urology 2024 (PubMed)- GeneRIF: Glycolate oxidase-1 gene variants influence the risk of hyperoxaluria and renal stone development.
- Mechanistic insights into the ROS-mediated inactivation of human aldehyde oxidase.
Esmaeeli, FEBS letters 2023 (PubMed)- GeneRIF: Mechanistic insights into the ROS-mediated inactivation of human aldehyde oxidase.
- Stabilization of an intermediate in the oxidative half-reaction of human liver glycolate oxidase.
Pennati, Biochemistry 2011 (PubMed)- GeneRIF: The study presents the first spectroscopic evidence of the formation of an intermediate with absorbance features resembling those of a flavosemiquinone in the oxidative half-reaction of glycolate oxidase.
- Genome-wide association study of childhood acute lymphoblastic leukemia in Korea.
Han, Leukemia research 2010 (PubMed)- GeneRIF: Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
- Structure of human glycolate oxidase in complex with the inhibitor 4-carboxy-5-[(4-chlorophenyl)sulfanyl]-1,2,3-thiadiazole.
Bourhis, Acta crystallographica. Section F, Structural biology and crystallization communications 2009 - GeneRIF: The inhibitor heteroatoms interact with five active-site residues that have been implicated in catalysis in homologous flavodehydrogenases of L-2-hydroxy acids. In addition, the chlorophenyl substituent is surrounded by nonconserved hydrophobic residues.
- Active site and loop 4 movements within human glycolate oxidase: implications for substrate specificity and drug design.
Murray, Biochemistry 2008 - GeneRIF: Active site and loop 4 movements within human glycolate oxidase.
- Purification and characterization of recombinant human liver glycolate oxidase.
Vignaud, Archives of biochemistry and biophysics 2007 (PubMed)- GeneRIF: These inhibitions suggest that glycolate binds to the active site of the reduced enzyme, and that DCIP also has affinity for the oxidized enzyme.
6gmbA / Q9UJM8 Structure of human hydroxyacid oxidase 1 bound with fmn and glycolate
43% identity, 90% coverage
- Ligands: flavin mononucleotide; glycolic acid (6gmbA)
HAOX1_ARATH / Q9LJH5 Peroxisomal (S)-2-hydroxyacid oxidase GLO4; Glycolate oxidase 4; AtGLO4; GOX 4; lHAOX1; EC 1.1.3.15 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
Q9LJH5 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Arabidopsis thaliana (see paper)
AT3G14130 (S)-2-hydroxy-acid oxidase, peroxisomal, putative / glycolate oxidase, putative / short chain alpha-hydroxy acid oxidase, putative from Arabidopsis thaliana
45% identity, 90% coverage
- function: Oxidase that catalyzes the oxidation of a broad range of 2- hydroxyacids to the corresponding 2-oxoacids, with a reduction of O2 to H2O2. Displays the highest activity with the long-chain fatty acid 2- hydroxydodecanoate and has intermediate activity with 2- hydroxyhexanoate, 2-hydroxyoctanote, and the short-chain hydroxyacid (S)-lactate (L-lactate). With much lower activity, it can also use glycolate, leucic acid, valic acid, and isoleucic acid as substrates in vitro. Cannot use 2-hydroxyhexadecanoate or D-lactate as substrates. May be involved in a general medium- and long-chain fatty acid catabolic pathway such as alpha-oxidation.
catalytic activity: a (2S)-2-hydroxycarboxylate + O2 = a 2-oxocarboxylate + H2O2 (RHEA:16789)
catalytic activity: 2-hydroxydodecanoate + O2 = 2-oxododecanoate + H2O2 (RHEA:69376)
catalytic activity: 2-hydroxyhexanoate + O2 = 2-oxohexanoate + H2O2 (RHEA:69372)
catalytic activity: 2-hydroxyoctanoate + O2 = 2-oxooctanoate + H2O2 (RHEA:67940)
catalytic activity: (S)-lactate + O2 = H2O2 + pyruvate (RHEA:55868)
cofactor: FMN
subunit: Homotetramer. - Identification and characterization of Glycolate oxidase gene family in garden lettuce (Lactuca sativa cv. 'Salinas') and its response under various biotic, abiotic, and developmental stresses
Mariyam,, Scientific reports 2023 - “...Arabidopsis Ortholog Gene ID AtGOX1, AtGLO1 AtGOX3, AtGLO5 AtHAOX1, AtGOX4, AtGLO4 Accession no AT3G14420 AT4G18360 AT3G14130 % Homology 90.51 89.97 85.08 75.99 74.01 Functions Regulating signal transduction pathway through ROS during nonhost resistance Metabolize l-lactate to pyruvate at low intracellular concentrations Encoding medium and long chain...”
- “...at Phytozome v13, which consisted of three AtGOX (AT3G14420, AT3G14415 and AT4G18360), and two AtHAOX (AT3G14130 and AT3G14150) genes. These sequences were then used to BLAST-P (Protein- basic local alignment search tool) search in Lactuca sativa v8 ( Lactuca sativa cv. Salinas ) proteome database at...”
- Enzymatic Properties of Recombinant Phospho-Mimetic Photorespiratory Glycolate Oxidases from Arabidopsis thaliana and Zea mays
Jossier, Plants (Basel, Switzerland) 2019 - “...]. In Arabidopsis , there are five GOX-related genes: At3g14420 , At3g14415 , At4g18360 , At3g14130 and At3g14150 (encoding At GOX1, At GOX2, At GOX3, At HAOX1 and At HAOX2, respectively). According to transcriptomic analyses, At3g14415 ( AtGOX2 ) and At3g14420 ( AtGOX1 ) are highly...”
- Multilevel Regulation of Peroxisomal Proteome by Post-Translational Modifications
Sandalio, International journal of molecular sciences 2019 - “...no; nt; ph; ro; ps AT2G13360 alanine:glyoxylate aminotransferase ac; na; no; nt; ph; ps; ntyr AT3G14130 Aldolase-type TIM barrel family protein/ glycolate oxidase ac; na AT3G14150 Aldolase-type TIM barrel family protein/ glycolate oxidase na AT3G14415 Aldolase-type TIM barrel family protein/ glycolate oxidase ac; na; ng; nt;...”
- Mechanisms of glacial-to-future atmospheric CO2 effects on plant immunity
Williams, The New phytologist 2018 - “...= 3). Expression of CAT2 ( AT4G35090 ), GOX1 ( AT3G14420 ) and HAOX1 ( AT3G14130 ) were measured in plants of the eightleaf stage, where each biological replicate consisted of shoot material from one plant ( n = 5). Differences in relative transcript levels were...”
- Developmental genetic mechanisms of C4 syndrome based on transcriptome analysis of C3 cotyledons and C4 assimilating shoots in Haloxylon ammodendron
Li, PloS one 2015 - “...At3g14420 911.87 3690.36 -2.02 AtGOX2 At3g14415 330.80 1326.77 -2.00 AtGOX3 At4g18360 151.29 679.40 -2.17 AtHAOX1 At3g14130 8.32 12.51 -0.59 AtHAOX2 At3g14150 9.20 16.56 -0.85 Ser:glyoxylate aminotransferase AtAGT1 At2g13360 362.28 2052.76 -2.50 Glu:glyoxylate aminotransferase AtGGT1 At1g23310 670.03 1607.05 -1.26 AtGGT2 At1g70580 527.48 1194.60 -1.18 Gly decarboxylase P-protein...”
- 2-Hydroxy Acids in Plant Metabolism
Maurino, The arabidopsis book 2015 - “...(L)-2-hydroxyacidoxidase gene family, GOX3 (At4g18360), lHAOX1 (At3g14130), and lHAOX2 (At3g14150), are involved in non-photosynthetic functions (Esser et al.,...”
- Effects of high temperature on photosynthesis and related gene expression in poplar
Song, BMC plant biology 2014 - “...AT1G73110 0.38 PTAC14 Potri.003G155100 Rubisco LSMT substrate-binding AT4G20130 0.30 HAOX1 Potri.003G069400 similar to (S)-2-hydroxy-acid oxidase; AT3G14130 0.40 GOX3 Potri.011G112700 similar to glycolate oxidase AT4G18360 0.08 AOAT2 Potri.008G187400 a protein with glyoxylate aminotransferase activity AT1G70580 0.14 AGT Potri.001G253300 similar to aminotransferase 2 AT2G13360 0.07 GDCST Potri.011G006800 similar...”
- Generation, annotation and analysis of first large-scale expressed sequence tags from developing fiber of Gossypium barbadense L
Yuan, PloS one 2011 - “...several G. barbadense- specific genes deserve to be highlighted. The contig sequence CO000339 (similar with AT3G14130) encoded (S)-2-hydroxy-acid oxidase, peroxisomal, which is mitochondrial type II peroxiredoxin F and essential for redox homeostasis and root growth of Arabidopsis thaliana under stress [65] . Some genes involved in...”
BN5_0696 alpha-hydroxy acid oxidase from Pseudomonas oleovorans CECT 5344
48% identity, 92% coverage
E1AXT8 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Nicotiana benthamiana (see 2 papers)
42% identity, 98% coverage
- Proteomics of PTI and Two ETI Immune Reactions in Potato Leaves
Resjö, International journal of molecular sciences 2019 - “...1.48 NA 1.48 PGSC0003DMP400044750 CXE carboxylesterase 1.07 NA 0.87 Q0WVD8 Adenylate translocator 0.63 NA 0.52 E1AXT8 Glycolate oxidase 1.71 NA NA PGSC0003DMP400000661 Beta-galactosidase 1.42 NA NA PGSC0003DMP400010835 MAR-binding protein 1.35 NA NA PGSC0003DMP400063324 DUF26 domain-containing protein 1 1.33 NA NA Q8LK04 Glyceraldehyde-3-phosphate dehydrogenase 1.02 NA NA...”
7r4pA / Q9UJM8 Structure of human hydroxyacid oxidase 1 bound with 6-amino-1-benzyl- 5-(methylamino)pyrimidine-2,4(1h,3h)-dione
44% identity, 90% coverage
- Ligands: flavin mononucleotide; 6-amino-1-benzyl-5-(methylamino)pyrimidine-2,4(1h,3h)-dione (7r4pA)
XP_006233084 2-Hydroxyacid oxidase 2 isoform X2 from Rattus norvegicus
42% identity, 92% coverage
GLO2_ARATH / Q9LRS0 Glycolate oxidase 2; AtGLO2; GOX2; (S)-2-hydroxy-acid oxidase GLO2; Short chain alpha-hydroxy acid oxidase GLO2; EC 1.1.3.15 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
NP_188059 Aldolase-type TIM barrel family protein from Arabidopsis thaliana
AT3G14415 (S)-2-hydroxy-acid oxidase, peroxisomal, putative / glycolate oxidase, putative / short chain alpha-hydroxy acid oxidase, putative from Arabidopsis thaliana
41% identity, 95% coverage
- function: Catalyzes the oxidation of glycolate to glyoxylate, with a reduction of O2 to H2O2 (PubMed:21828292, PubMed:25416784). Is a key enzyme in photorespiration in green plants (Probable). Glycolate is the preferred substrate, but to a lesser extent, this oxidase is also able to use hydroxypyruvate, L-lactate and glycerate as substrates in vitro (PubMed:21828292).
catalytic activity: glycolate + O2 = glyoxylate + H2O2 (RHEA:25311)
catalytic activity: a (2S)-2-hydroxycarboxylate + O2 = a 2-oxocarboxylate + H2O2 (RHEA:16789)
catalytic activity: (S)-lactate + O2 = H2O2 + pyruvate (RHEA:55868)
cofactor: FMN
subunit: Homotetramer. - Photorespiration: regulation and new insights on the potential role of persulfidation
Aroca, Journal of experimental botany 2023 - “...S (5) , N (10,11) AT3G14420 Q9LRR9 GLO1 Glycolate oxidase 1 (GOX1) P (1,2,3,4) AT3G14415 Q9LRS0 GLO2 Glycolate oxidase 2 (GOX2) P (1,2,3,4) , N (10) AT5G04140 Q9ZNZ7 GLU1 Ferredoxin-dependent glutamate synthase 1, chloroplastic/mitochondrial (Fd-GOGAT 1) P (2,3,4) , S (7) AT1G80380 Q944I4 GLYK d -Glycerate...”
- Profiling of advanced glycation end products uncovers abiotic stress-specific target proteins in Arabidopsis
Chaplin, Journal of experimental botany 2019 - “...AT4G02520/AT2G02930 9 - 10 ALDEHYDE DEHYDROGENASE 11A3 Q1WIQ6 AT2G24270 5 - 10 GLYCOLATE OXIDASE 2 Q9LRS0 AT3G14415 6 - 11 CYTOSOLIC NADP+-DEPENDENT ISOCITRATE DEHYDROGENASE Q9SRZ6 AT1G65930 11 - 13 LIGHT HARVESTING COMPLEX OF PHOTOSYSTEM II 5 Q9XF89 AT4G10340 7 - 11 PEROXISOMAL NAD-MALATE DEHYDROGENASE 2 Q9ZP05...”
- Lack of GLYCOLATE OXIDASE1, but Not GLYCOLATE OXIDASE2, Attenuates the Photorespiratory Phenotype of CATALASE2-Deficient Arabidopsis.
Kerchev, Plant physiology 2016 - GeneRIF: GOX2 role in photorespiration.
- Rewiring of primary metabolism for ammonium recycling under short-term low CO2 treatment - its implication for C4 evolution
Miao, Frontiers in plant science 2024 - “...ammonium refixation pathways. The expression of a number of photorespiratory genes, including glycolate oxidase (GOX2, AT3G14415), glutamate: glyoxylate aminotransferase (GGT2, AT1G70580), alanine: glyoxylate aminotransferase (AGT1, AT2G13360), glycine decarboxylase P-protein (GLDP1, AT4G33010; GLDP2, AT2G26080), and mitochondrial transporter A BOUT DE SOUFFLE (Bou, AT5G46800) (Eisenhut etal., 2013), were...”
- Removal of phosphoglycolate in hyperthermophilic archaea
Michimori, Proceedings of the National Academy of Sciences of the United States of America 2024 - “...to glyoxylate. On the T. kodakarensis genome, there was no homolog of the GOX (GOX, At3g14415 ) from A. thaliana . Cyanobacteria and some algae such as C. reinhardtii use a GLDH. As we observed NAD + -dependent GLDH activity in cell extracts, we searched for...”
- Identification and characterization of Glycolate oxidase gene family in garden lettuce (Lactuca sativa cv. 'Salinas') and its response under various biotic, abiotic, and developmental stresses
Mariyam,, Scientific reports 2023 - “...family genes were retrieved from TAIR at Phytozome v13, which consisted of three AtGOX (AT3G14420, AT3G14415 and AT4G18360), and two AtHAOX (AT3G14130 and AT3G14150) genes. These sequences were then used to BLAST-P (Protein- basic local alignment search tool) search in Lactuca sativa v8 ( Lactuca sativa...”
- Photorespiration: regulation and new insights on the potential role of persulfidation
Aroca, Journal of experimental botany 2023 - “..., S (5) , N (10,11) AT3G14420 Q9LRR9 GLO1 Glycolate oxidase 1 (GOX1) P (1,2,3,4) AT3G14415 Q9LRS0 GLO2 Glycolate oxidase 2 (GOX2) P (1,2,3,4) , N (10) AT5G04140 Q9ZNZ7 GLU1 Ferredoxin-dependent glutamate synthase 1, chloroplastic/mitochondrial (Fd-GOGAT 1) P (2,3,4) , S (7) AT1G80380 Q944I4 GLYK d...”
- Construction and analysis of protein-protein interaction networks based on nuclear proteomics data of the desiccation-tolerant Xerophyta schlechteri leaves subjected to dehydration stress
Shoko, Communicative & integrative biology 2023 - “...gi|7269239 AT4G23900 Nucleoside diphosphate kinase IV, chloroplastic/mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q8LAH8] gi|6227018 AT1G65930 Isocitrate dehydrogenase [NADP] [Source:UniProtKB/TrEMBL;Acc:A0A178W7K0] gi|62320779 AT3G14415 GOX2 [Source:UniProtKB/TrEMBL;Acc:A0A384L63] gi|114152861 ATCG00580 Cytochrome b559 subunit alpha [Source:UniProtKB/TrEMBL;Acc:A0A1B1W4W2]...”
- DspA/E-Triggered Non-Host Resistance against E. amylovora Depends on the Arabidopsis GLYCOLATE OXIDASE 2 Gene
Launay, International journal of molecular sciences 2022 - “...showed that only one gene had SNPs leading to non-synonymous mutations in both suppressors; the At3g14415 gene encoding GLYCOLATE OXIDASE 2 (GOX2). In the II-36 mutant the identified SNP led to a Ser27Phe mutation in the GOX2 protein, while in the I-18 mutant the identified SNP...”
- “...25 ]. The gox2-2 mutant bears a T-DNA insertion in the 5UTR region of the AT3G14415 gene and has been shown to be a knock-out mutant [ 27 ]. All the plant material used in this study is in the Col-0 accession. 4.2. Bacterial Strains and...”
- Peroxisome-Mediated Reactive Oxygen Species Signals Modulate Programmed Cell Death in Plants
Huang, International journal of molecular sciences 2022 - “...LOC_Os05g02530 [ 71 ] GOX1 AT3G14420 [ 20 ] Potri.011G112700 LOC_Os07g05820 [ 54 ] GOX2 AT3G14415 [ 19 ] Potri.011G112700 LOC_Os07g05820 [ 54 ] IBR3 AT3G06810 [ 25 ] Potri.T030600 LOC_Os07g47820 MDAR4/SDP2 AT3G27820 [ 56 ] Potri.001G346200 LOC_Os02g47800 PAO2 AT2G43020 [ 29 ] Potri.005G207300 LOC_Os04g53190 [...”
- Color recycling: metabolization of apocarotenoid degradation products suggests carbon regeneration via primary metabolic pathways
Koschmieder, Plant cell reports 2022 - “...3.1 Photorespiration At1g32080 PLGG1 Glycolate/glycerate translocator 1 11 5 At3g14420 GOX1 Glycolate oxidase 5 4 At3g14415 GOX2 Glycolate oxidase n.s n.s At2g13360 SGAT Serine:glutamate aminotransferase 4 8 Glycolysis At1g43670 FBP Fructose-1,6-bisphosphatase 2.2 2.2 At4g26520 FBA7 Fructose-bisphosphate aldolase n.s 3.2 At3g26650 GAPA1 Glycerinaldehyde-3-phosphate dehydrogenase n.s 2.0 At1g12900...”
- “...four- and eightfold, respectively (Table 3 ). Genes encoding proteins involved in photorespiration, namely GOX2 (At3g14415), GDC-T (At1g11860), GDC-P (At4g33010), SHM1 (At4g37930), HPR1 (At1g68010) and GLYK (At1g80380), were not considerably induced. These findings agree with recent reports on alternative functions of enzymes linked with photorespiration in...”
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M1VAT1 Glycolate oxidase, peroxysomal from Cyanidioschyzon merolae (strain NIES-3377 / 10D)
42% identity, 91% coverage
GLO1_ORYSJ / Q10CE4 Glycolate oxidase 1; GOX 1; OsGLO1; Peroxisomal (S)-2-hydroxy-acid oxidase GLO1; Short chain alpha-hydroxy acid oxidase GLO1; EC 1.1.3.15 from Oryza sativa subsp. japonica (Rice) (see 4 papers)
Q10CE4 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Oryza sativa Japonica Group (see paper)
45% identity, 92% coverage
- function: Catalyzes the oxidation of glycolate to glyoxylate, with a reduction of O2 to H2O2 (PubMed:16595582). Is a key enzyme in photorespiration in plants (By similarity). To a lesser extent, is also able to oxidize glyoxylate to oxalate in vitro (PubMed:16595582). Can exert a strong regulation over photosynthesis, possibly through a feed- back inhibition on Rubisco activase (PubMed:19264754). Does not seem to play a role in oxalate accumulation (PubMed:16595582).
catalytic activity: glycolate + O2 = glyoxylate + H2O2 (RHEA:25311)
cofactor: FMN
subunit: Homotetramer (By similarity). Interacts with rice dwarf virus (RDV) P8. This interaction promotes viral P8 relocation to virus factories peripheral to peroxisomes. Binds to CATB and CATC; these interactions are disturbed by alpha-hydroxy-2-pyridinemethanesulfonic acid (HPMS) and salicylic acid (SA) (PubMed:26900141). - ITRAQ-based quantitative proteomic analysis of japonica rice seedling during cold stress
Qing, Breeding science 2022 - “...environmental stress or stimuli ( Zhang et al. 2016 ). In the present study, GLO1 (Q10CE4) and GLO5 (Q6YT73) proteins up-regulation may affect H 2 O 2 levels in Kongyu131 to enhance cold resistance. Although other DEPs identified in the work were not reported to function...”
- “...31.99 0.47 Q6AVZ8 LOC_Os05g04380.1 Peroxidase 16 49.12 0.42 Q0DCP0 LOC_Os06g20150.1 Peroxidase (Fragment) 14 39.53 0.53 Q10CE4 LOC_Os03g57220 Peroxisomal (S)-2-hydroxy-acid oxidase GLO1 41 69.65 1.56 Q6YT73 LOC_Os07g05820 Peroxisomal (S)-2-hydroxy-acid oxidase GLO5 38 65.85 1.84 A0A0P0WP33 LOC_Os05g41640.1 Phosphoglycerate kinase 41 68.18 2.42 Q8LMR0 LOC_Os03g06200 Phosphoserine aminotransferase 10 26.76...”
A0A0P0KG57 4-hydroxymandelate oxidase (EC 1.1.3.46) from Streptomyces sp. (see paper)
50% identity, 88% coverage
B0BNF9 2-Hydroxyacid oxidase 1 from Rattus norvegicus
NP_001101250 2-Hydroxyacid oxidase 1 from Rattus norvegicus
42% identity, 90% coverage
LOC100646060 2-Hydroxyacid oxidase 1 from Bombus terrestris
40% identity, 95% coverage
5zbmB / E1AXT8 Structure of glycolate oxidase containing fmn from nicotiana benthamiana (see paper)
43% identity, 91% coverage
- Ligand: flavin mononucleotide (5zbmB)
HAOX2_RAT / Q07523 2-Hydroxyacid oxidase 2; HAOX2; (S)-2-hydroxy-acid oxidase, peroxisomal; Long chain alpha-hydroxy acid oxidase; Long-chain L-2-hydroxy acid oxidase; LCHAO; EC 1.1.3.15 from Rattus norvegicus (Rat) (see 5 papers)
42% identity, 92% coverage
- function: Oxidase that catalyzes the oxidation of medium and long chain hydroxyacids such as 2-hydroxyhexadecanoate, 2-hydroxyoctanoate, 2- hydroxyhexanoate and 2-hydroxybutanoate, to the correspondong 2- oxoacids (PubMed:15683236, PubMed:3061453, PubMed:8508789). Its role in the oxidation of 2-hydroxy fatty acids may contribute to the general pathway of fatty acid alpha-oxidation (By similarity). Can also use mandelate as substrate (PubMed:3061453). Active in vitro with the artificial electron acceptor 2,6-dichlorophenolindophenol (DCIP), but O2 is believed to be the physiological electron acceptor, leading to the production of H2O2 (PubMed:15683236, PubMed:3061453, PubMed:8508789).
catalytic activity: a (2S)-2-hydroxycarboxylate + O2 = a 2-oxocarboxylate + H2O2 (RHEA:16789)
catalytic activity: 2-hydroxyoctanoate + O2 = 2-oxooctanoate + H2O2 (RHEA:67940)
catalytic activity: 2-hydroxyhexadecanoate + O2 = 2-oxohexadecanoate + H2O2 (RHEA:67944)
catalytic activity: 2-hydroxyhexanoate + O2 = 2-oxohexanoate + H2O2 (RHEA:69372)
catalytic activity: mandelate + O2 = H2O2 + phenylglyoxylate (RHEA:68968)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Homotetramer (PubMed:8508789). Could also form homooctamer. - Flavin Mononucleotide-Dependent l-Lactate Dehydrogenases: Expanding the Toolbox of Enzymes for l-Lactate Biosensors
Tsvik, ACS omega 2022 - “...M1VAT1; FCB2 from Saccharomyces cerevisiae P00175; MDH from Pseudomonas putida P20932; HAO from Rattus norvegicus Q07523; HMO from Amycolatopsis orientalis O52792; and mLDH from Pseudomonas stutzeri ADL63037) were used as queries for individual database searches on NCBI and UniProt using blastp and phmmer 56 with maximum...”
- Diverse Roles of Mitochondria in Renal Injury from Environmental Toxicants and Therapeutic Drugs.
Lash, International journal of molecular sciences 2021 - “...anion-selective channel protein 1 (VDAC-1) 1.12 0.08 Oxidoreductase Activity Q6AYT0 Quinone oxidoreductase (zeta-crystallin) 1.21 0.23 Q07523 Hydroxyacid oxidase 2 1.47 0.74 Q68FT3 Pyridine nucleotide-disulfide oxidoreductase domain-containing protein 2 1.92 0.22 ijms-22-04172-t002_Table 2 Table 2 Selective list of chemicals and drugs whose nephrotoxicity is associated with mitochondrial...”
- Antioxidant, antiapoptotic and amino acid balance regulating activities of 1,7-dihydroxy-3,4,8-trimethoxyxanthone against dimethylnitrosamine-induced liver fibrosis.
Zheng, PloS one 2017 - “...P68136 Alpha skeletal muscle 5.09 0.22 P70473 Alpha-methylacyl-CoA racemase 0.28 3.99 Q03336 Regucalcin 0.17 5.61 Q07523 Hydroxyacid oxidase 2 0.48 4.23 Q07936 Annexin A2 4.12 0.31 Q0D2L3 Agmatinase 0.37 2.57 Q5FVR2 Thymidine phosphorylase 0.29 10.84 Q641W2 UPF0160 protein MYG1 2.70 0.46 Q64648 Cytochrome P450 2C12 7.86...”
- Functional proteomic analysis of corticosteroid pharmacodynamics in rat liver: Relationship to hepatic stress, signaling, energy regulation, and drug metabolism.
Ayyar, Journal of proteomics 2017 - “...of glutamine and 4-aminobutanoate UP P21213 Hal Histidine ammonia-lyase First reaction in histidine catabolism UP/DOWN Q07523 Hao2 Hydroxyacid oxidase 2 Oxidation of L-alpha-hydroxy acids as well as L-alpha-amino acids DOWN Q58FK9 Kat3 Kynurenine-oxoglutarate transaminase 3 L-kynurenine to kynurenic acid UP Q5XIT9 Mccc2 Methylcrotonoyl-CoA carboxylase beta chain...”
- GSTA3 Attenuates Renal Interstitial Fibrosis by Inhibiting TGF-Beta-Induced Tubular Epithelial-Mesenchymal Transition and Fibronectin Expression.
Xiao, PloS one 2016 - Proteomic profiling and pathway analysis of the response of rat renal proximal convoluted tubules to metabolic acidosis
Schauer, American journal of physiology. Renal physiology 2013 - “...dehydrogenase [NADP] cytoplasmic HAOX2_RAT ENOA_RAT Q66HT1_RAT D4AD25_RAT F16P1_RAT Q07523 P04764 Q66HT1 D4AD25 P19112 Hao2 Eno1 Aldob Cltc Fbp1 39 kDa 47 kDa...”
B9ST74 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Ricinus communis (see paper)
43% identity, 91% coverage
B9S0Y9 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Ricinus communis (see paper)
42% identity, 94% coverage
GOX1_MAIZE / A0A3L6E0R4 Glycolate oxidase 1; GOX; EC 1.1.3.15 from Zea mays (Maize) (see 2 papers)
44% identity, 92% coverage
- function: Catalyzes the oxidation of glycolate to glyoxylate, with a reduction of O2 to H2O2 (PubMed:25416784). Is an essential enzyme in photorespiration in plants (PubMed:18805949). Photorespiration plays a vital role in C4 photosynthesis in Z.mays and is essential for maize seedling development and maintaining low (non-toxic) levels of glycolate (PubMed:18805949).
catalytic activity: glycolate + O2 = glyoxylate + H2O2 (RHEA:25311)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Homotetramer.
disruption phenotype: The mutant shows deficiency in glycolate oxidase activity and is non-viable in air; leaves become necrotic within 7 days and plants die within 15 days. When the mutant cells are shifted from high CO2 to air in light, they accumulate glycolate linearly for 6 hours to levels 7-fold higher than wild type and 11-fold higher after 25 hours.
GLO1_ARATH / Q9LRR9 Glycolate oxidase 1; AtGLO1; GOX1; (S)-2-hydroxy-acid oxidase GLO1; Short chain alpha-hydroxy acid oxidase GLO1; EC 1.1.3.15 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
Q9LRR9 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Arabidopsis thaliana (see paper)
AT3G14420 (S)-2-hydroxy-acid oxidase, peroxisomal, putative / glycolate oxidase, putative / short chain alpha-hydroxy acid oxidase, putative from Arabidopsis thaliana
NP_188060 Aldolase-type TIM barrel family protein from Arabidopsis thaliana
42% identity, 94% coverage
- function: Catalyzes the oxidation of glycolate to glyoxylate, with a reduction of O2 to H2O2 (PubMed:25416784). Is a key enzyme in photorespiration in green plants (Probable).
catalytic activity: glycolate + O2 = glyoxylate + H2O2 (RHEA:25311)
cofactor: FMN
subunit: Homotetramer. - Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translation
Smith, The Plant journal : for cell and molecular biology 2024 - “..., AT4G32260 , AT5G60600 , AT5G42980 , AT3G55800 , AT3G46780 , AT3G16140 , AT4G20360 , AT3G14420 , AT1G56070 , AT5G66190 , AT3G02470 , AT1G30380 , AT4G03280 , AT2G30950 , AT5G60390 , AT4G04640 , AT1G55670 , AT3G60750 , AT1G44575 , AT5G35630 , AT4G28750 , AT1G20020 , AT3G12780...”
- Identification and characterization of Glycolate oxidase gene family in garden lettuce (Lactuca sativa cv. 'Salinas') and its response under various biotic, abiotic, and developmental stresses
Mariyam,, Scientific reports 2023 - “...LsHAOX1 LsHAOX2 Arabidopsis Ortholog Gene ID AtGOX1, AtGLO1 AtGOX3, AtGLO5 AtHAOX1, AtGOX4, AtGLO4 Accession no AT3G14420 AT4G18360 AT3G14130 % Homology 90.51 89.97 85.08 75.99 74.01 Functions Regulating signal transduction pathway through ROS during nonhost resistance Metabolize l-lactate to pyruvate at low intracellular concentrations Encoding medium and...”
- “...GLO family genes were retrieved from TAIR at Phytozome v13, which consisted of three AtGOX (AT3G14420, AT3G14415 and AT4G18360), and two AtHAOX (AT3G14130 and AT3G14150) genes. These sequences were then used to BLAST-P (Protein- basic local alignment search tool) search in Lactuca sativa v8 ( Lactuca...”
- The tomato chloroplast stromal proteome compendium elucidated by leveraging a plastid protein-localization prediction Atlas
Bhattacharya, Frontiers in plant science 2023 - “...Solyc11g066390 SOD3 Superoxide dismutase 47 0.250 At2g28190 nd Solyc07g056540 GLO1 Glycolate oxidase 1 48 0.238 At3g14420 nd Solyc07g044860 OEE2 Oxygen-evolving enhancer protein 2, PsbP 49 0.229 At1g06680 2 Solyc11g069790 CPN60A2 Chaperonin - RuBisCo LS binding protein (A 50 0.228 At2g28000 3 Solyc04g074750 CP33C Polyadenylate-binding protein 1-A...”
- Photosynthetic and transcriptome responses to fluctuating light in Arabidopsis thylakoid ion transport triple mutant
Gollan, Plant direct 2023 - “...transcription 1.4 0.1 0.046 NAC046 AT3G04060 NAC domaincontaining regulator 2.7 0.7 ** 0.005 Photorespiration GOX1 AT3G14420 Glycolate/glyoxylate catabolism 1.0 1.1 0.000 AGT1 AT2G13360 1.1 1.1 0.000 AGT3 AT2G38400 1.6 1.9 0.000 GGT2 AT1G70580 1.2 1.4 0.000 GLPD2 AT2G26080 1.7 1.8 0.000 GLN1;1 AT5G37600 1.4 1.7 0.000...”
- Photorespiration: regulation and new insights on the potential role of persulfidation
Aroca, Journal of experimental botany 2023 - “...(9) AT5G35630 Q43127 GLN2 Glutamine synthetase (GS2) P (2,3,4) , S (5) , N (10,11) AT3G14420 Q9LRR9 GLO1 Glycolate oxidase 1 (GOX1) P (1,2,3,4) AT3G14415 Q9LRS0 GLO2 Glycolate oxidase 2 (GOX2) P (1,2,3,4) , N (10) AT5G04140 Q9ZNZ7 GLU1 Ferredoxin-dependent glutamate synthase 1, chloroplastic/mitochondrial (Fd-GOGAT 1)...”
- Peroxisome-Mediated Reactive Oxygen Species Signals Modulate Programmed Cell Death in Plants
Huang, International journal of molecular sciences 2022 - “...30 ] Potri.015G082900 LOC_Os04g40040 DHAR1 AT1G19570 [ 60 ] Potri.008G049300 LOC_Os05g02530 [ 71 ] GOX1 AT3G14420 [ 20 ] Potri.011G112700 LOC_Os07g05820 [ 54 ] GOX2 AT3G14415 [ 19 ] Potri.011G112700 LOC_Os07g05820 [ 54 ] IBR3 AT3G06810 [ 25 ] Potri.T030600 LOC_Os07g47820 MDAR4/SDP2 AT3G27820 [ 56 ]...”
- Color recycling: metabolization of apocarotenoid degradation products suggests carbon regeneration via primary metabolic pathways
Koschmieder, Plant cell reports 2022 - “...13.4 At5g09660 MDH Malate dehydrogenase 3.6 3.1 Photorespiration At1g32080 PLGG1 Glycolate/glycerate translocator 1 11 5 At3g14420 GOX1 Glycolate oxidase 5 4 At3g14415 GOX2 Glycolate oxidase n.s n.s At2g13360 SGAT Serine:glutamate aminotransferase 4 8 Glycolysis At1g43670 FBP Fructose-1,6-bisphosphatase 2.2 2.2 At4g26520 FBA7 Fructose-bisphosphate aldolase n.s 3.2 At3g26650...”
- “...(Pick et al. 2013 ), was induced 11-fold. Moreover, the peroxisomal enzymes glycolate oxidase GOX1 (At3g14420), converting glycolate into glyoxylate, and serine:glutamate aminotransferase SGAT (At2g13360) were induced four- and eightfold, respectively (Table 3 ). Genes encoding proteins involved in photorespiration, namely GOX2 (At3g14415), GDC-T (At1g11860), GDC-P...”
- Protein-protein interactions in plant antioxidant defense
Melicher, Frontiers in plant science 2022 - “...etal., 2019 AT1G20620 CAT3, catalase 3 hydrogen peroxide detoxification peroxisome Y2H High Guo etal., 2019 AT3G14420 GOX1, Glycolate oxidase 1 catalyzes the oxidation of glycolate to glyoxylate peroxisome Y2H High Guo etal., 2019 Y2H, yeast two hybrid assay; SUS, split ubiquitin system. According to high-throughput Y2H...”
- More
- Lack of GLYCOLATE OXIDASE1, but Not GLYCOLATE OXIDASE2, Attenuates the Photorespiratory Phenotype of CATALASE2-Deficient Arabidopsis.
Kerchev, Plant physiology 2016 - GeneRIF: GOX1 role in photorespiration.
- Glycolate oxidase is an alternative source for H2O2 production during plant defense responses and functions independently from NADPH oxidase.
Rojas, Plant signaling & behavior 2012 - GeneRIF: GOX plays a role in nonhost resistance independent of NADPH oxidase. [GOX1]
- Photorespiration: regulation and new insights on the potential role of persulfidation
Aroca, Journal of experimental botany 2023 - “...AT5G35630 Q43127 GLN2 Glutamine synthetase (GS2) P (2,3,4) , S (5) , N (10,11) AT3G14420 Q9LRR9 GLO1 Glycolate oxidase 1 (GOX1) P (1,2,3,4) AT3G14415 Q9LRS0 GLO2 Glycolate oxidase 2 (GOX2) P (1,2,3,4) , N (10) AT5G04140 Q9ZNZ7 GLU1 Ferredoxin-dependent glutamate synthase 1, chloroplastic/mitochondrial (Fd-GOGAT 1) P...”
- Disclosing proteins in the leaves of cork oak plants associated with the immune response to Phytophthora cinnamomi inoculation in the roots: A long-term proteomics approach
Coelho, PloS one 2021 - “...0.015 -0.6 Protein translocase subunit SecA A0A1P8B485 P25697 8.890 6.489 0.015 -0.6 Phosphoribulokinase, chloroplastic KPPR/PRK Q9LRR9 1.487 0.662 0.002 -0.6 (S)-2-hydroxy-acid oxidase GLO1 GLO1/GOX1 B3H4S6 0.434 0.300 0.041 -0.3 Dicarboxylate transporter 1 B3H4S6 P56778 19.522 15.325 0.002 -0.3 Photosystem II CP43 reaction center protein PSBC P56761...”
- “...(RBS1A/RBCS1A) Chloroplast Photorespiration; Photosynthesis -3.1 3 P25697 Phosphoribulokinase (KPPR/PRK) Chloroplast Photosynthesis; Plant defense -0.6 3 Q9LRR9 (S)-2-hydroxy-acid oxidase GLO1 (GLO1/GOX1) Peroxisome Plant defense; Photorespiration -0.6 3.1 F4KDZ4 Malate dehydrogenase (F4KDZ4/PMDH2) Peroxisome Fatty acid -oxidation -0.3 Protein-DNA complex assembly (5) 5 A8MRL0 Histone superfamily protein H3.3 (A8MRL0/AT4G40030)...”
- Profiling of advanced glycation end products uncovers abiotic stress-specific target proteins in Arabidopsis
Chaplin, Journal of experimental botany 2019 - “...AT1G29910/AT1G29920/ AT1G29930 6 - 8 GLYCERATE KINASE Q944I4 AT1G80380 8 - 10 GLYCOLATE OXIDASE 1 Q9LRR9 AT3G14420 8 PHOTOSYSTEM II SUBUNIT Q Q9XFT3 AT4G21280 8 - 9 RIBOSOMAL L5P PROTEIN O04603 AT4G01310 7 - 9 NUCLEOSIDE DIPHOSPHATE KINASE 1 P39207 AT4G09320 8 - 9 MONODEHYDROASCORBATE REDUCTASE...”
- iTRAQ Mitoproteome Analysis Reveals Mechanisms of Programmed Cell Death in Arabidopsis thaliana Induced by Ochratoxin A
Wang, Toxins 2017 - “...1.81 0.23 Homocysteine methyltransferase O50008 CIMS 5.14 5.62 3 - 1.79 0.02 Peroxisomal (S)-2-hydroxy-acid oxidase Q9LRR9 GLO1 10.35 19.62 6 - 1.71 0.35 NADH dehydrogenase [ubiquinone] flavoprotein 2 O22769 At4g02580 8.40 18.04 4 - 1.67 0.15 Adenylate kinase 1 O82514 ADK1 15.95 36.99 7 1.55 0.14...”
HAOX1_MOUSE / Q9WU19 2-Hydroxyacid oxidase 1; HAOX1; Glycolate oxidase; GOX; Glyoxylate oxidase; EC 1.1.3.15; EC 1.2.3.5 from Mus musculus (Mouse) (see paper)
Q9WU19 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Mus musculus (see 3 papers)
NP_034533 2-Hydroxyacid oxidase 1 from Mus musculus
41% identity, 90% coverage
- function: Broad substrate specificity (S)-2-hydroxy-acid oxidase that preferentially oxidizes glycolate (PubMed:9891009). The glyoxylate produced by the oxidation of glycolate can then be utilized by alanine- glyoxylate aminotransferase for the peroxisomal synthesis of glycine; this pathway appears to be an important step for the detoxification of glyoxylate which, if allowed to accumulate, may be metabolized to oxalate with formation of kidney stones (By similarity). Can also catalyze the oxidation glyoxylate, and long chain hydroxyacids such as 2-hydroxyhexadecanoate and 2-hydroxyoctanoate (By similarity). Active in vitro with the artificial electron acceptor 2,6- dichlorophenolindophenol (DCIP), but O2 is believed to be the physiological electron acceptor, leading to the production of H2O2 (PubMed:9891009).
catalytic activity: a (2S)-2-hydroxycarboxylate + O2 = a 2-oxocarboxylate + H2O2 (RHEA:16789)
catalytic activity: glycolate + O2 = glyoxylate + H2O2 (RHEA:25311)
catalytic activity: glyoxylate + H2O + O2 = H(+) + H2O2 + oxalate (RHEA:14837)
catalytic activity: 2-hydroxyhexadecanoate + O2 = 2-oxohexadecanoate + H2O2 (RHEA:67944)
catalytic activity: 2-hydroxyoctanoate + O2 = 2-oxooctanoate + H2O2 (RHEA:67940)
cofactor: FMN
subunit: Homotetramer. - HAO1 negatively regulates liver macrophage activation via the NF-κB pathway in alcohol-associated liver disease.
Chen, Cellular signalling 2022 (PubMed)- GeneRIF: HAO1 negatively regulates liver macrophage activation via the NF-kappaB pathway in alcohol-associated liver disease.
- Metabolism of (13)C5-hydroxyproline in mouse models of Primary Hyperoxaluria and its inhibition by RNAi therapeutics targeting liver glycolate oxidase and hydroxyproline dehydrogenase.
Li, Biochimica et biophysica acta 2016 - GeneRIF: Decreasing hepatic glycolate oxidase and HYPDH expression decreases oxalate excretion.
- Comparative proteomic study of liver lipid droplets and mitochondria in mice housed at different temperatures
Liu, FEBS letters 2019 - “...Glutathione S transferase kappa 1 Gstk1 1.57 0.03 Q99MZ7 Peroxisomal trans2enoylCoA reductase Pecr 1.56 0.02 Q9WU19 Hydroxyacid oxidase 1 Hao1 1.53 0.04 Q9JKR6 Hypoxia upregulated protein 1 Hyou1 1.46 0.04 Q91WG0 Acylcarnitine hydrolase Ces2c 1.44 0.04 Downregulated 10 P12710 Fatty acidbinding protein Fabp1 0.74 0.09 F7A8H6...”
- Functional proteomic analysis of corticosteroid pharmacodynamics in rat liver: Relationship to hepatic stress, signaling, energy regulation, and drug metabolism.
Ayyar, Journal of proteomics 2017 - “...enzyme in the endoplasmic reticulum UP Q91Z53 Grhpr Glyoxylate reductase/hydroxypyruvate reductase Dicarboxylic acid metabolism UP/DOWN Q9WU19 Hao1 Hydroxyacid oxidase 1 Glycolate degradation UP O35952 Hagh Hydroxyacylglutathione hydrolase, mitochondrial Hydrolysis of S-D-lactoyl-glutathione to form glutathione UP Q5BJY9 Krt18 Keratin, type I cytoskeletal 18 Role in filament reorganization...”
- Identification and quantification of the basal and inducible Nrf2-dependent proteomes in mouse liver: biochemical, pharmacological and toxicological implications.
Walsh, Journal of proteomics 2014 - “...P08032 Spectrin alpha chain, erythrocyte 7 0.66 0.005 P21981 Protein-glutamine gamma-glutamyltransferase 2 16 0.66 0.049 Q9WU19 Hydroxyacid oxidase 1 9 0.65 <0.001 Q6ZWY9 Histone H2B type 1-C/E/G 30 0.65 0.020 O08917 Flotillin-1 2 0.63 0.002 0.69 0.018 P32020 Non-specific lipid-transfer protein 72 0.62 0.003 Q99P30 Peroxisomal...”
- Proteomic changes at 8 weeks after infection are associated with chronic liver pathology in experimental schistosomiasis
Manivannan, Journal of proteomics 2012 (secret)
GOX_SPIOL / P05414 Glycolate oxidase; GAO; GOX; Short chain alpha-hydroxy acid oxidase; EC 1.1.3.15 from Spinacia oleracea (Spinach) (see 5 papers)
P05414 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Spinacia oleracea (see paper)
42% identity, 94% coverage
- function: Catalyzes the oxidation of glycolate to glyoxylate, with a reduction of O2 to H2O2 (PubMed:1324737, PubMed:7705356). Is a key enzyme in photorespiration in green plants (Probable). To a lesser extent, is also able to use L-lactate and 2-hydroxbyutanoate as substrate in vitro, but shows almost no activity with L-mandelate (PubMed:7705356).
catalytic activity: glycolate + O2 = glyoxylate + H2O2 (RHEA:25311)
catalytic activity: a (2S)-2-hydroxycarboxylate + O2 = a 2-oxocarboxylate + H2O2 (RHEA:16789)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Homotetramer. - Flavin Mononucleotide-Dependent l-Lactate Dehydrogenases: Expanding the Toolbox of Enzymes for l-Lactate Biosensors
Tsvik, ACS omega 2022 - “...Chlamydomonas reinhardtii F8WQN2; LMO from Mycolicibacterium smegmatis P21795; GLO from Homo sapiens Q9UJM8, Spinacia oleracea P05414, and Cyanidioschyzon merolae M1VAT1; FCB2 from Saccharomyces cerevisiae P00175; MDH from Pseudomonas putida P20932; HAO from Rattus norvegicus Q07523; HMO from Amycolatopsis orientalis O52792; and mLDH from Pseudomonas stutzeri ADL63037)...”
- Enzymatic Properties of Recombinant Phospho-Mimetic Photorespiratory Glycolate Oxidases from Arabidopsis thaliana and Zea mays
Jossier, Plants (Basel, Switzerland) 2019 - “...GOX1, At GOX2 and Zm GO1 3D-structures were designed based on the spinach GOX (UniProtKB: P05414) 3D-structure (PDB: 1al7.1) using the SWISS-MODEL server ( https://swissmodel.expasy.org/ ) modelling service. Manipulation of 3D-structures was realized using Deepview (Swiss Pdb-viewer) ( https://spdbv.vital-it.ch/ ) and included the compute H-bond formation...”
- A functional genomics approach to dissect the mode of action of the Stagonospora nodorum effector protein SnToxA in wheat.
Vincent, Molecular plant pathology 2012 (no snippet) - EST analysis of the scaly green flagellate Mesostigma viride (Streptophyta): implications for the evolution of green plants (Viridiplantae)
Simon, BMC plant biology 2006 - “...were obtained from public databases ( Cyanidioschyzon merolae [KEGG:CMQ436C]; Chlamydomonas reinhardtii [JGI:C_340068]; Spinacia oleracea [Swiss-Prot: P05414 ]; Nostoc punctiforme PCC 73102 [Genbank: ZP_00106740.1 ]; Nostoc sp. PCC 7120 [Genbank: BAB77694.1 ]; Anabaena variabilis ATCC 29413 [Genbank: ZP_00160276.2 ]; Arabidopsis thaliana [Genbank: CAB78838 ], Oryza sativa [Genbank:...”
- Predicting functional family of novel enzymes irrespective of sequence similarity: a statistical learning approach.
Han, Nucleic acids research 2004 - “...EC class (F2) Sequence similarity (BLAST E -value) SVM functional family assignment Assignment status Glycolateoxidase (P05414) EC 1.1 IPP isomerase (Q8PW37) EC 5.3 3.00E07 E1->F1;E2->F2 + Creatine amidinohydrolase (P38488) EC 3.5 Prolinedipeptidase (O58885) EC 3.4 3.00E15 E1->F1;E2->F2 + Cystathionine gamma-synthase (P38675) EC 2.5 Methionine gamma-lyase (P13254)...”
- SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence.
Cai, Nucleic acids research 2003
3sgzA / Q07523 High resolution crystal structure of rat long chain hydroxy acid oxidase in complex with the inhibitor 4-carboxy-5-[(4-chiorophenyl) sulfanyl]-1, 2, 3-thiadiazole. (see paper)
42% identity, 92% coverage
- Ligands: flavin mononucleotide; 5-[(4-methylphenyl)sulfanyl]-1,2,3-thiadiazole-4-carboxylic acid (3sgzA)
Q6YT73 Glycolate oxidase 5 from Oryza sativa subsp. japonica
44% identity, 92% coverage
- ITRAQ-based quantitative proteomic analysis of japonica rice seedling during cold stress
Qing, Breeding science 2022 - “...stimuli ( Zhang et al. 2016 ). In the present study, GLO1 (Q10CE4) and GLO5 (Q6YT73) proteins up-regulation may affect H 2 O 2 levels in Kongyu131 to enhance cold resistance. Although other DEPs identified in the work were not reported to function in cold stress...”
- “...LOC_Os06g20150.1 Peroxidase (Fragment) 14 39.53 0.53 Q10CE4 LOC_Os03g57220 Peroxisomal (S)-2-hydroxy-acid oxidase GLO1 41 69.65 1.56 Q6YT73 LOC_Os07g05820 Peroxisomal (S)-2-hydroxy-acid oxidase GLO5 38 65.85 1.84 A0A0P0WP33 LOC_Os05g41640.1 Phosphoglycerate kinase 41 68.18 2.42 Q8LMR0 LOC_Os03g06200 Phosphoserine aminotransferase 10 26.76 1.72 Q8GT95 LOC_Os07g38130 Polygalacturonase inhibitor 1 8 32.83 0.54...”
- Lipid and Protein Oxidation of Brown Rice and Selenium-Rich Brown Rice during Storage.
Zhang, Foods (Basel, Switzerland) 2022 - “...Accession No. Name BR-0:Se-0 BR-0:BR-6 Se-0:Se-6 BR-6:Se-6 Peroxisome B7EAG0 136 Catalase 0.6026 0.5248 1.8030 2.0512 Q6YT73 738 Glycolate oxidase 5 - 1.5996 - - Q43008 352 Superoxide dismutase [Mn], mitochondrial - - 4.6989 2.6546 Glutathione metabolism Q93WM2 1508 Glutathione transferase - 2.8314 - 0.5445 Q945W6 2338...”
LOC101764130 peroxisomal (S)-2-hydroxy-acid oxidase GLO4 from Setaria italica
43% identity, 91% coverage
P93260 (S)-2-hydroxy-acid oxidase from Mesembryanthemum crystallinum
42% identity, 92% coverage
Q8H3I4 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Oryza sativa Japonica Group (see paper)
43% identity, 91% coverage
HAOX2_HUMAN / Q9NYQ3 2-Hydroxyacid oxidase 2; HAOX2; (S)-2-hydroxy-acid oxidase, peroxisomal; Cell growth-inhibiting gene 16 protein; Long chain alpha-hydroxy acid oxidase; Long-chain L-2-hydroxy acid oxidase; EC 1.1.3.15 from Homo sapiens (Human) (see paper)
Q9NYQ3 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Homo sapiens (see paper)
44% identity, 91% coverage
- function: Oxidase that catalyzes the oxidation of medium and long chain hydroxyacids such as 2-hydroxyhexadecanoate and 2-hydroxyoctanoate, to the correspondong 2-oxoacids (PubMed:10777549). Its role in the oxidation of 2-hydroxy fatty acids may contribute to the general pathway of fatty acid alpha-oxidation (Probable). Active in vitro with the artificial electron acceptor 2,6-dichlorophenolindophenol (DCIP), but O2 is believed to be the physiological electron acceptor, leading to the production of H2O2. Is not active on glycolate, glyoxylate, L- lactate and 2-hydroxybutanoate (PubMed:10777549).
catalytic activity: a (2S)-2-hydroxycarboxylate + O2 = a 2-oxocarboxylate + H2O2 (RHEA:16789)
catalytic activity: 2-hydroxyhexadecanoate + O2 = 2-oxohexadecanoate + H2O2 (RHEA:67944)
catalytic activity: 2-hydroxyoctanoate + O2 = 2-oxooctanoate + H2O2 (RHEA:67940)
cofactor: FMN
subunit: Homotetramer. - The cysteine proteome.
Go, Free radical biology & medicine 2015 - “...oxidase 1 HAOX1 HAO1 Q9UJM8 Px H 2 O 2 Hydroxyacid oxidase 2 HAOX2 HAO2 Q9NYQ3 Px H 2 O 2 Membrane primary amine oxidase AOC3 AOC3 Q16853 PM H 2 O 2 Peroxisomal N(1)-acetyl-spermine/spermidine oxidase PAOX PAOX Q6QHF9 Px, C H 2 O 2 Peroxisomal...”
- Global analysis of gene expression in mineralizing fish vertebra-derived cell lines: new insights into anti-mineralogenic effect of vanadate.
Tiago, BMC genomics 2011 - “...cell adhesion/- 4,35 0,19 23,12 No match -/- 6,28 0,28 22,13 Hydroxyacid oxidase 2 [Source:Uniprot/SWISSPROTAcc: Q9NYQ3 ] metabolic process, electron transport/oxidoreductase activity 5,21 0,24 21,38 No match -/- 7,70 0,39 19,85 No match -/- 7,35 0,37 19,79 Phosphatase and actin regulator 4 isoform 1 [Source:RefSeq_peptideAcc:NP_001041648] -/-...”
XP_015138965 hydroxyacid oxidase 1 isoform X3 from Gallus gallus
45% identity, 82% coverage
G4V4S8 4-hydroxymandelate oxidase (EC 1.1.3.46) from Amycolatopsis orientalis (see 2 papers)
47% identity, 89% coverage
Q7FAS1 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Oryza sativa Japonica Group (see paper)
B8AUI3 Glycolate oxidase 3 from Oryza sativa subsp. indica
42% identity, 90% coverage
- Carbon and nitrogen partitioning of transgenic rice T2A-1 (Cry2A*) with different nitrogen treatments
Ling, Scientific reports 2019 - “...0.027 Pyruvate kinase 2, cytosolic Q2QXR8 37 1 17 1.518 0.028 Peroxisomal (S)-2-hydroxy-acid oxidase GLO3 B8AUI3 10.35 2 4 1.516 0.029 Os08g0495800 protein Q6Z5C3 2.25 1 1 1.503 0.032 60S ribosomal protein L27 A2ZAB3 38.24 3 6 1.467 0.044 Peroxidase A3AB79 1.61 1 1 0.572 0.000...”
- “...1.374 0.000 Putative uncharacterized protein B8B184 3.58 1 1 1.366 0.000 Peroxisomal (S)-2-hydroxy-acid oxidase GLO3 B8AUI3 10.35 2 4 1.364 0.001 Lipoxygenase A3BUP8 34.27 13 24 1.336 0.001 Amine oxidase B8B7J8 2.84 1 1 1.323 0.002 Phenylalanine ammonia-lyase Q75HQ7 22.63 5 13 1.313 0.002 Phospho-2-dehydro-3-deoxyheptonate aldolase...”
- Knockout of Pi21 by CRISPR/Cas9 and iTRAQ-Based Proteomic Analysis of Mutants Revealed New Insights into M. oryzae Resistance in Elite Rice Line
Nawaz, Genes 2020 - “...if not timely repaired [ 61 ]. Photosynthesis-related proteins (E9KIQ4, Q8W0E6, Q6AVG2, Q2QTK0, Q67WJ2, Q10HD0, Q7FAS1, B9FFA5) were found to be upregulated in homozygous mutant line. Proteins related to response to stimulus (A0A0P0W9C3, Q6K8R2) were up-regulated in homozygous mutants, mainly involved in chitinase activity and defense...”
- Proteomic analysis of the rice (Oryza officinalis) provides clues on molecular tagging of proteins for brown planthopper resistance
Zhang, BMC plant biology 2019 - “...Os03g0733332 AACCAGGGGTGGGCGAGCTA ACCGAGCTGTCGCCGAAGCA Q7XRT6 OSJNBa0042F21.7 AAGCCTTCTGTTGCTCTGCC TGAAGATGAACCCAACAAAGTG Q2R1U4 Os11g0592800 GAGGCATACTTGGAGCTTGTG TTCCGATGAGCATGAGTCTTT Q6Z7B3 Os02g0115600 GGAAACCCACCATACATCAG GCACAGATGACTCACGATCA Q7FAS1 Os04g0623500 CGTCTCCGAGTATGAGCAGC TGGGCATGGAAATGTTGAAG To acquire a comprehensive representation of proteomic changes after BHP infestation, all 1084 DEPs were annotated using GO terms and subjected to GO functional analysis. Main biological...”
- “...analysis. Table 2 and Fig. 6 show that mRNA expression pattern of the gene encoding Q7FAS1 was similar to the protein expression pattern. Genes Q6AVH9, Q6K832 and Q6Z7B3 in PS_B-VS-PS,HR_B-VS-HR and PR_B-VS-PR groups showed similar expression profiles between mRNA and corresponding protein. On the other hand,...”
Q39640 (S)-2-hydroxy-acid oxidase from Cucurbita hybrid cultivar
41% identity, 97% coverage
GRMZM2G148194 aldolase-type TIM barrel family protein-like from Zea mays
44% identity, 89% coverage
- The dynamics of DNA methylation in maize roots under Pb stress
Ding, International journal of molecular sciences 2014 - “...Unknown GRMZM2G078389 0.19 0.16 0.23 Unknown GRMZM2G369243 0.14 0.12 0.22 Ribosomal RNA adenine methylase transferase GRMZM2G148194 5.06 4.68 5.51 Protein phosphatase 2C (PP2C)-like GRMZM2G422464 8.85 6.24 9.01 Mitochondrial carrier protein GRMZM2G057743 0.49 0.21 6.51 Kinesin, motor domain GRMZM2G385925 10,000 2.6 10,000 CTLH, C -terminal LisH motif...”
DMB42_RS42735 alpha-hydroxy acid oxidase from Nonomuraea sp. WAC 01424
47% identity, 89% coverage
- Genomic-Led Discovery of a Novel Glycopeptide Antibiotic by Nonomuraea coxensis DSM 45129
Yushchuk, ACS chemical biology 2021 - “...) (aa identity of protein product with noc homologue, %) encoded protein noc1 dbv1 (90.6%) DMB42_RS42735 (31) (60%) hydroxymandelate oxidase (Hmo) noc2 dbv2 (89.3%) DMB42_RS42740 (30) (62%) hydroxymandelate synthase (HmaS) noc3 dbv37 (90.9%) DMB42_RS42745 (29) (83%) hydroxyphenylglycine aminotransferase (HpgT) noc4 dbv35 (90.9%) DMB42_RS42730 (32) (63%) Na...”
PAAG_07725 peroxisomal (S)-2-hydroxy-acid oxidase from Paracoccidioides lutzii Pb01
40% identity, 84% coverage
- Interaction of Isocitrate Lyase with Proteins Involved in the Energetic Metabolism in Paracoccidioides lutzii
Freitas, Journal of fungi (Basel, Switzerland) 2020 - “...0.983 PAAG_03138 alanine-glyoxylate aminotransferase & 0.943 PAAG_02682 fructose-1,6-bisphosphatase * 0.933 PAAG_08203 phosphoenolpyruvate carboxykinase # 0.926 PAAG_07725 peroxisomal (S)-2-hydroxy-acid oxidase & 0.911 PAAG_03793 dihydrodipicolinate synthase & 0.900 PAAG_08075 citrate synthase * 0.899 PAAG_04550 2-methylcitrate synthase * 0.858 PAAG_06563 succinate/fumarate mitochondrial transporter & 0.835 PAAG_02653 acetyl-coenzyme A synthetase...”
HAOX2_MOUSE / Q9NYQ2 2-Hydroxyacid oxidase 2; HAOX2; (S)-2-hydroxy-acid oxidase, peroxisomal; Medium chain alpha-hydroxy acid oxidase; Medium-chain L-2-hydroxy acid oxidase; EC 1.1.3.15 from Mus musculus (Mouse) (see paper)
Q9NYQ2 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Mus musculus (see paper)
40% identity, 92% coverage
- function: Oxidase that catalyzes the oxidation of medium chain hydroxyacids such as 2-hydroxyoctanoate, to the correspondong 2- oxoacids. Its role in the oxidation of 2-hydroxy fatty acids may contribute to the general pathway of fatty acid alpha-oxidation. Active in vitro with the artificial electron acceptor 2,6- dichlorophenolindophenol (DCIP), but O2 is believed to be the physiological electron acceptor, leading to the production of H2O2. Is not active on glycolate, glyoxylate, L-lactate, 2-hydroxybutanoate and 2-hydroxyhexadecanoate.
catalytic activity: a (2S)-2-hydroxycarboxylate + O2 = a 2-oxocarboxylate + H2O2 (RHEA:16789)
catalytic activity: 2-hydroxyoctanoate + O2 = 2-oxooctanoate + H2O2 (RHEA:67940)
cofactor: FMN
subunit: Homotetramer. - Quantitative Proteomic Study Unmasks Fibrinogen Pathway in Polycystic Liver Disease.
Cordido, Biomedicines 2022 - “...4 P05208 CEL2A Cela2a 0.35 2.37 10 2 Q63836 SBP2 Selenbp2 0.39 3.27 10 5 Q9NYQ2 HAOX2 Hao2 0.42 2.40 10 11 Q9D1L0 CHCH2 Chchd2 0.45 1.79 10 7 P16015 CAH3 Ca3 0.47 1.19 10 4 Q8R1F5 HYI Hyi 0.49 5.79 10 3 1 Protein accession...”
- Dataset on the mass spectrometry-based proteomic profiling of the kidney from wild type and the dystrophic mdx-4cv mouse model of X-linked muscular dystrophy.
Dowling, Data in brief 2020 - “...9.1520 5.17E-06 1.24 Q3U4I7 Pyridine nucleotide-disulfide oxidoreductase domain-containing protein 2 Pyroxd2 3 10.0392 0.00151 1.24 Q9NYQ2 Hydroxyacid oxidase Hao2 3 11.4539 0.02747 1.24 O70475 UDP-glucose 6-dehydrogenase Ugdh 5 19.0586 0.00356 1.24 Q8BUV3 Gephyrin Gphn 2 6.3220 0.00830 1.22 Q99K51 Plastin-3 Pls3 2 6.6408 0.01267 1.21 Q9DBM2...”
- ITRAQ-based quantitative proteomic analysis of processed Euphorbia lathyris L. for reducing the intestinal toxicity.
Zhang, Proteome science 2018 - “...Ckmt1 1 0.7492 0.851 0.6657 Q6T707 Protein Scd4 (Stearoyl-CoA desaturase-4) Scd4 1 0.768 1.808 1.1152 Q9NYQ2 Hydroxyacid oxidase 2 (HAOX2) Hao2 Hao3 Haox2 1 0.771 0.721 0.658 P09036 Serine protease inhibitor Kazal-type 3 Spink3 1 0.7765 0.987 0.595 P98086 Complement C1q subcomponent subunit A C1qa 1...”
- Renal proteome in mice with different susceptibilities to fluorosis
Carvalho, PloS one 2013 - “...mitochondrial 36.5/5.1 35.8/5.4 8/434 129(0.011) Q9D051 Metabolism 175 Hydroxyacid oxidase 2 38.5/7.94 38.7/7.6 11/529 129(0.012) Q9NYQ2 Metabolism 217/221 Medium-chain specific acyl-CoA dehydrogenase, mitochondrial 42.5/8.055 43.6/7.69 15/715 129(0.001) P45952 Metabolism 269 Homogentisate 1,2-dioxygenase 50/7.2 50/6.85 6/105 129(0.011) O09173 Metabolism 384 Sarcosine dehydrogenase, mitochondrial 95/6.14 - 18/583 129(0.041)...”
- “...mitochondrial 33.5/9.28 32995.07/8.3 8/255 129(0.035) Q61425 Metabolism 175 Hydroxyacid oxidase 2 37/8.1 38.7/7.6 11/529 129(0.003) Q9NYQ2 Metabolism 184 Sorbitol dehydrogenase 40.5/6.805 38.2/6.56 10/586 129(0.003) Q64442 Metabolism 210 Aminoacylase-1 42.5/5.92 45.8/5.9 18/831 129(0.006) Q99JW2 Metabolism 217/221 Medium-chain specific acyl-CoA dehydrogenase, mitochondrial 41.5/8.22 43.6/7.69 15/715 129(0.009) P45952 Metabolism...”
LOX_NOSS1 / Q8Z0C8 L-lactate oxidase; LOX; Glyoxylate oxidase; No-LOX; EC 1.1.3.-; EC 1.2.3.5 from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (see 2 papers)
Q8Z0C8 L-lactate oxidase (EC 1.1.3.2) from Nostoc sp. PCC 7120 = FACHB-418 (see paper)
all0170 glycolate oxidase from Nostoc sp. PCC 7120
43% identity, 93% coverage
- function: Catalyzes the oxidation of (S)-lactate (L-lactate) to pyruvate, with a reduction of O2 to H2O2. In extant N2-fixing cyanobacteria such as Nostoc, this enzyme primarily serves as an O2- scavenging enzyme, protecting nitrogenase that is extremely sensitive to O2, and is therefore an essential partner in N2 fixation. Also shows clear oxidase activity with glyoxylate in vitro, and low activity with glycerate, hydroxypyruvate and glycolate. The very low glycolate oxidase activity indicates that this enzyme is unlikely to be involved in photorespiratory glycolate metabolism, a pathway that seems to exist in this cyanobacterium, but in which the oxidation of glycolate is taken over by glycolate dehydrogenase (GlcD). Is not able to use D- lactate as substrate and does not show any dehydrogenase activity with NAD(+) or NADP(+).
catalytic activity: (S)-lactate + O2 = H2O2 + pyruvate (RHEA:55868)
catalytic activity: glyoxylate + H2O + O2 = H(+) + H2O2 + oxalate (RHEA:14837)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Homotetramer.
disruption phenotype: Deletion of this gene does not affect growth in nitrate-containing medium under normal photorespiratory conditions. However, the mutant is unable to grow diazotrophically, caused by its inability to protect nitrogenase from O2 inhibition. - Flavin Mononucleotide-Dependent l-Lactate Dehydrogenases: Expanding the Toolbox of Enzymes for l-Lactate Biosensors
Tsvik, ACS omega 2022 - “...characterized HAOx sequences (LOx from Aerococcus viridans Q44467, Lactococcus lactis A0A4Y3JPV3, Nostoc sp. PCC 7120 Q8Z0C8, and Chlamydomonas reinhardtii F8WQN2; LMO from Mycolicibacterium smegmatis P21795; GLO from Homo sapiens Q9UJM8, Spinacia oleracea P05414, and Cyanidioschyzon merolae M1VAT1; FCB2 from Saccharomyces cerevisiae P00175; MDH from Pseudomonas putida...”
- The photorespiratory glycolate metabolism is essential for cyanobacteria and might have been conveyed endosymbiontically to plants
Eisenhut, Proceedings of the National Academy of Sciences of the United States of America 2008 - “...origin? (At5g06580) sll0404 slr0806 sll1559 alr5269 all4443 all0170 alr1004 At4g18360 At2g13360 At4 g18360 slr0293 sll0171 slr0879 slr1096 sll1931 slr0006...”
RL3578 putative L-lactate dehydrogenase from Rhizobium leguminosarum bv. viciae 3841
40% identity, 89% coverage
XP_502755 Hydroxyacid oxidase 1 from Yarrowia lipolytica
39% identity, 91% coverage
- [Synthesis and localization of L-lactate oxidase in yeasts].
Arinbasarova, Mikrobiologiia (PubMed)- GeneRIF: Centrifugation of the homogenate in Percoll gradient resulted in the isolation of purified fractions of the native mitochondria and peroxisomes. L-Lactate oxidase was shown to be localized in peroxisomes.
A8MS37 (S)-2-hydroxy-acid oxidase from Arabidopsis thaliana
43% identity, 83% coverage
LOX_CHLRE / F8WQN2 L-lactate oxidase; LOX; Cr-LOX; EC 1.1.3.- from Chlamydomonas reinhardtii (Chlamydomonas smithii) (see paper)
F8WQN2 L-lactate oxidase (EC 1.1.3.2) from Chlamydomonas reinhardtii (see paper)
42% identity, 90% coverage
- function: Catalyzes the oxidation of (S)-lactate (L-lactate) to pyruvate, with a reduction of O2 to H2O2. Also shows a low oxidase activity with glycolate in vitro. The very low glycolate oxidase activity indicates that this enzyme is unlikely to be involved in photorespiratory glycolate metabolism, a pathway in which the oxidation of glycolate is taken over by glycolate dehydrogenase (GlcD).
catalytic activity: (S)-lactate + O2 = H2O2 + pyruvate (RHEA:55868)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Homotetramer. - Flavin Mononucleotide-Dependent l-Lactate Dehydrogenases: Expanding the Toolbox of Enzymes for l-Lactate Biosensors
Tsvik, ACS omega 2022 - “...from Aerococcus viridans Q44467, Lactococcus lactis A0A4Y3JPV3, Nostoc sp. PCC 7120 Q8Z0C8, and Chlamydomonas reinhardtii F8WQN2; LMO from Mycolicibacterium smegmatis P21795; GLO from Homo sapiens Q9UJM8, Spinacia oleracea P05414, and Cyanidioschyzon merolae M1VAT1; FCB2 from Saccharomyces cerevisiae P00175; MDH from Pseudomonas putida P20932; HAO from Rattus...”
LOX_LYSSC / B1HZY7 L-lactate oxidase; LOX; (S)-2-hydroxy-acid oxidase; EC 1.1.3.-; EC 1.1.3.15 from Lysinibacillus sphaericus (strain C3-41) (see paper)
39% identity, 87% coverage
- function: Oxidase that catalyzes the oxidation of a broad range of 2- hydroxyacids in vitro, such as (S)-lactate, 2-hydroxyoctanoate, mandelate, 2-hydroxyoctadecanoate and (S)-2-hydroxyglutarate, to the corresponding 2-oxoacids, with a reduction of O2 to H2O2 (PubMed:34555022). May be involved in the utilization of L-lactate as an energy source for growth (By similarity).
catalytic activity: a (2S)-2-hydroxycarboxylate + O2 = a 2-oxocarboxylate + H2O2 (RHEA:16789)
catalytic activity: (S)-lactate + O2 = H2O2 + pyruvate (RHEA:55868)
catalytic activity: 2-hydroxyoctanoate + O2 = 2-oxooctanoate + H2O2 (RHEA:67940)
catalytic activity: mandelate + O2 = H2O2 + phenylglyoxylate (RHEA:68968)
catalytic activity: 2-hydroxyoctadecanoate + O2 = 2-oxooctadecanoate + H2O2 (RHEA:68964)
catalytic activity: (S)-2-hydroxyglutarate + O2 = 2-oxoglutarate + H2O2 (RHEA:27662)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Homotetramer.
LOX_LACJE / A0A5N1I561 L-lactate oxidase; LOX; (S)-2-hydroxy-acid oxidase; EC 1.1.3.-; EC 1.1.3.15 from Lactobacillus jensenii (see paper)
39% identity, 82% coverage
- function: Oxidase that catalyzes the oxidation of a broad range of 2- hydroxyacids in vitro, such as (S)-lactate, 2-hydroxyoctanoate, and to a lesser extent glycolate, mandelate and 2-hydroxyoctadecanoate, to the corresponding 2-oxoacids, with a reduction of O2 to H2O2 (PubMed:34555022). May be involved in the utilization of L-lactate as an energy source for growth (By similarity).
catalytic activity: a (2S)-2-hydroxycarboxylate + O2 = a 2-oxocarboxylate + H2O2 (RHEA:16789)
catalytic activity: (S)-lactate + O2 = H2O2 + pyruvate (RHEA:55868)
catalytic activity: 2-hydroxyoctanoate + O2 = 2-oxooctanoate + H2O2 (RHEA:67940)
catalytic activity: glycolate + O2 = glyoxylate + H2O2 (RHEA:25311)
catalytic activity: mandelate + O2 = H2O2 + phenylglyoxylate (RHEA:68968)
catalytic activity: 2-hydroxyoctadecanoate + O2 = 2-oxooctadecanoate + H2O2 (RHEA:68964)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Homotetramer.
Q9I197 L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) from Pseudomonas aeruginosa (see paper)
NP_251072 L-lactate dehydrogenase from Pseudomonas aeruginosa PAO1
PA14_33860 L-lactate dehydrogenase from Pseudomonas aeruginosa UCBPP-PA14
PA2382 L-lactate dehydrogenase from Pseudomonas aeruginosa PAO1
38% identity, 91% coverage
- Two NAD-independent l-lactate dehydrogenases drive l-lactate utilization in Pseudomonas aeruginosa PAO1.
Wang, Environmental microbiology reports 2018 (PubMed)- GeneRIF: Pseudomonas aeruginosa PAO1 contains a flavin-containing membrane-bound NAD-independent l-lactate dehydrogenase (l-iLDH) encoded by lldA. Loss of lldA has little effect on l-lactate utilization. However, deletion of both l-iLDH genes lldD and lldA completely impairs the l-lactate utilization capacity of the strain.
- The Pseudomonas aeruginosa Complement of Lactate Dehydrogenases Enables Use of d- and l-Lactate and Metabolic Cross-Feeding
Lin, mBio 2018 - “...contains four genes with the following annotation: ldhA (PA14_52270), lldD (PA14_63090), lldE (PA14_63100), and lldA (PA14_33860) ( Fig.1 ). ldhA encodes a lactate dehydrogenase that reduces pyruvate to lactate during anaerobic pyruvate fermentation ( 7 ) ( Fig.1 ). According to computational prediction ( 19 ),...”
- Development of liquid culture media mimicking the conditions of sinuses and lungs in cystic fibrosis and health
Ruhluel, F1000Research 2022 - “...Forward primer GTTCCTGGTGATGTACCTGTT mexB Reverse primer GTTCCTGGTGATGTACCTGTT PA2911 Forward primer AGCAACAACTCGCCCTATAC PA2911 Reverse primer CGAGCGGCTTTCGAAGTA PA2382 Forward primer TACACCCTGTCGACCATGA PA2382 Reverse primer GCATCACGTAGAGCTGGAAC rpoD Forward primer GGGCGAAGAAAGGAAATGGT rpoD Reverse primer CAGGTGGCGTAGGTGCAGA LESB65 algU Forward primer CAGGAACAGGATCAGCAACT algU Reverse primer CGCACGATCAATCCCAGTAT mexB Forward primer CGATCCATGAGGTAGTGAAGAC mexB Reverse...”
- “...genes of P. aeruginosa known to contribute to chronic infection. 45 , 46 PA2911 and PA2382 genes were also selected, as expression of these genes in clinical isolates in CF sputum is observed but expression has not previously been captured in in vitro CF models. 47...”
- Traditional Chinese Medicine Tanreqing Inhibits Quorum Sensing Systems in Pseudomonas aeruginosa
Yang, Frontiers in microbiology 2020 - “...Probable denitrification protein NorD PA1317 cyoA 1.5 1.3 + Cytochrome o ubiquinol oxidase subunit II PA2382 lldA 2.1 L -Lactate dehydrogenase PA2664 fhp 3.0 Flavohemoprotein PA3392 nosZ 2.9 + Nitrous-oxide reductase precursor PA3393 nosD 1.9 + NosD protein PA3872 narI 2.0 + Respiratory nitrate reductase gamma...”
- Two NAD-independent l-lactate dehydrogenases drive l-lactate utilization in Pseudomonas aeruginosa PAO1
Wang, Environmental microbiology reports 2018 (PubMed)- “...a novel flavin-containing membrane-bound L-iLDH encoded by lldA (PA2382) were both found to contribute to Llactate utilization by P. aeruginosa PAO1. In...”
- “...novel flavin-containing membranebound L-iLDH encoded by lldA (PA2382). Both L-iLDHs contribute to L-lactate utilization by P. aeruginosa PAO1. Furthermore,...”
- Pseudomonas aeruginosa transcriptome during human infection
Cornforth, Proceedings of the National Academy of Sciences of the United States of America 2018 - “...3.2 3.1 3.2 PA5535 4.1 3.7 4.4 PA1414 4.6 5.4 3.2 PA0781 2.9 2.6 3.2 PA2382 lldA 4.9 2.1 5.7 PA4835 2.8 2.2 3.1 PA2943 3.2 1.8 3.7 PA3598 3.5 2.3 4.0 PA4063 2.9 2.0 3.4 PA1797 2.8 3.2 2.5 PA4570 2.8 2.0 3.2 PA3237 7.0...”
- A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm
Sigurdsson, PloS one 2012 - “...Methionine metabolism MetX (PA0390) NAD biosynthesis NadD (PA4006) Oxidative phosphorylation SdhA (PA1583), SdhB (PA1584), LldA (PA2382) Peptidoglycan biosynthesis BacA (PA1959) Phenylalanine, tyrosine and tryptophan biosynthesis TrpF (PA3113) Purine and pyrimidine biosynthesis PyrF (PA2876) PurH (PA4854), PurB (PA2629), PurF (PA3108), PurM (PA0945), PurC (PA1013) Pyridoxine metabolism ThrC...”
NMA1592 L-lactate dehydrogenase from Neisseria meningitidis Z2491
37% identity, 85% coverage
- Metabolic shift in the emergence of hyperinvasive pandemic meningococcal lineages
Watkins, Scientific reports 2017 - “...(20), 213 (12) USA, 1964 Type III restriction/modification system enzyme Genetic Information Processing H 1499437 NMA1592 765 Exact match 11 (601), 41/44 (83), 8 (19), 5 (10) Denmark, 1962 L-lactate dehydrogenase Metabolism H 1501374 NMA1594 861 Exact match 11 (829), 5 (10) Denmark, 1962 NifS-like aminotranfserase...”
- Transcriptome analysis of Neisseria meningitidis during infection
Dietrich, Journal of bacteriology 2003 - “...NMA0569 NMA0453 NMA0147 NMA0142 NMA0825 NMA0879 NMA1202 NMA1592 NMA1727 NMA1740 NMA1763 NMA1765 NMA1766 NMA1770 NMA0612 NMA0600/NMA1174 NMA0596 NMA0570 NMA0513...”
lldA / AAB09666.1 lactate dehydrogenase from Neisseria meningitidis (see paper)
NMB1377 L-lactate dehydrogenase from Neisseria meningitidis MC58
37% identity, 85% coverage
- Fur-mediated global regulatory circuits in pathogenic Neisseria species
Yu, Journal of bacteriology 2012 - “...NMB1472 NMB0740 NMB0101 NMB1798 NMB1395 and -1396 NMB1377 NMB1458 NMB0343 NMB0394 NMB0396 NMB1381 NMB1380 Regulators Hypothetical NMB0034 to -0036 NMB0744...”
- Transcriptional profiling of serogroup B Neisseria meningitidis growing in human blood: an approach to vaccine antigen discovery
Hedman, PloS one 2012 - “...not reflected in regulated expression of NMB0543 ( lctP ) encoding lactate permease, nor of NMB1377 ( lldA ) and NMB0901 (both encoding lactate dehydrogenases). Meningococcal genes contributing to complement evasion are highly expressed in blood-grown organisms LOS (lipooligosaccharide), as well as polysaccharide capsule, has been...”
- Modeling Neisseria meningitidis metabolism: from genome to metabolic fluxes
Baart, Genome biology 2007 - “...be utilized by different meningococcal lactate dehydrogenases (LDH). In the MenB genome, an LDH gene (NMB1377) specific for L-lactate (EC1.1.2.3, EC 1.1.1.27) has been annotated. The predicted amino-acid sequence of this gene, lldA , is homologous to that of the Escherichia coli lldD gene (43% similarity)...”
- Effect of Neisseria meningitidis fur mutations on global control of gene transcription
Delany, Journal of bacteriology 2006 - “...frpB probes, at 68 and 137 nM Fur in the nmb0034, nmb1377, hmbR, and tonB probes and the recN, fumC probes, and finally at 275 nM in the nmb1395 probe. In...”
- Transcriptome analysis of Neisseria meningitidis during infection
Dietrich, Journal of bacteriology 2003 - “...NMB0126 NMB0132 NMB0617 Metabolism NMB0678 NMB0994 NMB1377 NMB1527 NMB1541 NMB1574 NMB1576 NMB1577 NMB1581 NMB1845 NMB1857/NMB0977 NMB1861 Transport Protein...”
- “...NMB0788, NMB0880, NMB0881, NMB0977, NMB0994, NMB0995, NMB1017, NMB1377, NMB1845, NMB1857, and NMB1940. The genes differentially regulated after the adherence to...”
- Analysis of the heat shock response of Neisseria meningitidis with cDNA- and oligonucleotide-based DNA microarrays
Guckenberger, Journal of bacteriology 2002 - “...NMB0906 NMB0907 NMB0946 NMB0947 NMB1056 NMB1231 NMB1334 NMB1377 NMB1468 NMB1469 NMB1472 NMB1563 NMB1564 NMB1789 NMB1790 NMB1796 NMB2000 NMB2013 Genes...”
NGK_1275 putative L-lactate dehydrogenase from Neisseria gonorrhoeae NCCP11945
37% identity, 85% coverage
NGO0639 putative L-lactate dehydrogenase from Neisseria gonorrhoeae FA 1090
37% identity, 85% coverage
- Global Network Analysis of Neisseria gonorrhoeae Identifies Coordination between Pathways, Processes, and Regulators Expressed during Human Infection
McClure, mSystems 2020 - “...genes were also regulated via iron based on a previous analysis ( 17 ), including NGO0639, NGO2071, NGO2092, and NGO2111. In addition, several of these same genes were also regulated as a function of the absence of Fur, including NGO0639, NGO2092, and NGO2111 ( 17 )....”
- Transcriptional regulation of a gonococcal gene encoding a virulence factor (L-lactate permease)
Ayala, PLoS pathogens 2019 - “...specifically L-lactate utilization and lactate dehydrogenase (LDH) activity, [ 33 ]. Moreover, expression of lldD (NGO0639), encoding a NAD-independent membrane-bound LDH, was enhanced in gonococci exposed to sub-lethal levels of hydrogen peroxide [ 34 ]. These results suggest that lactate metabolism is important for resistance to...”
- Phase variable DNA repeats in Neisseria gonorrhoeae influence transcription, translation, and protein sequence variation
Zelewska, Microbial genomics 2016 - “...Replacement tract nifS NGO0636 CCACACCC NGK_1278 CCACACCC CCACACCC CCACACCC CCACACCC CCACACCC No. Replacement tract lldD NGO0639 (G)7 NGK_1275 (G)7 (G)7 (G)7 (G)7 (G)7 No. No variation. Methylase NlalV NGO0676 (A)9 NGK_1230 (A)9 (A)9 (A)9 (A)9 (A)9 No. No variation. dnaX NGO0743 (C)7 NGK_1135 (C)7 (C)7 (C)7...”
- A role for lactate dehydrogenases in the survival of Neisseria gonorrhoeae in human polymorphonuclear leukocytes and cervical epithelial cells
Atack, The Journal of infectious diseases 2014 - “...of N. gonorrhoeae strain FA1090 reveals that 3 genes (NGO0639, NGO0890, and NGO1336) are annotated as potential LDHs. The first 2 genes are predicted to be...”
- “...and transfer electrons to the quinone pool. NGO0639 (lldD) and NGO0890 (ldhD) are, respectively, predicted to encode respiratory L- and D-lactate-specific...”
- Proteomic analysis of Neisseria gonorrhoeae biofilms shows shift to anaerobic respiration and changes in nutrient transport and outermembrane proteins
Phillips, PloS one 2012 - “...subunit alpha; F-type H+-transporting ATPase subunit alpha ATP-proton motive force interconversion 1.392 (3) 1.621 (1) NGO0639 d putative L-lactate dehydrogenase; L-lactate dehydrogenase (cytochrome) Anaerobic 1.096 (3) 0.849 (3) NGO0565 AceE; pyruvate dehydrogenase subunit E1 Pyruvate dehydrogenase 0.875 (3) 1.178 (3) Protein fate NGO1422 heat shock protein...”
- “...replicates) averaged. d Protein with more than one functional role assignment provided (Main role/JCVI sub-role): NGO0639, Energy metabolism/Glycolysis/gluconeogenesis. e Protein functional role category tentatively assigned in the present study by orthology to an N. meningitidis protein (see Supplementary Table S6 for details). Fifteen of the 43...”
- Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae
Isabella, BMC genomics 2011 - “...SNF family sodium-dependent transporter Energy metabolism/Oxidation-Reduction NGO0108 -4.0 -5.9 NADPH-dependent FMN reductase Fur, Lrp lldD NGO0639 -7.1 -11.1 L-lactate dehydrogenase eda NGO0713 -3.0 -5.6 KHG-KDPG bifunctional aldolase rpeC NGO0758 -4.8 -3.8 Ribulose-phosphate 3-epimerase fdx NGO0825 -5.3 -5.3 Ferredoxin cisY NGO0918 -3.6 -3.8 Type II citrate synthase...”
- “...are anaerobically repressed (Figure 2 H, I ). RT-PCR confirmed that NGO0108, L-lactate dehydrogenase, lldD (NGO0639), thioredoxin, trx1 (NGO0652), heme oxygenase, hemO (NGO1318), and NADH dehydrogenase component, nqrA (NGO1413) were also anaerobically repressed (Figure 3 ). Analysis of raw RNA-seq data allows for the prediction of...”
CNAG_01080 glycolate oxidase from Cryptococcus neoformans var. grubii H99
40% identity, 90% coverage
CND02080 hypothetical protein from Cryptococcus neoformans var. neoformans JEC21
40% identity, 90% coverage
SM_b20850 L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) from Sinorhizobium meliloti 1021
36% identity, 93% coverage
- mutant phenotype: Specifically important for utilizing L-Rhamnose monohydrate. Automated validation from mutant phenotype: the predicted function (1.1.2.3) was linked to the condition via a SEED subsystem. This annotation was also checked manually.
FUB9_FUSO4 / A0A0D2YG00 Oxidase FUB9; Fusaric acid biosynthesis protein 9; EC 1.-.-.- from Fusarium oxysporum f. sp. lycopersici (strain 4287 / CBS 123668 / FGSC 9935 / NRRL 34936) (Fusarium vascular wilt of tomato) (see 8 papers)
38% identity, 89% coverage
- function: Oxidase; part of the gene cluster that mediates the biosynthesis of fusaric acid, a mycotoxin with low to moderate toxicity to animals and humans, but with high phytotoxic properties (PubMed:25372119). L-aspartate is suggested as fusaric acid amino acid precursor that is activated and further processed to O-acetyl-L- homoserine by cluster enzymes aspartate kinase FUB3 and homoserine O- acetyltransferase FUB5, as well as enzymes of the primary metabolism (By similarity). The polyketide synthase (PKS) FUB1 generates the triketide trans-2-hexenal which is presumptively released by the hydrolase FUB4 and linked to the NRPS-bound amino acid precursor by NAD(P)-dependent dehydrogenase FUB6 (By similarity). FUB1, FUB4, and the non-canonical NRPS Fub8 may form an enzyme complex (By similarity). Further processing of the NRPS-bound intermediate might be carried out by FUB6 and the sulfhydrylase FUB7, enabling a spontaneous electrocyclization to close the carbon backbone of fusaric acid (By similarity). Dihydrofusaric acid is likely to be released via reduction by the thioester reductase (TR) domain of FUB8 whereupon the final oxidation to fusaric acid may (also) be performed by the FMN-dependent dehydrogenase FUB9 (By similarity).
cofactor: FMN
FUB9_GIBM7 / W7NCP1 Oxidase FUB9; Fusaric acid biosynthesis protein 9; EC 1.-.-.- from Gibberella moniliformis (strain M3125 / FGSC 7600) (Maize ear and stalk rot fungus) (Fusarium verticillioides) (see 9 papers)
38% identity, 89% coverage
- function: Oxidase; part of the gene cluster that mediates the biosynthesis of fusaric acid, a mycotoxin with low to moderate toxicity to animals and humans, but with high phytotoxic properties (PubMed:25372119). L-aspartate is suggested as fusaric acid amino acid precursor that is activated and further processed to O-acetyl-L- homoserine by cluster enzymes aspartate kinase FUB3 and homoserine O- acetyltransferase FUB5, as well as enzymes of the primary metabolism (By similarity). The polyketide synthase (PKS) FUB1 generates the triketide trans-2-hexenal which is presumptively released by the hydrolase FUB4 and linked to the NRPS-bound amino acid precursor by NAD(P)-dependent dehydrogenase FUB6 (By similarity). FUB1, FUB4, and the non-canonical NRPS Fub8 may form an enzyme complex (By similarity). Further processing of the NRPS-bound intermediate might be carried out by FUB6 and the sulfhydrylase FUB7, enabling a spontaneous electrocyclization to close the carbon backbone of fusaric acid (By similarity). Dihydrofusaric acid is likely to be released via reduction by the thioester reductase (TR) domain of FUB8 whereupon the final oxidation to fusaric acid may (also) be performed by the FMN-dependent dehydrogenase FUB9 (By similarity).
cofactor: FMN
disruption phenotype: Does not alter fusaric acid production (PubMed:25372119).
SLG_34570 alpha-hydroxy acid oxidase from Sphingobium sp. SYK-6
42% identity, 91% coverage
- Iron acquisition system of Sphingobium sp. strain SYK-6, a degrader of lignin-derived aromatic compounds
Fujita, Scientific reports 2020 - “...squares. Genes: SLG_34530, hypothetical protein; tonB2 , TonB-like protein; fiuA , TBDR; SLG_34560, putative hydroxylase; SLG_34570, putative oxidoreductase; SLG_34580, putative oxidoreductase. ( B D ) -galactosidase activities of SYK-6 cells harbouring pS-t2 ( B ), pS-fiuA ( C ), and pSEVA225 ( D ) grown in...”
LOX_ALIDK / F4G5A4 L-lactate oxidase; LOX; Glycolate oxidase; EC 1.1.3.-; EC 1.1.3.15 from Alicycliphilus denitrificans (strain DSM 14773 / CIP 107495 / K601) (see paper)
45% identity, 91% coverage
- function: Catalyzes the oxidation of (S)-lactate (L-lactate) to pyruvate, with a reduction of O2 to H2O2. To a lesser extent is also able to use glycolate as substrate.
catalytic activity: (S)-lactate + O2 = H2O2 + pyruvate (RHEA:55868)
catalytic activity: glycolate + O2 = glyoxylate + H2O2 (RHEA:25311)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Homotetramer.
C9Y9E7 L-lactate dehydrogenase [cytochrome] from Curvibacter symbiont subsp. Hydra magnipapillata
35% identity, 91% coverage
BOV_RS14715 alpha-hydroxy acid oxidase from Brucella ovis ATCC 25840
36% identity, 92% coverage
BAB2_0315 FMN-dependent alpha-hydroxy acid dehydrogenase:FMN/related compound-binding core from Brucella melitensis biovar Abortus 2308
36% identity, 92% coverage
BMEII0377 L-LACTATE DEHYDROGENASE (CYTOCHROME) from Brucella melitensis 16M
36% identity, 92% coverage
AORI_1496 alpha-hydroxy acid oxidase from Amycolatopsis keratiniphila
47% identity, 89% coverage
- Complete genome sequence and comparative genomic analyses of the vancomycin-producing Amycolatopsis orientalis
Xu, BMC genomics 2014 - “...synthetase lcl|AJ223998.1_cdsid_CAA11773.1 83.57 AORI_1494 oxyD Cytochrome P450 lcl|Y16952.3_cdsid_CAC48370.1 85.35 AORI_1495 hmaS 4-hydroxymandelate synthase lcl|AJ223998.1_cdsid_CAA11761.1 75.56 AORI_1496 hmo 4-hydroxymandelate oxidase lcl|Y16952.3_cdsid_CAC48372.1 85.24 AORI_1497 Antipoter lcl|Y16952.3_cdsid_CAC48373.1 80 AORI_1498 vcaA Oxidase lcl|Y16952.3_cdsid_CAC48374.1 88.04 AORI_1499 vcaE Reductase lcl|Y16952.3_cdsid_CAC48375.1 84.21 AORI_1500 vcaB Aminotransferase lcl|AJ223998.1_cdsid_CAA11782.1 88.62 AORI_1501 vcaD Epimerase lcl|Y16952.3_cdsid_CAC48377.1 85.57 AORI_1502...”
FTN_0217 L-lactate dehydrogenase from Francisella tularensis subsp. novicida U112
33% identity, 91% coverage
- Francisella-arthropod vector interaction and its role in patho-adaptation to infect mammals
Akimana, Frontiers in microbiology 2011 - “...unknown function containing a von Willebrand factor type A (vWA) domain FTN_0214 Valyl-tRNA synthetase valS FTN_0217 l -lactate dehydrogenase lldD FTN_0266 Chaperone Hsp90, heat shock protein HtpG htpG FTN_0275 Hypothetical protein FTN_0330 Septum formation inhibitor-activating ATPase minD FTN_0331 Septum formation inhibitor minC FTN_0337 Fumarate hydratase, class...”
- Molecular bases of proliferation of Francisella tularensis in arthropod vectors
Asare, Environmental microbiology 2010 - “...glutathione synthase/ribosomal protein S6 modification enzyme 3 tnfn1_pw060328p01q150 FTN_0168 lysU lysyl-tRNA synthetase 2 # tnfn1_pw060510p02q178 FTN_0217 L-lactate dehydrogenase 2 tnfn1_pw060323p07q113 FTN_0362 deoxyribodipyrimidine photolyase-related protein 4 tnfn1_pw060323p04q144 FTN_0406 sterol desaturase 3 # tnfn1_pw060418p01q189 FTN_0406 sterol desaturase 6 # tnfn1_pw060328p06q134 FTN_0443 maeA NAD-dependent malic enzyme 5 # tnfn1_pw060328p06q125...”
- “...membrane protein tnfn1_pw060418p03q133 FTN_0199 cyoE heme O synthase tnfn1_pw060323p04q102 FTN_0211 pcp pyrrolidone carboxylylate peptidase tnfn1_pw060510p02q178 FTN_0217 L-lactate dehydrogenase tnfn1_pw060420p04q134 FTN_0297 conserved protein of unknown function tnfn1_pw060418p03q147 FTN_0299 putP proline:Na+ symporter tnfn1_pw060420p02q146 FTN_0300 glycosyl transferase, group 2 tnfn1_pw060328p01q167 FTN_0330 minD septum formation inhibitor-activating ATPase tnfn1_pw060323p08q146 FTN_0331 minC...”
- Molecular complexity orchestrates modulation of phagosome biogenesis and escape to the cytosol of macrophages by Francisella tularensis
Asare, Environmental microbiology 2010 - “...glutathione synthase/ribosomal protein S6 modification enzyme 3 tnfn1_pw060328p01q150 FTN_0168 lysU lysyl-tRNA synthetase 2 # tnfn1_pw060510p02q178 FTN_0217 L-lactate dehydrogenase 2 tnfn1_pw060323p07q113 FTN_0362 deoxyribodipyrimidine photolyase-related protein 4 tnfn1_pw060323p04q144 FTN_0406 sterol desaturase 3 # tnfn1_pw060418p01q189 FTN_0406 sterol desaturase 6 # tnfn1_pw060328p06q134 FTN_0443 maeA NAD-dependent malic enzyme 5 # tnfn1_pw060328p06q125...”
- “...membrane protein tnfn1_pw060418p03q133 FTN_0199 cyoE heme O synthase tnfn1_pw060323p04q102 FTN_0211 pcp pyrrolidone carboxylylate peptidase tnfn1_pw060510p02q178 FTN_0217 L-lactate dehydrogenase tnfn1_pw060420p04q134 FTN_0297 conserved protein of unknown function tnfn1_pw060418p03q147 FTN_0299 putP proline:Na+ symporter tnfn1_pw060420p02q146 FTN_0300 glycosyl transferase, group 2 tnfn1_pw060328p01q167 FTN_0330 minD septum formation inhibitor-activating ATPase tnfn1_pw060323p08q146 FTN_0331 minC...”
- Reciprocal analysis of Francisella novicida infections of a Drosophila melanogaster model reveal host-pathogen conflicts mediated by reactive oxygen and imd-regulated innate immune response
Moule, PLoS pathogens 2010 - “...histidine kinase qsec x FTN_1582 FFF0134 hypothetical membrane protein x FTN_0210 FTT0295 hypothetical protein x FTN_0217 FTT0303c L-lactate dehydrogenase lldD x FTN_0493 FTT0397 5-methylthioadenosine\S-adenosylhomocysteine nucleosidase mtn x FTN_0494 FTT0398c hypothetical membrane protein x FTN_0495 FTT0399c BNR/Asp-box repeat protein x FTN_0554 FTT0463 tRNA/rRNA methyltransferase yibK x x...”
- Working toward the future: insights into Francisella tularensis pathogenesis and vaccine development
Pechous, Microbiology and molecular biology reviews : MMBR 2009 - “...FTN_0198 FTN_0199 FTN_0202 FTN_0205 FTN_0208 FTN_0210 FTN_0211 FTN_0217 FTN_0229 FTN_0240 FTN_0241 FTN_0248 FTN_0265 FTN_0266 purA cyoB cyoC cyoD cyoE pdxY...”
- Genome-wide screen in Francisella novicida for genes required for pulmonary and systemic infection in mice
Kraemer, Infection and immunity 2009 - “...and/or spleena FTN FTN_0169 FTN_0199 FTN_0205 FTN_0208 FTN_0217 FTN_0280 FTN_0281 FTN_0292 FTN_0297 FTN_0298 tmpT tyrA ribH Defense mechanisms Hypothetical,...”
NP_879338 L-lactate dehydrogenase from Bordetella pertussis Tohama I
BP0484 alpha-hydroxy acid oxidase from Bordetella pertussis Tohama I
37% identity, 90% coverage
H1A07_09050 alpha-hydroxy-acid oxidizing protein from Lactobacillus taiwanensis
36% identity, 88% coverage
1huvA / P05414,P20932 Crystal structure of a soluble mutant of the membrane-associated (s)- mandelate dehydrogenase from pseudomonas putida at 2.15a resolution (see paper)
38% identity, 92% coverage
- Ligand: flavin mononucleotide (1huvA)
bll6401 L-lactate dehydrogenase from Bradyrhizobium japonicum USDA 110
37% identity, 85% coverage
LJ1826 glycolate oxidase from Lactobacillus johnsonii NCC 533
38% identity, 81% coverage
FUB9_GIBF5 / S0DRI9 Oxidase FUB9; Fusaric acid biosynthesis protein 9; EC 1.-.-.- from Gibberella fujikuroi (strain CBS 195.34 / IMI 58289 / NRRL A-6831) (Bakanae and foot rot disease fungus) (Fusarium fujikuroi) (see 8 papers)
37% identity, 92% coverage
- function: Oxidase; part of the gene cluster that mediates the biosynthesis of fusaric acid, a mycotoxin with low to moderate toxicity to animals and humans, but with high phytotoxic properties (PubMed:26662839). L-aspartate is suggested as fusaric acid amino acid precursor that is activated and further processed to O-acetyl-L- homoserine by cluster enzymes aspartate kinase FUB3 and homoserine O- acetyltransferase FUB5, as well as enzymes of the primary metabolism (PubMed:26662839). The polyketide synthase (PKS) FUB1 generates the triketide trans-2-hexenal which is presumptively released by the hydrolase FUB4 and linked to the NRPS-bound amino acid precursor by NAD(P)-dependent dehydrogenase FUB6 (PubMed:26662839). FUB1, FUB4, and the non-canonical NRPS Fub8 may form an enzyme complex (PubMed:26662839). Further processing of the NRPS-bound intermediate might be carried out by FUB6 and the sulfhydrylase FUB7, enabling a spontaneous electrocyclization to close the carbon backbone of fusaric acid (PubMed:26662839). Dihydrofusaric acid is likely to be released via reduction by the thioester reductase (TR) domain of FUB8 whereupon the final oxidation to fusaric acid may (also) be performed by the FMN- dependent dehydrogenase FUB9 (PubMed:26662839).
cofactor: FMN
STY1444 putative glycolate oxidase from Salmonella enterica subsp. enterica serovar Typhi str. CT18
39% identity, 82% coverage
- Genomic Comparison of the Closely Related Salmonella enterica Serovars Enteritidis and Dublin
Betancor, The open microbiology journal 2012 - “...in S . Dublin strains include a membrane transport protein (SG3368), a putative glycolate oxidase (STY1444) and several phage-related proteins. Microarray methodology allowed us to detect only presence or absence/divergence of genes, but not small variations in gene sequences. Considering that pseudogene accumulation has been postulated...”
- “...SPA possible membrane transport protein Sing Du3 STY0602 SDT, SBG, SPA phage integrase Sing Du4 STY1444 TY2, STM, SDT, SL, SBG, SPA putative glycolate oxidase Sing Du5 STY2690 TY2, STM, SDT,SL hypothetical protein Sing Du6 STY3029 NO transposase CT18: S. Typhi CT18, TY2: S. Typhi Ty2,...”
- Prevalence of Salmonella enterica in poultry and eggs in Uruguay during an epidemic due to Salmonella enterica serovar Enteritidis
Betancor, Journal of clinical microbiology 2010 - “...STY0302-0310 STY0313-0314 STY0756-0768 STY0894 STY1413 STY1444 STY1911 STY2043-2044 STY2349-2350 STY2361 STY2364 STY2690 STY3092 STY3093 STY3277 STY3291-3292...”
E0NE46 L-lactate oxidase from Pediococcus acidilactici DSM 20284
37% identity, 92% coverage
STM1620 putative oxidase from Salmonella typhimurium LT2
STM14_1959 lactate oxidase from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
38% identity, 81% coverage
- Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits
Seif, Nature communications 2018 - “...) Glycerophosphodiester phosphodiesterase (C-O2+/, P-O2+/) Sn-Glycero-3-phosphocholine STM2037 ( pduF ) (R)-Propane-1,2-diol facilitated transport (C-O2+) (R)-Propane-1,2-diol STM1620 Glycolate oxidase (C-O2+) Glycolate STM0154 ( lpdA ) Pyruvate dehydrogenase and 2-Oxogluterate dehydrogenase (C-O2-) DCMP and Deoxyuridine and DUMP and Deoxycytidine Our predictions indicate that the serovars adapted to cold-blooded...”
- A Trade-Off for Maintenance of Multidrug-Resistant IncHI2 Plasmids in Salmonella enterica Serovar Typhimurium through Adaptive Evolution
Zhang, mSystems 2022 - “...and populations. These genes were primarily associated with oxidative stress ( ahpC , ybgS , STM14_1959 , and STM14_2022 ), DNA repair ( umuC and alkB ), outer membrane permeability ( ompC ), osmotic stress ( osmY ), and sugar transporter ( yjiJ ), as well...”
- “...protein YbgS containing two cysteine residues was probably associated with redox reactions ( 12 ). STM14_1959 and STM14_2022 encode a putative oxidoreductase and oxidase, respectively. These two genes act together with ahpC and ybgS as antioxidant-related genes, and inactivation of these genes most likely alters the...”
SC1616 putative oxidase from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
39% identity, 82% coverage
6r9vA / E0NE46 Crystal structure of pediococcus acidilactici lactate oxidase a94g mutant (see paper)
37% identity, 92% coverage
- Ligand: flavin mononucleotide (6r9vA)
Q43775 (S)-2-hydroxy-acid oxidase (Fragment) from Solanum lycopersicum
43% identity, 77% coverage
- Comparative Membrane-Associated Proteomics of Three Different Immune Reactions in Potato
Burra, International journal of molecular sciences 2018 - “...1.39 0.98 1.22 E2FAG4 COSII_At5g14320 1.15 1.2 1.73 Q9ZWH9 Elongation factor 1- 0.78 0.35 0.48 Q43775 Glycolate oxidase (EC 1.1.3.15) 1.01 0.18 0.67 PGSC0003DMP400009092 Glyoxisomal malate dehydrogenase 1.65 1.01 1.34 Q9LLE0 Hexose transporter 0.7 0.15 0.24 PGSC0003DMP400035078 Hydrolase, acting on ester bonds 1.91 2.36 2.58 B2D2G3...”
LSA1399 L-Lactate oxidase from Lactobacillus sakei subsp. sakei 23K
37% identity, 93% coverage
G3I6D1 3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type 2 from Cricetulus griseus
43% identity, 41% coverage
W1QKE8 L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) from Ogataea angusta (see 2 papers)
36% identity, 61% coverage
QULF_PENCI / P0DUR7 FMN-dependent alpha-hydroxy acid dehydrogenase qulF; Quinolactacin A2 biosynthesis cluster protein F; EC 1.13.12.- from Penicillium citrinum (see paper)
37% identity, 84% coverage
- function: FMN-dependent alpha-hydroxy acid dehydrogenase; part of the gene cluster that mediates the biosynthesis of quinolactacin A2 (QUL A2), a fungal alkaloid that features a quinolone-gamma-lactam hybrid, which is a potential pharmacophore for the treatment of cancer and Alzheimer's disease (PubMed:32663343). The quinolone-gamma-lactam hybrid scaffold is synthesized from the combination of L-isoleucine (L- Ile) and the nonproteinogenic amino acid L-kynurenine, followed by quinolone cyclization, oxidative decarboxylation, and lactam formation (PubMed:32663343). Additionally, the N-methyl group is derived from methionine, which might be catalyzed by an S-adenosylmethionine (SAM)- dependent methyltransferase (PubMed:32663343). Bioconversion of L- tryptophan to L-kynurenine could be catalyzed by the indoleamine-2,3- dioxygenase (IDO) qulI to produce an unstable product, N-formyl-L- kynurenine, followed by kynurenine formamidase catalyzed hydrolysis (PubMed:32663343). QulM then acts as a methyltransferase that methylates L-kynurenine at the N-4 position (PubMed:32663343). The FMN- dependent alpha-hydroxy acid dehydrogenase qulF than functions as an oxidative decarboxylase which converts N-methylkynurenine into 2- aminobenzoylacetamide via 2 tandem reactions, including dehydrogenation and decarboxylation (PubMed:32663343). An amidase located outside of the qul gene cluster further produces the unstable beta-keto acid precursor N-methyl-2-aminobenzoylacetate, which could be spontaneously dehydrated to form N-methyl-4-hydroxy-2-quinolone (PubMed:32663343). The NRPS qulB is able to incorporate N-methyl-2-aminobenzoylacetate and efficiently compete with the spontaneous reaction (PubMed:32663343). By further extending the beta-keto acid with L-Ile, qulA performs a Dieckmann condensation to form the gamma-lactam ring and release a 4- ketopyrrolidinone intermediate from the assembly line (PubMed:32663343). This intermediate could plausibly further undergo a spontaneous cyclization to yield the final quinolone-gamma-lactam hybrid structure (PubMed:32663343).
cofactor: FMN
disruption phenotype: Impairs the production of quinolactacin A2 and leads to the accumulatin of N-methylkynurenine.
FGSG_03984 hypothetical protein from Fusarium graminearum PH-1
37% identity, 79% coverage
- Transcriptome-Based Discovery of Fusarium graminearum Stress Responses to FgHV1 Infection
Wang, International journal of molecular sciences 2016 - “...acid transporter protein FGSG_06127 0.146473 6.70 10 85 Formate dehydrogenase FGSG_07582 0.152292 0 MFS transporter FGSG_03984 0.152931 1.161 10 3 l -lactate dehydrogenase FGSG_01450 0.157498 6.18 10 57 Domain: Calcipressin FGSG_11272 0.178327 1.05 10 13 ABC transporter FGSG_07598 0.183762 2.45 10 32 Domain: Alcohol acetyltransferase FGSG_07509...”
CH_124019 putative FMN dependent dehydrogenase [Aspergillus fumigatus Af293] from Magnaporthe grisea 70-15 (see paper)
39% identity, 78% coverage
A0A099P7X2 L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) from Pichia kudriavzevii (see paper)
38% identity, 57% coverage
LOX_LENH9 / C0XIJ3 L-lactate oxidase; LOX; EC 1.1.3.- from Lentilactobacillus hilgardii (strain ATCC 8290 / DSM 20176 / CCUG 30140 / JCM 1155 / KCTC 3500 / NBRC 15886 / NCIMB 8040 / NRRL B-1843 / 9) (see paper)
38% identity, 89% coverage
- function: Catalyzes the oxidation of (S)-lactate (L-lactate) to pyruvate, with a reduction of O2 to H2O2 (PubMed:34555022). May be involved in the utilization of L-lactate as an energy source for growth (By similarity).
catalytic activity: (S)-lactate + O2 = H2O2 + pyruvate (RHEA:55868)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Homotetramer.
Bphy_5156 L-lactate dehydrogenase (cytochrome) from Burkholderia phymatum STM815
38% identity, 78% coverage
PAJ_p0276 FMN-dependent L-lactate dehydrogenase LldD from Pantoea ananatis AJ13355
38% identity, 88% coverage
Bphy_5156 alpha-hydroxy acid oxidase from Paraburkholderia phymatum STM815
38% identity, 79% coverage
Ac3H11_1623 L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) from Acidovorax sp. GW101-3H11
35% identity, 89% coverage
- mutant phenotype: Specifically important for utilizing Sodium D,L-Lactate; Sodium L-Lactate. Automated validation from mutant phenotype: the predicted function (1.1.2.3) was linked to the condition via a SEED subsystem. This annotation was also checked manually.
lctO / D4YFM2 lactate oxidase monomer (EC 1.1.3.2) from Aerococcus viridans (strain ATCC 11563 / DSM 20340 / CCUG 4311 / JCM 20461 / NBRC 12219 / NCTC 8251 / M1) (see 29 papers)
D4YFM2 L-lactate oxidase (EC 1.1.3.2) from Aerococcus viridans (see 2 papers)
WP_003142047 L-lactate oxidase from Aerococcus viridans
36% identity, 92% coverage
6bfgA / P20932 Crystal structure of monotopic membrane protein (s)-mandelate dehydrogenase (see paper)
35% identity, 92% coverage
- Ligand: flavin mononucleotide (6bfgA)
mdlB / P20932 (S)-mandelate dehydrogenase (EC 1.1.99.31) from Pseudomonas putida (see 2 papers)
MDLB_PSEPU / P20932 (S)-mandelate dehydrogenase; MDH; L(+)-mandelate dehydrogenase; EC 1.1.99.31 from Pseudomonas putida (Arthrobacter siderocapsulatus) (see 5 papers)
P20932 (S)-mandelate dehydrogenase (EC 1.1.99.31) from Pseudomonas putida (see 5 papers)
35% identity, 88% coverage
- function: Catalyzes the dehydrogenation of (S)-mandelate to phenylglyoxylate (benzoylformate) (PubMed:10493804, PubMed:19465768). Is likely involved in the utilization of mandelate as a sole source of carbon and energy for growth (Probable). Active in vitro with the artificial electron acceptors 2,6-dichlorophenolindophenol (DCPIP) or ferricyanide, but in vivo most likely transfer the electron pair from the reduced flavin to a component of the electron transport chain in the membrane, possibly a quinone (PubMed:10493804, PubMed:19465768). Shows very low activity with oxygen as the electron acceptor, and also with 3-indolelactate and medium chain 2-hydroxyacids as substrates (PubMed:10493804, PubMed:19465768).
catalytic activity: (S)-mandelate + A = AH2 + phenylglyoxylate (RHEA:15749)
cofactor: FMN
subunit: Homotetramer. - Flavin Mononucleotide-Dependent l-Lactate Dehydrogenases: Expanding the Toolbox of Enzymes for l-Lactate Biosensors
Tsvik, ACS omega 2022 - “...oleracea P05414, and Cyanidioschyzon merolae M1VAT1; FCB2 from Saccharomyces cerevisiae P00175; MDH from Pseudomonas putida P20932; HAO from Rattus norvegicus Q07523; HMO from Amycolatopsis orientalis O52792; and mLDH from Pseudomonas stutzeri ADL63037) were used as queries for individual database searches on NCBI and UniProt using blastp...”
- Divergent evolution of a beta/alpha-barrel subclass: detection of numerous phosphate-binding sites by motif search
Bork, Protein science : a publication of the Protein Society 1995 - “...mdlbgsepu 297 GKPVLIDSGFRRGSDIVKAL.ALGAEAVLLGRATLYGLAARGETGVDE P20932 lctd-ecoli 300 DIAILADSGIRNGLDWRMI.ALGADTVLLGRAFLYALATA(3QAGVAN P33232 la2m_mycsm 314...”
H16_B0460 L-Lactate cytochrome reductase from Ralstonia eutropha H16
H16_B0460 alpha-hydroxy acid oxidase from Cupriavidus necator H16
34% identity, 92% coverage
LOX_AERVM / Q44467 L-lactate oxidase; LOD; LOX; Lactate oxidase; EC 1.1.3.- from Aerococcus viridans (strain ATCC 11563 / DSM 20340 / CCUG 4311 / JCM 20461 / NBRC 12219 / NCTC 8251 / M1) (see 11 papers)
Q44467 L-lactate dehydrogenase (EC 1.1.1.27); L-lactate oxidase (EC 1.1.3.2) from Aerococcus viridans (see 18 papers)
2du2A / Q44467 Crystal structure analysis of the l-lactate oxidase (see paper)
36% identity, 92% coverage
- function: Catalyzes the oxidation of (S)-lactate (L-lactate) to pyruvate, with a reduction of O2 to H2O2 (PubMed:25423902, PubMed:26260739, PubMed:27302031, PubMed:2818595, PubMed:8589073, Ref.1). Cannot oxidize D-lactate, glycolate, and D,L-2-hydroxybutanoate (PubMed:2818595). May be involved in the utilization of L-lactate as an energy source for growth (By similarity).
catalytic activity: (S)-lactate + O2 = H2O2 + pyruvate (RHEA:55868)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Homotetramer. - Ligand: flavin mononucleotide (2du2A)
- Flavin Mononucleotide-Dependent l-Lactate Dehydrogenases: Expanding the Toolbox of Enzymes for l-Lactate Biosensors
Tsvik, ACS omega 2022 - “...Sequence Similarity Networks In July 2020, 13 experimentally characterized HAOx sequences (LOx from Aerococcus viridans Q44467, Lactococcus lactis A0A4Y3JPV3, Nostoc sp. PCC 7120 Q8Z0C8, and Chlamydomonas reinhardtii F8WQN2; LMO from Mycolicibacterium smegmatis P21795; GLO from Homo sapiens Q9UJM8, Spinacia oleracea P05414, and Cyanidioschyzon merolae M1VAT1; FCB2...”
SP_0715 lactate oxidase from Streptococcus pneumoniae TIGR4
35% identity, 97% coverage
- The Streptococcus pneumoniae transcriptome in patient cerebrospinal fluid identifies novel virulence factors required for meningitis
Wall, 2024 - Role of the pyruvate metabolic network on carbohydrate metabolism and virulence in Streptococcus pneumoniae
Echlin, Molecular microbiology 2020 - “...insertion of the cassette and deletion of the gene. Deletion mutants of the genes lctO (Sp_0715), spxB (Sp_0730), and pdhC (Sp_1163-1164) were generated in a similar manner as previously described ( Echlin et al., 2016 ). Mouse studies For bacterial burden and survival studies, TIGR4 and...”
- Multi-omic profiling to assess the effect of iron starvation in Streptococcus pneumoniae TIGR4
Jiménez-Munguía, PeerJ 2018 - “...proteolytic subunit 81 Cytoplasmic TS7 Decreased SP_2190 Choline binding protein A 174 Extracellular TS8 Decreased SP_0715 Lactate oxidase 686 Cytoplasmic TS9 Decreased SP_2216 Secreted 45 kd protein 512 Extracellular TS10 Decreased SP_1456 Peptide deformylase (PDF) 251 Cytoplasmic TS11 Decreased SP_0459 Formate acetyltransferase 152 Cytoplasmic TS12 Decreased...”
- Expression of the lux genes in Streptococcus pneumoniae modulates pilus expression and virulence
Herbert, PloS one 2018 - “...Frameshift. Removal of stop codon SP_0491 Hypothetical protein C deletion Frameshift. Removal of stop codon SP_0715 Lactate oxidase (LctO) SNP (G>T Glycine > stop codon SP_0730 Pyruvate oxidase (SpxB) SNP (G>T) Glutamine > stop codon SP_1715 Hypothetical protein G Insertion Frameshift. Premature stop codon SP_1732 Serine/Threonine...”
- Pyruvate Oxidase as a Critical Link between Metabolism and Capsule Biosynthesis in Streptococcus pneumoniae
Echlin, PLoS pathogens 2016 - “...in this study are listed in S4 Table . Bacterial Constructs The spxB (Sp_0730), lctO (Sp_0715), and pdhc (E1 alpha and beta subunits; Sp_1163 and Sp_1164) mutants were created via splicing by overhang extension PCR (SOE-PCR) [ 57 ]. Briefly, 1-kb upstream and downstream fragments of...”
lp_3586 lactate oxidase from Lactobacillus plantarum WCFS1
38% identity, 89% coverage
CIMG_08907 cytochrome b2 from Coccidioides immitis RS
34% identity, 71% coverage
C0J08_14140 alpha-hydroxy acid oxidase from Marinomonas sp. CT5
37% identity, 84% coverage
- Genomic insights into indole-3-acetic acid catabolism in the marine algae-associated bacterium, Marinomonas sp. NFXS50
Bertrand, Access microbiology 2024 - “...C0J08_14150 Oxidoreductase iacF MMWYL1_RS09290, 95.9% ABY62762.1, 61.8% C0J08_14145 Flavin reductase iacG MMWYL1_RS09295, 98.8% ABY62763.1, 62.8% C0J08_14140 Alpha-hydroxy-acid oxidizing enzyme MMWYL1_RS09300, 96.1% n.f. C0J08_14135 Amidase iacH MMWYL1_RS09305, 92.5% ABY62765.1, 28.6% n.f.not found Fig. 2. Representation of Marinomonas sp. MWYL1 and Marinomonas sp. NFXS50 iac gene clusters and...”
- “...429 aa vs P. putida 1290, 374 aa) and overall characteristics. Moreover, the NFXS50 gene (C0J08_14140, iac? ) found in the upstream region of the iacH homolog was not detected in the P. putida 1290 iac gene cluster. This gene encoded an alpha-hydroxy acid dehydrogenase family...”
SPD_0621 lactate oxidase from Streptococcus pneumoniae D39
spr0627 Lactate oxidase from Streptococcus pneumoniae R6
SPND141_00711 L-lactate oxidase from Streptococcus pneumoniae
35% identity, 97% coverage
- Transcriptional and metabolic effects of glucose on Streptococcus pneumoniae sugar metabolism
Paixão, Frontiers in microbiology 2015 - “...eno Enolase 0.61 SPD_1823 gap Glyceraldehyde-3-phosphate dehydrogenase 0.53 DOWNSTREAM PYRUVATE SPD_0420 pflB Pyruvate formate-lyase 1.25 SPD_0621 lcto Lactate oxidase 0.38 SPD_0985 pta Phosphotransacetylase 0.64 SPD_1834 adh Bifunctional acetaldehyde-CoA/alcohol dehydrogenase 1.00 SUGAR-SPECIFIC TRANSPORTERS c SPD_0088 ABC transporter, permease protein 0.73 SPD_0089 ABC transporter, permease protein 0.80 SPD_0279...”
- Host glycan sugar-specific pathways in Streptococcus pneumoniae: galactose as a key sugar in colonisation and infection [corrected]
Paixão, PloS one 2015 - “...IID 4.4 SPD_1496 PTS system transporter subunit IIBC 4.4 SPD_1006 glgC Glucose 1-phosphate adenylyltransferase 4.4 SPD_0621 lctO Lactate oxidase 4.0 SPD_1935 malC Maltodextrin ABC transporter permease 3.9 SPD_0420 pflB Formate acetyltransferase 3.7 SPD_1007 glgD Glucose 1-phosphate adenylyltransferase, GlgD subunit 3.5 SPD_1005 glgB Glycogen branching protein 2.9...”
- iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6
Dias, Frontiers in microbiology 2019 - “...in mixed-acid fermentation, namely pfl (spr0415), pflF (spr0232), ackA (spr1854), adh (spr1866), pta (spr1007), lctO (spr0627), and activates ldh (spr1100). When galactose is used as the carbon source, the enzymes downstream of pyruvate exhibit alleviation of repression of the genes involved mixed-acid fermentation. Simulations Software Optflux...”
- “...shown in study 1, and were therefore set to 10% of the RDFs while lctO (spr0627) was reduced to 0%. Likewise, for study 2, the flux of pfl genes (spr0415 and spr0232), adh (spr1866), pta (spr1007), and lctO (spr0627) were restricted to zero, to simulate growth...”
- Long Persistence of a Streptococcus pneumoniae 23F Clone in a Cystic Fibrosis Patient
Rieger, mSphere 2017 - “...were absent in D122 and D141. One gene cluster, SPND122_00705 to SPND122_00709 and SPND141_00707 to SPND141_00711 related to the R6 genes spr0623 to spr062 7 (ABC transporter, lactate monooxygenase, 2-lysyl-tRNA synthetase) were not found in D219. However, since these genes are all located on small contigs,...”
Snov_0680 alpha-hydroxy acid oxidase from Ancylobacter novellus DSM 506
35% identity, 91% coverage
E6SCX5 (S)-2-hydroxy-acid oxidase from Intrasporangium calvum (strain ATCC 23552 / DSM 43043 / JCM 3097 / NBRC 12989 / NCIMB 10167 / NRRL B-3866 / 7 KIP)
38% identity, 86% coverage
LOX_STRIN / O33655 L-lactate oxidase; LOX; EC 1.1.3.- from Streptococcus iniae (Streptococcus shiloi) (see paper)
O33655 L-lactate oxidase (EC 1.1.3.2) from Streptococcus iniae (see paper)
35% identity, 89% coverage
- function: Catalyzes the oxidation of (S)-lactate (L-lactate) to pyruvate, with a reduction of O2 to H2O2. Is likely involved in the L- lactate aerobic metabolism of S.iniae that enables the bacterium to utilize L-lactate as an energy source for growth under aerobic conditions in the absence (or at low concentrations) of glucose.
catalytic activity: (S)-lactate + O2 = H2O2 + pyruvate (RHEA:55868)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Homotetramer.
2j6xH / Q44467 The crystal structure of lactate oxidase (see paper)
34% identity, 92% coverage
- Ligand: flavin mononucleotide (2j6xH)
VDAG_08961 cytochrome b2 from Verticillium dahliae VdLs.17
34% identity, 69% coverage
- The bZip Transcription Factor VdMRTF1 is a Negative Regulator of Melanin Biosynthesis and Virulence in Verticillium dahliae
Lai, Microbiology spectrum 2022 - “...of DEGs (VDAG_00117, VDAG_00767, VDAG_02942, VDAG_03485, VDAG_03495, VDAG_03909, VDAG_04020, VDAG_04798, VDAG_06349, VDAG_06717, VDAG_06722, VDAG_07197, and VDAG_08961) enriched in oxidoreductase activity were upregulated, the expression of the rest of DEGs (VDAG_01286, VDAG_03335, VDAG_03969, VDAG_07187, VDAG_07587, VDAG_08214, VDAG_10051, VDAG_10407, and VDAG_10485) were downregulated ( Fig.6D ). These results...”
CNAG_05169 L-lactate dehydrogenase (cytochrome) from Cryptococcus neoformans var. grubii H99
38% identity, 65% coverage
W6W585 (S)-2-hydroxy-acid oxidase from Rhizobium sp. (strain CF080)
36% identity, 82% coverage
CNL04570 hypothetical protein from Cryptococcus neoformans var. neoformans JEC21
38% identity, 65% coverage
A9QH69 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15); L-lactate oxidase (EC 1.1.3.2) from Streptococcus iniae (see paper)
34% identity, 92% coverage
- Discovery of Two Novel Oxidases Using a High-Throughput Activity Screen
Rembeza, Chembiochem : a European journal of chemical biology 2022 - “...for expression of a HexNAcO (A3RXB7), and a control protein, peroxide producing lactate oxidase (LacO, A9QH69), were transformed into E. coli BL21(DE3) cells. Overnight cultures were set up in LB medium with 100g/mL carbenicillin at 30C. Next morning the OD 600 of the cultures was set...”
BPSS1800 putative dehydrogenase from Burkholderia pseudomallei K96243
36% identity, 86% coverage
RL0444 putative lactate dehydrogenase from Rhizobium leguminosarum bv. viciae 3841
37% identity, 90% coverage
6m73A / I6SYK8 Crystal structure of enterococcus hirae l-lactate oxidase in complex with d-lactate form ligand
35% identity, 90% coverage
- Ligand: 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydro-2h-benzo[g]pteridin-1-id-10(5h)-yl)-5-o-phosphonato-d-ribitol (6m73A)
Q9CG58 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Lactococcus lactis (see 2 papers)
38% identity, 83% coverage
R7SNP0 Glyoxylate dehydrogenase from Dichomitus squalens (strain LYAD-421)
35% identity, 69% coverage
LLKF_1317 L-lactate oxidase from Lactococcus lactis subsp. lactis KF147
38% identity, 83% coverage
Q87G18 L-lactate dehydrogenase from Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
VPA1499 L-lactate dehydrogenase from Vibrio parahaemolyticus RIMD 2210633
35% identity, 90% coverage
- Comparative Proteomics and Secretomics Revealed Virulence and Antibiotic Resistance-Associated Factors in Vibrio parahaemolyticus Recovered From Commonly Consumed Aquatic Products
Zhu, Frontiers in microbiology 2020 - “...4.65 (3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity,3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity, trans-2-decenoyl-acyl-carrier-protein isomerase activity, fatty acid biosynthetic process, cytoplasm P86 Q87G18 L -Lactate dehydrogenase lldD 41,399.35 6.04 9.50 FMN binding, lactate dehydrogenase activity, lactate oxidation, cell inner membrane, Peripheral membrane protein, plasma membrane P87 A0A0D1GKR8 Glycerol-3-phosphate dehydrogenase glpD 58,535.82 6.09 18.88...”
- Bacterial dormancy: A subpopulation of viable but non-culturable cells demonstrates better fitness for revival
Wagley, PLoS pathogens 2021 - “...the significantly upregulated proteins belonged to metabolic functional categories and included a lactate dehydrogenase (LldD; VPA1499) one of the most highly abundant proteins in both P1 and P2 subpopulations. We demonstrated that deletion of the lactate dehydrogenase encoding gene caused the cells to enter the VBNC...”
- “...VP0622, VP0589 (YajC) involved in intracellular trafficking and secretion, VP2817 (HfQ) assigned to translation category, VPA1499 (LldD), VP1161 and VP1053 involved in energy production and conversion, VP0240 involved in carbohydrate metabolism and VP0171 and VP0174 involved in inorganic ion transport and metabolism. We identified another 90...”
- Insights into Vibrio parahaemolyticus CHN25 response to artificial gastric fluid stress by transcriptomic analysis
Sun, International journal of molecular sciences 2014 - “...VP0325 Chn25_0313 3.5504 Malate dehydrogenase VP2519 ( aceE ) Chn25_2453 2.132 Pyruvate dehydrogenase subunit E1 VPA1499 ( lldD ) Chn25A_1389 8.5267 l -lactate dehydrogenase Oxidative phosphorylation VPA0631 Chn25A_1023 0.464 Putative protoheme IX farnesyltransferase VPA0544 Chn25A_1156 0.4221 Protoheme IX farnesyltransferase VP2841 Chn25_2763 2.102 Fumarate reductase iron-sulfur subunit...”
- “...stress. Of these, five genes were down-regulated, and the others were up-regulated. Interestingly, the lldD (VPA1499) gene encoding an l -lactate dehydrogenenase displayed an increase of 8.53-fold in expression, which degrades l -lactate to pyruvate. Moreover, the conversion of malate to pyruvate catalyzed by a malate...”
WU75_03655 FMN-dependent L-lactate dehydrogenase LldD from Vibrio parahaemolyticus
35% identity, 90% coverage
HD0084 L-lactate dehydrogenase from Haemophilus ducreyi 35000HP
35% identity, 90% coverage
- Haemophilus ducreyi Seeks Alternative Carbon Sources and Adapts to Nutrient Stress and Anaerobiosis during Experimental Infection of Human Volunteers
Gangaiah, Infection and immunity 2016 - “...359 139 165 174 134 223 194 97 410 183 HD0084 HD0953 HD1000 HD1027 glpC HD1171 HD1226 hhdA HD1622 HD1765 HD0085 HD0954 HD1001 HD1028 ribD HD1172 HD1227 HD1328...”
- The Haemophilus ducreyi Fis protein is involved in controlling expression of the lspB-lspA2 operon and other virulence factors
Labandeira-Rey, Infection and immunity 2013 - “...previously (23, 34) on three independent biological replicates, using HD0084 (ldh) to normalize the amount of cDNA per sample. The fold change of each gene was...”
- Activation of CpxRA in Haemophilus ducreyi primarily inhibits the expression of its targets, including major virulence determinants
Gangaiah, Journal of bacteriology 2013 - “...ackA fumC Lipid biosynthesis, HD1253 Anaerobic respiration HD0084 HD0344-47h HD1110-12h HD1393-4h HD1456-7h HD1986 ATP synthase, HD0003-11h HD0003, atpB, atpE,...”
LOX_LACRM / C2K1F0 L-lactate oxidase; LOX; EC 1.1.3.- from Lacticaseibacillus rhamnosus (strain LMS2-1) (see paper)
39% identity, 86% coverage
- function: Catalyzes the oxidation of (S)-lactate (L-lactate) to pyruvate, with a reduction of O2 to H2O2. To a lesser extent is also able to use 2-hydroxyoctanoate as substrate (PubMed:34555022). May be involved in the utilization of L-lactate as an energy source for growth (By similarity).
catalytic activity: (S)-lactate + O2 = H2O2 + pyruvate (RHEA:55868)
catalytic activity: 2-hydroxyoctanoate + O2 = 2-oxooctanoate + H2O2 (RHEA:67940)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Homotetramer.
An04g01450 uncharacterized protein from Aspergillus niger
35% identity, 81% coverage
AFUA_4G03120 mitochondrial cytochrome b2, putative from Aspergillus fumigatus Af293
34% identity, 70% coverage
CND03480 hypothetical protein from Cryptococcus neoformans var. neoformans JEC21
34% identity, 64% coverage
- Unisexual reproduction drives meiotic recombination and phenotypic and karyotypic plasticity in Cryptococcus neoformans
Sun, PLoS genetics 2014 - “...CND03160 CND03170 17 854912 JOHE40301 JOHE40302 BsaHI Inter- CND03240 CND03250 18 878777 JOHE40303 JOHE40304 AccI CND03480 19 944503 JOHE23353 JOHE23354 HphI CND03960 20 1096841 JOHE23357 JOHE23358 AflIII Inter- CND04040 CND04050 21 8 1129340 JOHE40317 JOHE40318 EcoRV CND04340 22 1203443 JOHE23361 JOHE23362 Sau96I CND04760 23 1307202 JOHE27442...”
- “...17/18 Inter- CND03160 CND03170 Inter- CND03240 CND03250 0 24 >240 2 18/19 Inter- CND03240 CND03250 CND03480 7.5 66 8.8 <LGII> 20/21 CND03960 Inter- CND04040 CND04050 0 32 >320 2 21/22 Inter- CND04040 CND04050 CND04340 11.7 74 6.32 22/23 CND04340 CND04760 10.8 104 9.63 23/24 CND04760 Inter-...”
- Chromosomal rearrangements between serotype A and D strains in Cryptococcus neoformans
Sun, PloS one 2009 - “...192 0.6 0.31 CND01190 CND02060 211 5 2.36 CND02060 CND03160 SI(4)A 299 6.1 2.04 CND03160 CND03480 91 1.6 1.76 CND03480 AD030 78 2.2 2.82 AD030 CND03960 74 2.2 2.96 CND03960 CND04540 154 2.2 1.43 CND04540 CND05140 157 4.3 2.75 CND05140 MAT CR(4)B 165 6.2 3.76 MAT...”
A4TKI4 L-lactate dehydrogenase from Yersinia pestis (strain Pestoides F)
36% identity, 90% coverage
SPy0414, SPy_0414 putative lactate oxidase from Streptococcus pyogenes M1 GAS
35% identity, 85% coverage
- Glucose Levels Alter the Mga Virulence Regulon in the Group A Streptococcus
Valdes, Scientific reports 2018 - “...FC SF370 Microarray * M5005_spy0143 hypothetical protein 2.54 SPy0169 1.95 M5005_spy0340 lctO L-lactate oxidase 2.47 SPy0414 1.30 M5005_spy1632 lacG 6-phospho-beta-galactosidase 2.06 SPy1916 1.59 M5005_spy1714 fba fibronectin-binding surface protein 3.20 SPy2009 5.59 M5005_spy1715 scpA C5A peptidase 3.43 SPy2010 5.67 M5005_spy1718 sic1 . 0 secreted inhibitor of complement...”
- Genome-wide identification of genes required for fitness of group A Streptococcus in human blood
Le, Infection and immunity 2013 - “...with excised pCRS.0220 5448 insertional inactivation of Spy0414; Spr 5448.0414 with excised pCRS.0414 5448 insertional inactivation of fruA; Spr 5448.fruA with...”
- “...Spr pCRS derivative for insertional inactivation of Spy0414; Spr pCRS derivative for insertional inactivation of Spy0662(fruA); Spr pCRS derivative for...”
- Murine vaginal colonization model for investigating asymptomatic mucosal carriage of Streptococcus pyogenes
Watson, Infection and immunity 2013 - “...by rpsL. b (SPy_0514) and pCK37 for lctO (SPy_0414) (33). Generation of spontaneous streptomycin-resistant isolates was performed by plating a high density of...”
- “...b The recA (SPy_2116), speB (SPy_2039), lctO (SPy_0414), hasA (SPy_2200), sagA (SPy_0738), malM (SPy_1292), cfa (SPy_1273), ackA (SPy_0109), and arcA (SPy_1543)...”
- Surface export of GAPDH/SDH, a glycolytic enzyme, is essential for Streptococcus pyogenes virulence
Jin, mBio 2011 - “...downregulation of 11 genes ( SPy0148 to SPy0151 , SPy0154 , SPy0155 , SPy0157 , SPy0414 , SPy0739 , SPy1128 , and SPy1849 ) and upregulation of three genes ( SPy0755 , SPy0757 , and SPy0759 ) related to energy production and conversion (see TableS3 in...”
- Distinct time-resolved roles for two catabolite-sensing pathways during Streptococcus pyogenes infection
Kietzman, Infection and immunity 2011 - “...corresponding to the genes are as follows: for lctO, SPy_0414; for malM, SPy_1292; for ackA, SPy_0109; for xpt, SPy_1136; for dexS, SPy_2096; and for arcA,...”
- CcpA and LacD.1 affect temporal regulation of Streptococcus pyogenes virulence genes
Kietzman, Infection and immunity 2010 - “...mutations in the genes encoding CcpA (SPy_0514) and LctO (SPy_0414) were generated using allelic replacement and the PCR primers listed in Table S1 in the...”
- “...pyogenes M1 genome revealed a single gene (lctO, SPy_0414) with significant homology to the characterized lactate oxidase gene of Streptococcus iniae (19). This...”
M5005_RS01875 L-lactate oxidase from Streptococcus pyogenes MGAS5005
M5005_Spy_0340 L-lactate oxidase from Streptococcus pyogenes MGAS5005
35% identity, 85% coverage
C645_RS09865 FMN-dependent L-lactate dehydrogenase LldD from Haemophilus influenzae 2019
34% identity, 90% coverage
- Access to highly specialized growth substrates and production of epithelial immunomodulatory metabolites determine survival of Haemophilus influenzae in human airway epithelial cells
Hosmer, PLoS pathogens 2022 - “...were constructed using a two-stage process where either a single gene fragment ( lldD , C645_RS09865, WP_005657875.1) or two gene fragment ( dld , C645_RS09380, WP_046067851.1; ldhA , C645_RS00700, WP_005672300; guaB , C645_RS01605, WP_005660592.1) were cloned into pGEMT-Easy (Promega) or pBluescriptIISK (Stratagene), respectively, yielding pGEM-Hi lldD...”
Swit_1643 FMN-dependent alpha-hydroxy acid dehydrogenase from Sphingomonas wittichii RW1
39% identity, 89% coverage
YKN3_SCHPO / Q9HDX2 FMN-dependent alpha-hydroxy acid dehydrogenase PB1A11.03; EC 1.13.12.- from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
SPAPB1A11.03 FMN dependent dehydrogenase from Schizosaccharomyces pombe
36% identity, 77% coverage
FOXG_11687 L-lactate dehydrogenase (cytochrome) from Fusarium oxysporum f. sp. lycopersici 4287
37% identity, 71% coverage
P09437 L-lactate dehydrogenase (cytochrome) from Wickerhamomyces anomalus
33% identity, 61% coverage
ML2046 L-lactate dehydrogenase from Mycobacterium leprae TN
35% identity, 83% coverage
Q9HV37 L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) from Pseudomonas aeruginosa (see paper)
PA4771 L-lactate dehydrogenase from Pseudomonas aeruginosa PAO1
NP_253459 L-lactate dehydrogenase from Pseudomonas aeruginosa PAO1
36% identity, 90% coverage
- 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 - “...Phosphoenolpyruvate synthase PA3471 NP_252161 1,695 Malic enzyme NAD-dependent malic enzyme PA5046 NP_253733 1,269 Malic enzyme PA4771 NP_253459 1,146 lldD Lactate dehydrogenase L-lactate dehydrogenase PA4812 YP_003933614 3,081 fdnG Formate dehydrogenase-O major subunit PA5322 NP_254009 1,392 algC Phosphomannomutase Krebs cycle and glyoxylate cycle PA5015 NP_253702 2,649 aceE Pyruvate...”
- “...oxidase, along with the two cbb3 oxidases are also core proteins. Additionally, lactate dehydrogenase (lld, PA4771) and malate dehydrogenase (mqo) are consistently found across all growth conditions, as well as F 1 -F 0 ATP synthase. Interestingly, the A-type cytochrome c oxidase (coxB, PA0105) was identified...”
- Reverse diauxie phenotype in Pseudomonas aeruginosa biofilm revealed by exometabolomics and label-free proteomics
Yung, NPJ biofilms and microbiomes 2019 - “...Unique peptides Sequence coverage Log 2 ( x LCSP / x CSP ) Planktonic LldD PA4771 L-lactate dehydrogenase 14 44.4% 4.9 MmsA PA3570 Methylmalonate-semialdehyde dehydrogenase [acylating] 18 50.1% 5.5 MmsB PA3569 3-Hydroxyisobutyrate dehydrogenase 9 52.7% 4.5 HutH PA5098 Histidine ammonia-lyase 8 27.5% 4.0 Glk PA3193 Glucokinase...”
- “...9 52.1% 1.5 Hfq PA4944 RNA-binding protein in P. aeruginosa 16 51.3% 1.5 Biofilm LldD PA4771 L-lactate dehydrogenase 12 39.60% 5.3 FolE2 PA5539 GTP cyclohydrolase 6 36.20% 2.9 PvdA PA2386 L-ornithine N(5)-monooxygenase 4 12.40% 2.1 SpeE1 PA1687 Polyamine aminopropyltransferase 1 3 23.80% 2.0 Mqo1 PA3452 Malate:quinone...”
- Two NAD-independent l-lactate dehydrogenases drive l-lactate utilization in Pseudomonas aeruginosa PAO1
Wang, Environmental microbiology reports 2018 (PubMed)- “...NAD-independent L-lactate dehydrogenase (L-iLDH) encoded by lldD (PA4771) and a novel flavin-containing membrane-bound L-iLDH encoded by lldA (PA2382) were both...”
- “...NAD-independent L-lactate dehydrogenase (L-iLDH) encoded by lldD (PA4771) and a novel flavin-containing membranebound L-iLDH encoded by lldA (PA2382). Both...”
- Protein complex formation during denitrification by Pseudomonas aeruginosa
Borrero-de, Microbial biotechnology 2017 - “...(PA2638 to PA2644), proline dehydrogenase PutA (PA0782) (Nakada etal ., 2002 ), l lactate dehydrogenase (PA4771) (Eschbach etal ., 2004 ) and the Damino acid dehydratase (PA3357) (Ikeno etal ., 2006 ). Diverse subunits of the F o F 1 ATP synthase (PA5553 to 5560) (Cook...”
- Protein Network of the Pseudomonas aeruginosa Denitrification Apparatus
Borrero-de, Journal of bacteriology 2016 - “...proline dehydrogenase PutA (PA0782), L-lactate dehydrogenase (PA4771), succinate dehydrogenase (PA1582 to -1584), D-amino acid dehydratase (PA3357), and...”
- Pseudomonas aeruginosa ceftolozane-tazobactam resistance development requires multiple mutations leading to overexpression and structural modification of AmpC
Cabot, Antimicrobial agents and chemotherapy 2014 - “...PA4556 PA4571 Intergenic PA4622 PA4659 PA4673.1 Intergenic PA4745 PA4771 PA4783 PA4819 Intergenic PA4840 PA4846 PA4848 PA4856 gcpE acoR opmD pilB yfiT pilE nusA...”
- Transcriptome profiling defines a novel regulon modulated by the LysR-type transcriptional regulator MexT in Pseudomonas aeruginosa
Tian, Nucleic acids research 2009 - “...Conserved hypothetical protein PA4623 74 <2 Hypothetical protein PA4770 lldP 43 46 l -lactate permease PA4771 lldD 28 70 l -lactate dehydrogenase PA4772 7.0 19 Probable ferredoxin PA4881 751 <2 Hypothetical protein a Gene number from the Pseudomonas Genome Project ( http://www.pseudomonas.com ). b Fold change...”
- Cystic fibrosis sputum supports growth and cues key aspects of Pseudomonas aeruginosa physiology
Palmer, Journal of bacteriology 2005 - “...PA4230 PA4231 PA4471 PA4498 PA4514 PA4570 PA4633 PA4770 PA4771 PA4772 PA4811 PA4834 PA4835 PA4836 PA4837 PA4838 PA4929 PA5303 PA5532 PA5534 PA5535 PA5536 PA5538...”
- 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 - “...synthase PA3471 NP_252161 1,695 Malic enzyme NAD-dependent malic enzyme PA5046 NP_253733 1,269 Malic enzyme PA4771 NP_253459 1,146 lldD Lactate dehydrogenase L-lactate dehydrogenase PA4812 YP_003933614 3,081 fdnG Formate dehydrogenase-O major subunit PA5322 NP_254009 1,392 algC Phosphomannomutase Krebs cycle and glyoxylate cycle PA5015 NP_253702 2,649 aceE Pyruvate dehydrogenase...”
- “...cyoA Cytochrome o ubiquinol oxidase subunit II PA2290 NP_250980 2,412 gcd gcd Glucose dehydrogenase PA4771 NP_253459 1,146 lldD lldD L-lactate dehydrogenase PA4640 NP_253330 1,524 mqoB mqo Malate:quinone oxidoreductase PA3452 NP_252142 1,572 mqoA Malate:quinone oxidoreductase PA0139 NP_248829 564 ahpC Alkyl hydroperoxide reductase PA1475 NP_250166 702 ccmA Cytochrome...”
- Two NAD-independent l-lactate dehydrogenases drive l-lactate utilization in Pseudomonas aeruginosa PAO1.
Wang, Environmental microbiology reports 2018 (PubMed)- GeneRIF: Pseudomonas aeruginosa PAO1 contains a membrane-bound NAD-independent l-lactate dehydrogenase (l-iLDH) encoded by lldD. Disruption of the lldD gene impairs the growth of this strain in l-lactate, but the mutant strain can still grow after a long lag phase. Deletion of both l-iLDH genes lldD and lldA completely impairs the l-lactate utilization capacity of the strain.
6dvhA / P21795 Lactate monooxygenase from mycobacterium smegmatis - c203a mutant (see paper)
36% identity, 89% coverage
- Ligand: flavin mononucleotide (6dvhA)
CE2762 putative L-lactate dehydrogenase from Corynebacterium efficiens YS-314
36% identity, 84% coverage
HI1739.1 L-lactate dehydrogenase (lctD) from Haemophilus influenzae Rd KW20
P46454 L-lactate dehydrogenase from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
34% identity, 90% coverage
- Characterization of lactate utilization and its implication on the physiology of Haemophilus influenzae
Lichtenegger, International journal of medical microbiology : IJMM 2014 - “...l -lactate pathway, i.e. permease ( lctP ; HI1218), l -lactate dehydrogenase ( lctD ; HI1739.1), and characterized their influence on bacterial physiology. Materials and methods Bacterial strains, culture conditions and growth analysis Strains used in this study were Rd KW20 (gift of A. Wright, Tuffs...”
- “...medium is available. To test lactate utilization in H. influenzae , defined lctP (HI1218), lctD (HI1739.1) and arcA (HI0884) knockout mutants were generated in strain Rd KW20 replacing the genes by a kanamycin or chloramphenicol resistance gene cassette of plasmids pACYC177/184 ( Rose, 1988a , Rose,...”
- The ArcA regulon and oxidative stress resistance in Haemophilus influenzae
Wong, Molecular microbiology 2007 - “...( argG ) 4.8 5.02E-07 4.8 3.56E-07 HI1728 Conserved hypothetical protein 3.5 1.54E-06 3.1 2.58E-05 HI1739.1 l -lactate dehydrogenase ( lldD ) 3.2 1.79E-10 4.5 1.07E-11 HI1730 Conserved hypothetical protein 3.0 1.48E-06 7.0 3.32E-08 HI1661 2-oxoglutarate dehydrogenase E2 component ( sucB ) 2.8 5.33E-07 3.0 1.14E-06...”
- “...5 and 3 primer pairs for ndh ( HI0747 ) (5-ATGAAAAACGTCGTGATC and 5-ATGCAATTTTAATCTTGGTTTTAAATAAC), lldD ( HI1739.1 ) (5-ATGATTATTTCATCAGCTAG and 5-AAGTTTACTTAGATCAACC), fdxH ( HI0007 ) (5-ATGGCTGGAACTGCTCAAGGCG and 5-GAAACACGATCTACACAAAGAG), fdxI ( HI0008 ) (5-ATGAGTAAAATTGAAATTAGCAAC and 5-AGATACCAGTGAATAACATAAAAG), fdhE ( HI0009 ) (5-ATGAGTATCAAAATCTTATC and 5-TGCTTCTTCTGCAGGAAAAATAAATG), lldP ( HI1218 ) (5-ATGCTGTCTTTTATTCTAAG...”
- Redox signal transduction by the ArcB sensor kinase of Haemophilus influenzae lacking the PAS domain
Georgellis, Journal of bacteriology 2001 - “...gene, lctD (The Institute for Genomic Research gene name HI1739.1), in response to changes in redox conditions of growth. The promoter of the lctD gene...”
- Cloning of a Neisseria meningitidis gene for L-lactate dehydrogenase (L-LDH): evidence for a second meningococcal L-LDH with different regulation
Erwin, Journal of bacteriology 1996 - “...distance from the L-LDH gene, identified as lctD (ORF HI1739.1). No homolog of lldR has been found in Haemophilus influenzae. We looked for biochemical evidence...”
- Two-component systems in Haemophilus influenzae: a regulatory role for ArcA in serum resistance
De, Infection and immunity 2003 - “...ArcA represses L-lactate dehydrogenase (SwissProt accession no. P46454) only under anaerobic growth conditions (19). Interestingly, in H. influenzae we observed...”
LMO_MYCSM / P21795 L-lactate 2-monooxygenase; LMO; Lactate monooxygenase; EC 1.13.12.4 from Mycolicibacterium smegmatis (Mycobacterium smegmatis) (see 2 papers)
MSMEG_3962 lactate 2-monooxygenase from Mycobacterium smegmatis str. MC2 155
36% identity, 89% coverage
- function: Catalyzes the oxidative decarboxylation of (S)-lactate (L- lactate) to acetate and carbon dioxide. Its physiological role remains unknown.
catalytic activity: (S)-lactate + O2 = acetate + CO2 + H2O (RHEA:16513)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Homotetramer. - Flavin Mononucleotide-Dependent l-Lactate Dehydrogenases: Expanding the Toolbox of Enzymes for l-Lactate Biosensors
Tsvik, ACS omega 2022 - “...lactis A0A4Y3JPV3, Nostoc sp. PCC 7120 Q8Z0C8, and Chlamydomonas reinhardtii F8WQN2; LMO from Mycolicibacterium smegmatis P21795; GLO from Homo sapiens Q9UJM8, Spinacia oleracea P05414, and Cyanidioschyzon merolae M1VAT1; FCB2 from Saccharomyces cerevisiae P00175; MDH from Pseudomonas putida P20932; HAO from Rattus norvegicus Q07523; HMO from Amycolatopsis...”
- Biochemical and phenotypic characterisation of the Mycobacterium smegmatis transporter UspABC
Karlikowska, Cell surface (Amsterdam, Netherlands) 2021 - “...DNA helicase Information pathways 1.3 MSMEG_1940 Rv3203 hydrolase, alpha/beta fold family protein Lipid metabolism 1.2 MSMEG_3962 lactate 2-monooxygenase Virulence, detoxification and adaptation 1.1 Table 3 Differentially abundant proteins in uspAEC. Gene name Rv homologue Product Functional category Log 2 FC MSMEG_1392 alcohol dehydrogenase, class IV Intermediary...”
- Lack of mycothiol and ergothioneine induces different protective mechanisms in Mycobacterium smegmatis
Singh, Biochemistry and biophysics reports 2016 - “...MSMEG_0447 95 21.51 14.85 MSMEG_4272 Rv2204c HesB/YadR/YfhF family protein/ iron sulfur proteins 36 10.46 26.52 MSMEG_3962 Lactate-2-monooxygenase 72 8.58 6.61 MSMEG_4891 Rv2428 AhpC alkylhydroperoxide reductase 82 5.36 6.82 MSMEG_6361 MarR, transcriptional regulator, upstream of quinone reductase 78 3.62 6.47 MSMEG_0965 MspA, Chain A, Rim Domain Of...”
- The growth and survival of Mycobacterium smegmatis is enhanced by co-metabolism of atmospheric H2
Greening, PloS one 2014 - “...the same RNA samples. Genes were chosen that were downregulated (MSMEG_1203, MSMEG_3706), upregulated (MSMEG_3194, MSMEG_3249, MSMEG_3962, MSMEG_3769, MSMEG_5059), or unchanged (MSMEG_4640) in the microarray. All bars show the expression ratio of genes in hyd 2 vs. wild-type strains. Yellow bars show microarray data. Green bars show...”
- Functional analyses of mycobacterial lipoprotein diacylglyceryl transferase and comparative secretome analysis of a mycobacterial lgt mutant
Tschumi, Journal of bacteriology 2012 - “...SP MSMEG_1403 SP MSMEG_0361 SP MSMEG_0645 SP MSMEG_3962 MSMEG_6398 SP MSMEG_5789 MSMEG_3580 MSMEG_5345 Lip MSMEG_0216 glcB (MSMEG_3640) tkt (MSMEG_3103)...”
- Acid stress response of a mycobacterial proteome: insight from a gene ontology analysis
Roxas, International journal of clinical and experimental medicine 2009 (secret) - Lsr2 of Mycobacterium tuberculosis is a DNA-bridging protein
Chen, Nucleic acids research 2008 - “...higher level in the lsr2 mutant than the WT was identified as lactate 2-monoxygenase (LMO) (MSMEG_3962 in the recent annotation of M. smegmatis genome at TIGR center http://tigrblast.tigr.org/ ), by trypsin digestion followed by mass spectrometric (MALDI-TOF) analysis (data not shown). Although the functional significance of...”
PA14_63090 L-lactate dehydrogenase from Pseudomonas aeruginosa UCBPP-PA14
36% identity, 90% coverage
AO090023000871 No description from Aspergillus oryzae RIB40
35% identity, 89% coverage
NTHI2049 L-lactate dehydrogenase from Haemophilus influenzae 86-028NP
34% identity, 90% coverage
WP_005545672 FMN-dependent L-lactate dehydrogenase LldD from Aggregatibacter actinomycetemcomitans
33% identity, 90% coverage
An11g03500 uncharacterized protein from Aspergillus niger
35% identity, 90% coverage
A9QH71 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Streptococcus iniae (see paper)
33% identity, 88% coverage
WP_011728393 lactate 2-monooxygenase from Mycolicibacterium smegmatis MC2 155
38% identity, 88% coverage
HELO_1220 FMN-dependent L-lactate dehydrogenase LldD from Halomonas elongata DSM 2581
34% identity, 89% coverage
NCgl2817 quinone-dependent L-lactate dehydrogenase from Corynebacterium glutamicum ATCC 13032
cg3227 putative L-lactate dehydrogenase from Corynebacterium glutamicum ATCC 13032
35% identity, 82% coverage
- The role of the transcriptional repressor CssR in Corynebacterium glutamicum in response to phenolic compounds
Zhang, Heliyon 2024 - “...uppP Undecaprenyl-diphosphatase 1.92 0.03 NCgl2786 Putative transposase 2.17 7.72E-04 NCgl2807 Glycerophosphoryl diester phosphodiesterase 1.32 2.79E-05 NCgl2817 L-lactate dehydrogenase 1.23 1.39E-04 NCgl2844 23S RNA-specific pseudouridylate synthase 1.50 3.00E-05 NCgl2858 Hypothetical protein 1.31 1.18E-03 NCgl2861 Hypothetical protein 1.67 2.21E-03 NCgl2868 Crp/Fnr family transcriptional regulator 11.12 8.07E-04 NCgl2869 Copper...”
- Metabolic Engineering of Shikimic Acid-Producing Corynebacterium glutamicum From Glucose and Cellobiose Retaining Its Phosphotransferase System Function and Pyruvate Kinase Activities
Sato, Frontiers in bioengineering and biotechnology 2020 - “...), almost the same as SA-7. C. glutamicum has another putative lactate dehydrogenase gene (cg3227, NCgl2817), which might contribute lacate accumulation. A gene lldD (cg3227, NCgl2817) encoding quinone-dependent L-lactate dehydrogenase has the ability to utilize lactate as a carbon source ( Stansen et al., 2005 ),...”
- Accelerated Growth of Corynebacterium glutamicum by Up-Regulating Stress- Responsive Genes Based on Transcriptome Analysis of a Fast-Doubling Evolved Strain
Park, Journal of microbiology and biotechnology 2020 - “...Ncgl2437 ctaD Cytochrome aa 3 oxidase, subunit I 1.43 NCgl2810 ldh NAD-dependent Lactate dehydrogenase 1.39 Ncgl2817 lldD L-Lactate dehydrogenase (using MQ as acceptor) 0.96 B. TCA cycle NCgl0355 lpd Pyruvate dehydrogenase complex, LPD subunit 1.26 NCgl0359 sdhCD Succinate: menaquinone oxidoreductase 2.59 NCgl0360 sdhA Succinate: menaquinone oxidoreductase...”
- Understanding the high L-valine production in Corynebacterium glutamicum VWB-1 using transcriptomics and proteomics
Zhang, Scientific reports 2018 - “...0.00 800.97 NC 6 NCgl0658 cg0790 lpdA Flavoprotein disulfide reductase 5.61/49540.59 536.62 0.00 NC 7 NCgl2817 cg3227 lldA L-lactate dehydrogenase 5.72/45714.48 278.17 1249.10 NC 13 NCgl0960 cg1139 Allophanate hydrolase subunit 2 7.93/31668.91 0.00 1094.03 2.4 15 NCgl0360 cg0446 sdhA Succinate dehydrogenase A 5.37/74679.26 183.01 555.53 NC...”
- Citrate utilization by Corynebacterium glutamicum is controlled by the CitAB two-component system through positive regulation of the citrate transport genes citH and tctCBA
Brocker, Journal of bacteriology 2009 - “...NCgl0066 NCgl1173 NCgl1174 NCgl1175 NCgl1176 NCgl2816 NCgl2817 NCgl2881 NCgl0676 NCgl1383 NCgl1341 NCgl1342 NCgl1343 NCgl2635 NCgl2636 NCgl2637 NCgl2638...”
- Regulation of L-lactate utilization by the FadR-type regulator LldR of Corynebacterium glutamicum
Georgi, Journal of bacteriology 2008 - “...NCgl2737 NCgl2810 (ldhA) NCgl2814 (lldR) NCgl2816 NCgl2817 (lldD) Sulfate adenyltransferase subunit Putative membrane protease subunit LdhA, NAD-dependent...”
- Structural and functional characterization of the LldR from Corynebacterium glutamicum: a transcriptional repressor involved in L-lactate and sugar utilization
Gao, Nucleic acids research 2008 - “...l -lactate. cgl2917 (or NCgl2816 ) encodes a permease CGL2917 and lldD ( cgl2918 / NCgl2817 ) encode a quinone-dependent l -lactate dehydrogenase (LldD). During cultivation of C. glutamicum 2262 in continuous mode, excreted l -lactate is re-utilized after an increase in activity of LldD; such...”
- Two-component systems of Corynebacterium glutamicum: deletion analysis and involvement of the PhoS-PhoR system in the phosphate starvation response
Kocan, Journal of bacteriology 2006 - “...tag no. NCgl2553 NCgl2717 NCgl2718 NCgl2731 NCgl2787 NCgl2817 NCgl2859 NCgl2860 NCgl2864 NCgl2865 NCgl2877 NCgl2897 NCgl2904 NCgl2952 NCgl2953 NCgl2956 NCgl2957...”
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- CRISPRi-Library-Guided Target Identification for Engineering Carotenoid Production by Corynebacterium glutamicum
Göttl, Microorganisms 2021 - “...plasmid carrying the idsA (cg2384) sgRNA This work pS_dCas9_ IIdD pS_dCas9 plasmid carrying the IIdD (cg3227) sgRNA This work pS_dCas9_ ispE pS_dCas9 plasmid carrying the ispE (cg1039) sgRNA This work pS_dCas9_ ispF pS_dCas9 plasmid carrying the ispF (cg2944) sgRNA This work pS_dCas9_ ispG pS_dCas9 plasmid carrying...”
- Metabolic Engineering of Shikimic Acid-Producing Corynebacterium glutamicum From Glucose and Cellobiose Retaining Its Phosphotransferase System Function and Pyruvate Kinase Activities
Sato, Frontiers in bioengineering and biotechnology 2020 - “...S2 ), almost the same as SA-7. C. glutamicum has another putative lactate dehydrogenase gene (cg3227, NCgl2817), which might contribute lacate accumulation. A gene lldD (cg3227, NCgl2817) encoding quinone-dependent L-lactate dehydrogenase has the ability to utilize lactate as a carbon source ( Stansen et al., 2005...”
- Production of Food and Feed Additives From Non-food-competing Feedstocks: Valorizing N-acetylmuramic Acid for Amino Acid and Carotenoid Fermentation With Corynebacterium glutamicum
Sgobba, Frontiers in microbiology 2018 - “...L -lactate requires quinone-dependent L -lactate dehydrogenase which is encoded in the LldR repressed operon cg3227 - lldD ( Engels et al., 2008 ; Georgi et al., 2008 ). L -Lactate is secreted by C. glutamicum under certain conditions, e.g., during growth with glucose when oxygen...”
- Harnessing novel chromosomal integration loci to utilize an organosolv-derived hemicellulose fraction for isobutanol production with engineered Corynebacterium glutamicum
Lange, Microbial biotechnology 2018 - “...( cysZ ) g cg3111 CgLP11 3077633 10 cg3212 cg3213 yes h CgLP12 3094266 20 cg3227 ( lldD ) cg3228 araBAD CgLP13 3191992 10 cg3344 cg3345 yes h CgLP14 f 3213531 10 cg3365 ( rmpC ) cg3364 ( trpA ) g CgLP15 3229705 10 cg3385 (...”
- Understanding the high L-valine production in Corynebacterium glutamicum VWB-1 using transcriptomics and proteomics
Zhang, Scientific reports 2018 - “...800.97 NC 6 NCgl0658 cg0790 lpdA Flavoprotein disulfide reductase 5.61/49540.59 536.62 0.00 NC 7 NCgl2817 cg3227 lldA L-lactate dehydrogenase 5.72/45714.48 278.17 1249.10 NC 13 NCgl0960 cg1139 Allophanate hydrolase subunit 2 7.93/31668.91 0.00 1094.03 2.4 15 NCgl0360 cg0446 sdhA Succinate dehydrogenase A 5.37/74679.26 183.01 555.53 NC 16...”
- Citrate utilization by Corynebacterium glutamicum is controlled by the CitAB two-component system through positive regulation of the citrate transport genes citH and tctCBA
Brocker, Journal of bacteriology 2009 - “...cg3127 cg2380 cg0088 cg1376 cg1377 cg1379 cg1380 cg3226 cg3227 cg3308 cg0810 cg1628 cg1581 cg1582 cg1583 cg3026 cg3027 cg3028 cg3029 cg1156 cg1451 cg0576 cg2894...”
- Elastase digests: new ammunition for shotgun membrane proteomics
Rietschel, Molecular & cellular proteomics : MCP 2009 - “...Cg1437 Cg1790 Cg2958 61 62 63 64 9 3 7 3 8 8 8 8 Cg2211 Cg3227 Cg1429 Cg1685 65 66 67 68 0 8 8 8 8 7 6 6 Cg2444 Cg2405 Cg1791 Cg1001 69 70 71 72 73 74 3 1 0 2 0...”
- Functional genomics of pH homeostasis in Corynebacterium glutamicum revealed novel links between pH response, oxidative stress, iron homeostasis and methionine synthesis
Follmann, BMC genomics 2009 - “...DH 0 1.83 0.12 5.1 3.1 4.8 4.3 1.3 2.3 - - -0.4 GlxR* 84 cg3227 lldD Aerobic FMN-L-lactate DH 0 1.14 0.45 1.2 2.1 0.7 5.2 4.1 4.0 1.5 -0.6 - GlxR* 85 cg3236 msrA Methionine sulfoxide reductase 0 1.27 1.01 - - -0.8 -...”
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LOX_ROSS0 / B7RR92 L-lactate oxidase; LOX; (S)-2-hydroxy-acid oxidase; EC 1.1.3.-; EC 1.1.3.15 from Roseobacter sp. (strain GAI101) (see paper)
40% identity, 92% coverage
- function: Catalyzes the oxidation of (S)-lactate (L-lactate) to pyruvate, with a reduction of O2 to H2O2. Is also able to use glycolate and to a lesser extent 2-hydroxyoctadecanoate as substrate.
catalytic activity: (S)-lactate + O2 = H2O2 + pyruvate (RHEA:55868)
catalytic activity: a (2S)-2-hydroxycarboxylate + O2 = a 2-oxocarboxylate + H2O2 (RHEA:16789)
catalytic activity: glycolate + O2 = glyoxylate + H2O2 (RHEA:25311)
catalytic activity: 2-hydroxyoctadecanoate + O2 = 2-oxooctadecanoate + H2O2 (RHEA:68964)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Homotetramer.
VCA0984 L-lactate dehydrogenase from Vibrio cholerae O1 biovar eltor str. N16961
35% identity, 90% coverage
- Modulation of Host-Microbe Metabolism by Cholera Toxin
Chapman, Infection and immunity 2023 (secret) - IurV, Encoded by ORF VCA0231, Is Involved in the Regulation of Iron Uptake Genes in Vibrio cholerae
Sachman-Ruiz, Genes 2020 - “...Bacterioferritinassociated ferredoxin VC0286 gntU 2.22969 <5.00E05 Lowaffinity gluconate/H+ symporter GntU VCA0976 2.23539 <5.00E05 Hypotetical protein VCA0984 ildD 2.27194 <5.00E05 Llactate dehydrogenase | lldD VC1332 2.34818 <5.00E05 Tripartite tricarboxylate transporter TctA family VCA0983 2.43475 <5.00E05 Llactate permease VCA0227 vctP 2.47329 <5.00E05 Ferric vibriobactin, enterobactin transport system, substratebinding...”
- Cholera toxin promotes pathogen acquisition of host-derived nutrients
Rivera-Chávez, Nature 2019 - “...TCA cycle (VC0432, VC1573, VC2084-VC2092, VC2738), LCFA utilization (VC1043, VC2758, VC2231), and L-Lactate utilization (VCA0983, VCA0984), and all open reading frames (ORFs) of wild type C6706 during colonization of the ileum relative to the cecum. (c) Differential expression of V . cholerae genes involved in TCA...”
- Metabolic Reprogramming of Vibrio cholerae Impaired in Respiratory NADH Oxidation Is Accompanied by Increased Copper Sensitivity
Toulouse, Journal of bacteriology 2018 - “...5 2.6 2.6 2.5 2.4 A0A0H3AFI4 A0A0H3ALG0 A0A0H3AI86 VCA0984 VC2763 VC0194 lldD atpC ggt 2.2 2.2 2 Cytochrome c551 peroxidase Acyl-CoA thioesterase I Nicotinate...”
- A novel phase variant of the cholera pathogen shows stress-adaptive cryptic transcriptomic signatures
Lambert, BMC genomics 2016 - “...), which encodes a periplasmic nitrate reductase, VC2656 ( frdA ), encoding fumarate reductase, and VCA0984 ( lldD ), encoding lactate dehydrogenase (Additional file 13 : Table S9). In the case of the latter function, it is possible that down-regulation of lactate production in N16961SD allows...”
- Inhibition of the sodium-translocating NADH-ubiquinone oxidoreductase [Na+-NQR] decreases cholera toxin production in Vibrio cholerae O1 at the late exponential growth phase
Minato, Microbial pathogenesis 2014 - “...to fumarate and dehyroxyacetone-P, respectively. Other bacteria-specific respiration-linked dehydrogenases [such as Ndh2 (VC1890), L-lactate dehydrogenase (VCA0984), and D-amino acid dehydrogenase (VC0786)] are shown collectively (DHs). The bd- type cytochrome (bd cyt) oxidase-1 (VC1843-44) and oxidase-2 (VCA0872-73) oxidize the reduced form of UQ coupled to oxygen reduction...”
- Central metabolism controls transcription of a virulence gene regulator in Vibrio cholerae
Minato, Microbiology (Reading, England) 2013 - “...to encode an inducible L-lactateubiquinone oxidoreductase enzyme (VCA0984); thus, the addition of L-lactate would be predicted to stimulate respiration even in...”
CNAG_01229 L-mandelate dehydrogenase from Cryptococcus neoformans var. grubii H99
33% identity, 64% coverage
LGG_02356 L-lactate dehydrogenase (FMN-dependent) related alpha-hydroxy acid dehydrogenase from Lactobacillus rhamnosus GG
LGG_02356 lactate oxidase from Lacticaseibacillus rhamnosus GG
36% identity, 91% coverage
- Impact of electro-activated whey on growth, acid and bile resistance of Lacticaseibacillus rhamnosus GG and Lactobacillus acidophilus ATCC 4356
Aider-Kaci, Heliyon 2023 - “...37 ]. Most of upregulated genes have no defined function except for l -lactate oxidase (LGG_02356) and thioredoxin (LGG_00775). It is known that the enzymatic oxidation of lactate by l -lactate oxidase occurs with the release of H 2 O 2 as a reaction product [...”
- Adaptation of Lacticaseibacillus rhamnosus CM MSU 529 to Aerobic Growth: A Proteomic Approach
Dinarieva, Microorganisms 2023 - “...( ) 1, () 2, ( ) 3, ( ) 4. LGG_01836 ( pox ), LGG_02356 ( lctO ), and LGG_02295 (LRHMDP2_2713). Figure 2 Pyruvate conversion pathways in L. rhamnosus CM MSU 529. LdhL/D, lactate dehydrogenase; LctO, lactate oxidase; Cit, citrate lyase; Xfp, phosphoketolase; AckA, acetate...”
Q6DAY3 L-lactate dehydrogenase from Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672)
35% identity, 89% coverage
APL_1849 L-lactate dehydrogenase (cytochrome) from Actinobacillus pleuropneumoniae L20
APPSER1_RS10140 FMN-dependent L-lactate dehydrogenase LldD from Actinobacillus pleuropneumoniae serovar 1 str. 4074
33% identity, 90% coverage
PMPD1_1350 FMN-dependent L-lactate dehydrogenase LldD from Paramixta manurensis
35% identity, 91% coverage
Rv1872c POSSIBLE L-LACTATE DEHYDROGENASE (CYTOCHROME) LLDD2 from Mycobacterium tuberculosis H37Rv
35% identity, 83% coverage
- Ongoing evolution of the Mycobacterium tuberculosis lactate dehydrogenase reveals the pleiotropic effects of bacterial adaption to host pressure
Stanley, PLoS pathogens 2024 - “...of functional genetic diversity in response to host challenge. We focus here on lldD2 ( rv1872c ), an Mtb gene that encodes the lactate dehydrogenase (LDH) LldD2, which has been shown to be required for Mtb grown on lactate as a sole carbon source [ 20...”
- “...show that it is formed and accumulates. Reviewer #2:This manuscript argues that the gene lldD2 (Rv1872c) which encodes a lactate dehydrogenase, has been positively selected for in the human host. Clearly, Mtb has continued to evolve, with selective pressures, but the authors claim that BCG vaccination...”
- Genomic characteristics of Mycobacterium tuberculosis isolates of cutaneous tuberculosis
Mei, Frontiers in microbiology 2023 - “...drug targets (INH, RFP, EMB, PNZ, STR, FLQ, and PASA) and loci under convergent evolutionary (Rv1872c (c.757G>A), 2123281; Rv1873 (c.8C>T), 2122395) are marked with a black dot. The branches in the yellow and blue range of the tree belong to Lineage 4 and Lineage 2, respectively....”
- “...that were supposed to be homoplastic SNPs. They were also detected in PTB strains, namely, Rv1872c (c.757G>A), the coding gene of lldD2 , had variation in 72.41% of CTB (42/58) and 95.21% of PTB (179/188) and Rv1873 (c.8C>T) was in the subsequent region of Rv1872c, was...”
- The cause-effect relation of tuberculosis on incidence of diabetes mellitus
Bisht, Frontiers in cellular and infection microbiology 2023 - “...resistance ( Wang etal., 2020 ). Mtb can utilize lactate with L-lactate dehydrogenase gene, lldD2 (Rv1872c) and facilitate its intracellular survival. It has been shown that lldD2 knock-out Mtb fails to efficiently replicate in human macrophages ( Billig etal., 2017 ). The tuberculosis necrotizing toxin (TNT)...”
- Analysis of Genome-Wide Mutational Dependence in Naturally Evolving Mycobacterium tuberculosis Populations
Green, Molecular biology and evolution 2023 - “...2011 ) 1722228 Rv1527c pks5 Mediates surface remodeling ( Boritsch et al. 2016 ) 2122395 Rv1872c lldD2 Promotes survival inside macrophages ( Billig et al. 2017 ) 2338994 Rv2082 Rv2082 Unknown 2626011 Rv2346c esxO Inferred to increase risk of resistance evolution ( Ortiz et al. 2021...”
- Transcriptional Biomarkers of Differentially Detectable Mycobacterium tuberculosis in Patient Sputum
Zainabadi, mBio 2022 - “...24.0 98.6 pks15 (Rv2947c) Probable polyketide synthase Lipid metabolism 16.0 h 2.6 25.5 60 lldD2 (Rv1872c) Possible l -lactate dehydrogenase (cytochrome) Intermediary metabolism and respiration 10.0 h 3.6 Yes 24.0 95.1 Upregulated arsC (Rv2643) Probable arsenic-transport integral membrane protein Cell wall and cell processes 7.7 2.6...”
- Shotgun proteomic profiling of dormant, 'non-culturable' Mycobacterium tuberculosis
Nikitushkin, PloS one 2022 - “...glyoxylate and methylcitrate pathways. Mtb used to have annotated two lactate dehydrogenases, LldD 2 ( Rv1872c , p < 0.05, log 2 FC = 1.04) and LldD1 ( Rv0694 , p < 0.05, log 2 FC = 2.67); however, lactate dehydrogenase activity was confirmed for LldD2...”
- Immunogenicity of Mycobacterial Extracellular Vesicles Isolated From Host-Related Conditions Informs About Tuberculosis Disease Status
Schirmer, Frontiers in microbiology 2022 - “...PPE18 0.1 Intermediary metabolism 301 Rv2220 GlnA1 1.76 90 Rv2220 GlnA1 1.57 Rv2215 DlaT 0.88 Rv1872c LldD2 1.33 Rv1023 Eno 0.81 Rv3841 BfrB 1.32 Rv3841 BfrB 0.75 Rv1327c GlgE 1.16 Rv3248c SahH 0.74 Rv1133c MetE 1.1 Unknown 1 Rv2818c Hypothetical protein 0.02 0 Regulatory proteins 19...”
- Lactate cross-talk in host-pathogen interactions
Llibre, The Biochemical journal 2021 - “...inhibits M.tb growth [ 117 ]. Further confirming this, deletion of ldh ( lldD2 , Rv1872c) in M.tb is detrimental to growth in lactate containing media, suggesting potential lactate toxicity when M.tb cannot metabolise it. Inside the infected macrophage, lactate concentrations have been estimated to be...”
- “...Colombian clinical isolate UT127 was shown to cope with scarce lipid availability by up-regulating lldD2 (Rv1872c), suggesting the potential use of lactate as an alternative carbon source [ 125 ]. In summary, the evidence converges towards increased glycolysis and lactate release in the context of TB...”
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SMLT_RS13830 FMN-dependent L-lactate dehydrogenase LldD from Stenotrophomonas maltophilia K279a
36% identity, 90% coverage
Mb1903c POSSIBLE L-LACTATE DEHYDROGENASE (CYTOCHROME) LLDD2 from Mycobacterium bovis AF2122/97
BCG_1908c putative L-lactate dehydrogenase (cytochrome) lldD2 from Mycobacterium bovis BCG str. Pasteur 1173P2
35% identity, 83% coverage
B8MMC0 Oxidoreductase, putative from Talaromyces stipitatus (strain ATCC 10500 / CBS 375.48 / QM 6759 / NRRL 1006)
34% identity, 68% coverage
MAP1585c LldD2 from Mycobacterium avium subsp. paratuberculosis str. k10
34% identity, 87% coverage
H16_B1817 alpha-hydroxy acid oxidase from Cupriavidus necator H16
37% identity, 83% coverage
PP4736, PP_4736 L-lactate dehydrogenase from Pseudomonas putida KT2440
36% identity, 90% coverage
CYB2 / P00175 L-lactate dehydrogenase subunit (EC 1.1.2.3) from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (see 2 papers)
CYB2_YEAST / P00175 L-lactate dehydrogenase (cytochrome); Cytochrome b2; Flavocytochrome b2; FCB2; L-lactate ferricytochrome c oxidoreductase; L-LCR; EC 1.1.2.3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 8 papers)
P00175 L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) from Saccharomyces cerevisiae (see 9 papers)
NP_013658 L-lactate dehydrogenase (cytochrome) from Saccharomyces cerevisiae S288C
YML054C Cyb2p from Saccharomyces cerevisiae
33% identity, 59% coverage
- function: Catalyzes the oxidation of (S)-lactate (L-lactate) to pyruvate with subsequent transfer of electrons to cytochrome c (PubMed:11914072). Is involved in the utilization of (S)-lactate as a sole source of carbon for growth (PubMed:3004948). Can also use ferricyanide as an electron acceptor in vitro (PubMed:3004948, PubMed:4593578).
catalytic activity: (S)-lactate + 2 Fe(III)-[cytochrome c] = 2 Fe(II)-[cytochrome c] + 2 H(+) + pyruvate (RHEA:19909)
cofactor: FMN
cofactor: heme b (Binds 1 heme b (iron(II)-protoporphyrin IX) group non-covalently per subunit.)
subunit: Homotetramer.
disruption phenotype: Inactivation of this gene leads to a deficiency in L-lactate dehydrogenase activity and consequently to the inability to use L-lactate as a sole source of carbon. - Whitening of brown adipose tissue inhibits osteogenic differentiation via secretion of S100A8/A9.
Wang, iScience 2024 - “...USA) for immunoblotting with relevant antibodies, or silver staining using the Fast Silver Stain kit (P00175, Beyotime) according to the manufacturers instructions. For bone histology and histomorphometric analysis, femora and tibiae were decalcified for 2030days in decalcification solution (1.45% ETDA, 1.25% NaOH, 1.5% glycerol, pH 7.3)...”
- Annotation of biologically relevant ligands in UniProtKB using ChEBI.
Coudert, Bioinformatics (Oxford, England) 2023 - “...below shows one such case, where amino acid 146 of yeast L-lactate dehydrogenase (UniProtKB/Swiss-Prot entry P00175) binds to the iron atom (CHEBI: 18248) of heme b (CHEBI: 60344) (this form of heme b represents the predominant protonation state at pH7.3, the form chosen by convention in...”
- Flavin Mononucleotide-Dependent l-Lactate Dehydrogenases: Expanding the Toolbox of Enzymes for l-Lactate Biosensors
Tsvik, ACS omega 2022 - “...from Homo sapiens Q9UJM8, Spinacia oleracea P05414, and Cyanidioschyzon merolae M1VAT1; FCB2 from Saccharomyces cerevisiae P00175; MDH from Pseudomonas putida P20932; HAO from Rattus norvegicus Q07523; HMO from Amycolatopsis orientalis O52792; and mLDH from Pseudomonas stutzeri ADL63037) were used as queries for individual database searches on...”
- A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs
Dingerdissen, Biology direct 2014 - “...P36871 P37012 Q9BUP3 P40008 P34949 P29952 Q9UBZ9 P12689 P54098 P15801 Q7L211 P42840 Q9HBY8 P12688 Q9UJM8 P00175 P07741 P49435 P07902 P08431 Q8WUX2 P32656 P13716 P05373 Q9Y2L1 Q08162 Q14249 P08466 P48449 P38604 Q96C11 Q04585 Q5VTY9 Q08929 P49336 P39073 O14818 P40303 Q86YJ6 P16120 Q8IZ73 Q12362 O00743 P20604 P12081 P07263...”
- Structural evidence for the functional importance of the heme domain mobility in flavocytochrome b2.
Diêp, Journal of molecular biology 2010 (PubMed)- GeneRIF: The present results support the idea that the heme domain mobility is an inherent component of the Fcb2 functioning.
- Improvement of L-lactate production by CYB2 gene disruption in a recombinant Saccharomyces cerevisiae strain under low pH condition.
Ookubo, Bioscience, biotechnology, and biochemistry 2008 (PubMed)- GeneRIF: Disruption of the CYB2 gene encoding L-lactate dehydrogenase improved the L-lactate production by S. cerevisiae under low pH condition.
- Mechanistic and structural studies of H373Q flavocytochrome b2: effects of mutating the active site base.
Tsai, Biochemistry 2007 - GeneRIF: The combination of an altered active site and the small kinetic isotope effects is consistent with the slowest step in turnover being a conformational change involving a conformation in which lactate is bound unproductively.
- Flavocytochrome b2: reactivity of its flavin with molecular oxygen.
Boubacar, Biochemistry 2007 (PubMed)- GeneRIF: separately engineered flavodehydrogenase domain produces superoxide anion in its slow reaction with oxygen. This reaction also takes place in the holoenzyme when oxygen is the sole electron acceptor, because the heme domain autoxidation is also slow.
- The Role of Ancestral Duplicated Genes in Adaptation to Growth on Lactate, a Non-Fermentable Carbon Source for the Yeast Saccharomyces cerevisiae
Mattenberger, International journal of molecular sciences 2021 - “...core set (altered genes shared by all three populations), we found Idp2 (YLR174W; WGD), Cyb2 (YML054C; singleton), Mls1 (YNL117W; SSD), Acs1 (YAL054C; SSD), and Rgi2 (YIL057C; WGD) genes implied in the utilization of non-fermentable carbon sources, with affected growth parameters even under vegetative growth and decreased...”
- Lachancea fermentati Strains Isolated From Kombucha: Fundamental Insights, and Practical Application in Low Alcohol Beer Brewing
Bellut, Frontiers in microbiology 2020 - “...KBI 5.3 ( Supplementary Data Sheet S1 ). LAFE_0E15192G shows some similarities with S. cerevisiae YML054C CYB2 , a cytochrome b2 (L-lactate cytochrome-c oxidoreductase) component of the mitochondrial intermembrane space which is required for lactate utilization (and repressed by glucose and anaerobic conditions) ( Sauer et...”
- A High-Resolution Luminescent Assay for Rapid and Continuous Monitoring of Protein Translocation across Biological Membranes
Pereira, Journal of molecular biology 2019 - “...f). As an import substrate, we used the classical yeast import precursor cytochrome B2 (CytB2; YML054C) with its hydrophobic sorting domain removed (CytB2 4365 ), causing it to localize to the matrix [20] . We found that standard in vitro import reaction conditions [4] , [8]...”
- The stress-regulatory transcription factors Msn2 and Msn4 regulate fatty acid oxidation in budding yeast
Rajvanshi, The Journal of biological chemistry 2017 - “...YDR256C YCR005C YNL009W YLR151C YFL030W YNL242W YIL146C YML054C YIR004W YIL065C YDL022W YGR154C YIR034C YDR234W YDL078C YNL117W YBR222C YGL037C YPR165W YLR389C...”
- Different Toxicity Mechanisms for Citrinin and Ochratoxin A Revealed by Transcriptomic Analysis in Yeast
Vanacloig-Pedros, Toxins 2016 - “...10 6 Type II nitroreductase YEL072W RMD6 8.7 6.39 10 7 Protein required for sporulation YML054C CYB2 8.5 2.74 10 6 Cytochrome b2 ( l -lactate cytochrome-c oxidoreductase) YNL187W SWT21 8.5 6.08 10 6 Protein involved in mRNA splicing YNR064C - 8.5 1.99 10 5 Epoxide...”
- The flavoproteome of the yeast Saccharomyces cerevisiae
Gudipati, Biochimica et biophysica acta 2014 - “...l -Lactate:cytochrome c oxidoreductase (flavocytochrome b 2 ) FMN/heme TIM_barrel (FMN_dh) Mito. intermembr. sp. cyb2 YML054C 2 1.1.2.4 d -Lactate dehydrogenase FAD/heme I. mito. membr. dld1 YDL174C Mito. matrix dld2 YDL178W Cytoplasm dld3 YEL071W 3 1.1.3.37 d -Arabino-1,4-lactone oxidase 8-(N3-His) -FAD FAD_PCMH O. mito. membr. alo1...”
- Transcriptional response to mitochondrial NADH kinase deficiency in Saccharomyces cerevisiae
Stuart, Mitochondrion 2009 - “...SSA4 -4.23 -4.36 -4.42 9.23 1.53 Heat shock protein that is highly induced upon stress YML054C CYB2 -4.20 -1.93 -1.94 11.78 19.79 Cytochrome b2 ; lactate use; repressed by glucose, anaerobic conditions YDL085W NDE2 -3.99 -3.11 -2.66 8.80 18.07 With Nde1p, provides cytosolic NADH to mitochondrial...”
- “...Anaerobic expression : YJR047C ANB1 7.94 134.40 Translation initiation factor eIF-5A; expressed under anaerobic conditions YML054C CYB2 -4.20 1.11 Mitochondrial cytochrome b2 ; required for lactate utilization; repressed by glucose, anaerobic conditions YJR150C DAN1 12.74 2214.79 Cell wall mannoprotein expressed under anaerobic conditions; repressed during aerobic...”
- Construction and application of a protein and genetic interaction network (yeast interactome)
Stuart, Nucleic acids research 2009 - “...21.12 Plasma membrane glycerol proton symporter; subject to glucose-induced inactivation; transiently induced by osmotic shock YML054C CYB2 19.79 Cytochrome b2; mitochondrial intermembrane space; required for lactate utilization; repressed by glucose YMR280C CAT8 17.69 Transcriptional activator; derepresses a variety of genes under non-fermentative growth conditions, active after...”
- More
Z5032 L-lactate dehydrogenase from Escherichia coli O157:H7 EDL933
35% identity, 86% coverage
Lct / b3605 L-lactate dehydrogenase from Escherichia coli K-12 substr. MG1655 (see 7 papers)
lldD / P33232 L-lactate dehydrogenase from Escherichia coli (strain K12) (see 6 papers)
LLDD_ECOLI / P33232 L-lactate dehydrogenase; EC 1.1.-.- from Escherichia coli (strain K12) (see 2 papers)
lldD L-lactate dehydrogenase [cytochrome]; EC 1.1.2.3 from Escherichia coli K12 (see paper)
lctD / AAA03585.1 L-lactate dehydrogenase from Escherichia coli (see paper)
NP_418062 L-lactate dehydrogenase from Escherichia coli str. K-12 substr. MG1655
b3605 L-lactate dehydrogenase, FMN-linked from Escherichia coli str. K-12 substr. MG1655
35% identity, 86% coverage
- function: Catalyzes the conversion of L-lactate to pyruvate. Seems to be a primary dehydrogenase in the respiratory chain. To a lesser extent, can also oxidize DL-alpha-hydroxybutyrate, but not D-lactate.
catalytic activity: (S)-lactate + A = AH2 + pyruvate (RHEA:45816)
cofactor: FMN
subunit: Forms homooligomers.
disruption phenotype: Cells lacking this gene lose the ability to grow on L-lactate as the sole source of carbon and energy, but can still utilize D-lactate. - Dual role of LldR in regulation of the lldPRD operon, involved in L-lactate metabolism in Escherichia coli.
Aguilera, Journal of bacteriology 2008 - GeneRIF: These results are consistent with the hypothesis that LldR has a dual role, acting as a repressor or an activator of lldPRD operon.
- Biodistribution of 89Zr-DFO-labeled avian pathogenic Escherichia coli outer membrane vesicles by PET imaging in chickens
Li, Poultry science 2023 - “...wall/membrane/envelope biogenesis Cell inner membrane 427 P0AC78 WECA Cell wall/membrane/envelope biogenesis Cell inner membrane 428 P33232 LLDD Energy production and conversion Cell inner membrane 429 P0AC75 KDTA Cell wall/membrane/envelope biogenesis Cell inner membrane 430 P43341 LPXH Function unknown Cell inner membrane 431 P14175 PROV Amino acid...”
- Computational Proteome-Wide Study for the Prediction of Escherichia coli Protein Targeting in Host Cell Organelles and Their Implication in Development of Colon Cancer
Khan, ACS omega 2020 - “...weight (dalton) pI value protein targeting results using LocTree3 expected accuracy (%) functions in bacteria P33232 l -lactate dehydrogenase 42728.19 6.33 peroxisome 83 induced by l -lactate, aerobically P0AET8 7-hydroxysteroid dehydrogenase 26778.59 5.22 peroxisome 83 7-dehydroxylation of cholic acid, yielding deoxycholic acid and lithocholic acid, respectively....”
- Analysis of pleiotropic transcriptional profiles: a case study of DNA gyrase inhibition
Jeong, PLoS genetics 2006 - “...(P30125) , leuC (P30127) , leuD (P30126) , leuO (P10151) , lexA (P03033) , lldD (P33232) , lldP (P33232) , malE (P02928) , metK (P04384) , ompF (P02931) , parC (P20082) , parE (P20083) , pdhR (P06957) , pps (P23538) , proV (P14175) , proW (P14176)...”
- The Escherichia coli proteome: past, present, and future prospects
Han, Microbiology and molecular biology reviews : MMBR 2006 - “...no.b Descriptionb pI/MW Theoreticalc Experimentald P33232 P61316 L-Lactate dehydrogenase Outer-membrane lipoprotein carrier protein 6.33/42,728.19...”
- LEON: multiple aLignment Evaluation Of Neighbours
Thompson, Nucleic acids research 2004 - “...constructed using the L-lactate dehydrogenase from Escherichia coli (P33232) as the query. Two subfamilies are included in the alignment, one containing the...”
- “...E < 10 using the L-lactate dehydrogenase from E.coli (P33232) as the query. Conserved columns are shaded (black, 100%; dark grey, 80%; light grey, 60%). Two...”
- Proteome of Salmonella typhimurium SL1344: identification of novel abundant cell envelope proteins and assignment to a two-dimensional reference map
Qi, Journal of bacteriology 1996 - “...Protein (Swiss-Prot accession number)b Remarksd pIc Mrc dehydrogenase (P33232) OmpA protein of S. typhimurium (P02936) ATP synthase d chain (P00831) 6.33 42,728...”
- Divergent evolution of a beta/alpha-barrel subclass: detection of numerous phosphate-binding sites by motif search
Bork, Protein science : a publication of the Protein Society 1995 - “...lctd-ecoli 300 DIAILADSGIRNGLDWRMI.ALGADTVLLGRAFLYALATA(3QAGVAN P33232 la2m_mycsm 314 DTPVLFDSGIRTGADWKAL.AMGASAVGIGRPYAWGAALGGSKG1EH P21795 orf5/erwhe 272...”
- A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011
Orth, Molecular systems biology 2011 - “...growth was used to determine essentiality instead, only one additional essential gene was predicted: lldD (b3605) on lactate minimal medium. Knockout strains were taken from the Keio Collection ( Baba et al, 2006 ; Yamamoto et al, 2009 ) (supplied by Open Biosystems), a genome-scale collection...”
- Control and benefits of CP4-57 prophage excision in Escherichia coli biofilms
Wang, The ISME journal 2009 - “...synthase, -protein Carbohydrate metabolism lldP b3603 3.0 L-lactate permease lldR b3604 2.5 Transcriptional regulator lldD b3605 2.3 L-lactate dehydrogenase sdhA b0723 1.9 Succinate dehydrogenase, flavoprotein subunit sdhB b0724 1.9 Succinate dehydrogenase, iron sulfur protein sdhC b0721 1.7 Succinate dehydrogenase, cytochrome b556 sdhD b0722 1.7 Succinate dehydrogenase,...”
- The HU regulon is composed of genes responding to anaerobiosis, acid stress, high osmolarity and SOS induction
Oberto, PloS one 2009 - “...0.79 15.07 1 0.07 0.13 0.33 1 0.73 0.54 0.86 This work transcriptional regulator lldD b3605 lldPRD 1 12.6 0.79 7.63 1 0.21 0.15 0.56 1 0.68 0.58 0.82 This work L-lactate dehydrogenase fimA b4314 fimAICDFGH 1 0.34 0.81 2.8 1 0.22 0.63 2.56 1 0.49...”
- Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro
Stepanova, Journal of bacteriology 2007 - “...2.5 2.7 Dipeptide transport protein lldP lldR lldD b3603 b3604 b3605 2 2.5 3.1 2.6 3.5 2 L-Lactate glpK b3926 2.3 4.4 Glycerol kinase glpF b3927 2.9 4.9...”
- Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation
Selinger, Genome research 2003 - “...Labile mRNAs B# Name HL 0 2.5 5 10 20 b4188 b3605 b3914 b0990 b3913 b0553 b2398 b3494 b3556 b3685 b0726 b1205 b3362 b0162 b1060 b2080 b2377 b3361 b4132 b4396...”
1kbiA / P00175 Crystallographic study of the recombinant flavin-binding domain of baker's yeast flavocytochrome b2: comparison with the intact wild- type enzyme (see paper)
33% identity, 69% coverage
- Ligands: protoporphyrin ix containing fe; flavin mononucleotide (1kbiA)
PFLU4305 L-lactate dehydrogenase from Pseudomonas fluorescens SBW25
35% identity, 89% coverage
- Experimental evolution reveals hidden diversity in evolutionary pathways
Lind, eLife 2015 - “...desaturase (PFLU0184) located upstream. Eight deletions generating in-frame fusions were also found between PFLU4306 and PFLU4305. PFLU4306 encodes a DGC domain protein and the upstream gene encodes a putative L-lactate dehydrogenase. A third example was defined by a single mutation that fused the GGDEF domain protein...”
- “...PFLU1349 ins TC -47/48, PFLU5698 C-73T), and gene fusions (PFLU0184 M1-T328 fused to PFLU0183 A29-G335; PFLU4305 M1-Y340 fused to PFLU4306 S21-G489; PFLU4313 M1-F115 fused to PFLU4308 A189-R820) were reconstructed in the SBW25 background to prove that they are the cause of the WS phenotype and to...”
ABUW_3812 FMN-dependent L-lactate dehydrogenase LldD from Acinetobacter baumannii
34% identity, 90% coverage
- Lactate metabolism promotes in vivo fitness during Acinetobacter baumannii infection
Morris, FEMS microbiology letters 2024 - “...strain AB5075-UW, encoding the D-lactate dehydrogenase ( dld , ABUWs_3811), L-lactate dehydrogenase ( lldD , ABUW_3812), transcriptional repressor ( lldR , ABUW_3813) and lactate permease ( lldP , ABUW_3814). (B) Relative expression of lactate permease, lldP , compared to the house keeping gene recA , in...”
ABTJ_03740 FMN-dependent L-lactate dehydrogenase LldD from Acinetobacter baumannii MDR-TJ
34% identity, 90% coverage
ACIAD0108 L-lactate dehydrogenase, FMN linked from Acinetobacter sp. ADP1
32% identity, 91% coverage
PS417_19130 L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) from Pseudomonas simiae WCS417
35% identity, 91% coverage
- mutant phenotype: Specifically important for utilizing Sodium L-Lactate. Automated validation from mutant phenotype: the predicted function (1.1.2.3) was linked to the condition via a SEED subsystem. This annotation was also checked manually.
DW68_005145 FMN-dependent L-lactate dehydrogenase LldD from Pseudomonas mendocina S5.2
36% identity, 90% coverage
- Phenotypic and genomic survey on organic acid utilization profile of Pseudomonas mendocina strain S5.2, a vineyard soil isolate
Chong, AMB Express 2017 - “...(cytochrome b560 subunit) sdhC 2,793,3922,793,766 374 Lactic acid DW68_005140 d -Lactate dehydrogenase dld 1,090,0881,091,806 1719 DW68_005145 l -Lactate dehydrogenase lldD 1,091,8111,092,950 1140 DW68_005150 l -Lactate permease lldP 1,093,0351,094,726 1692 DW68_005155 Lactate responsive regulator lldR 1,095,0221,095,789 768 Malic acid (malateoxaloacetate) DW68_020815 Malate dehydrogenase sfcA 4,486,2444,487,512 1269 Malic...”
AN479_RS14060 FMN-dependent L-lactate dehydrogenase LldD from Serratia marcescens
34% identity, 90% coverage
CNH01230 cytochrome b2, mitochondrial precursor from Cryptococcus neoformans var. neoformans JEC21
34% identity, 59% coverage
- Allergen1 regulates polysaccharide structure in Cryptococcus neoformans
Jain, Molecular microbiology 2013 - “...all1 exo-PS in H99-wt cells resulted in up-regulation of FTR1 , FRE1 , CNM02430, CNM02420, CNH01230, CNG00950, CIG1 , and CNB00400 transcripts ( Fig 5E , white bars). Up-regulation was also seen if the mutant exo-PS was added to mutant cells ( Fig 5E , Black...”
- “...in microarray analysis related to iron-transport i.e., FTR1 , FRE1 , CNM02430, CNM02420, CNB02540, CNG00120, CNH01230, CNG00110, CNG00950, CNC01660, CNK02840, CNB00400, CNI01980 and -actin as control. The mRNA levels were normalized against their respective -actin and expression was calculated using the delta-delta CT method. The fold...”
H16_B1817 L-Lactate cytochrome c reductase from Ralstonia eutropha H16
37% identity, 91% coverage
LKW31_15200 FMN-dependent L-lactate dehydrogenase LldD from Pantoea agglomerans
34% identity, 91% coverage
BP1669 lactate dehydrogenase from Bordetella pertussis Tohama I
33% identity, 88% coverage
- Investigating genome reduction of Bordetella pertussis using a multiplex PCR-based reverse line blot assay (mPCR/RLB)
Lam, BMC research notes 2014 - “...isolates. Other genes, which were absent from at least one isolate, were BP0330, BP1553, BP1664, BP1669, BP1673, BP2102, BP2627, BP2825, BP3107, BP3319, BP3322, which collectively represent 10 RDs (Figure 2 ). Not all genes within an RD were always absent. For example, two isolates (L655 and...”
- “...exported protein RD24 BP1638-BP1639 BP1638 Hypothetical protein RD25 RD7 BP1663-BP1674/77 BP1664 Glutathione S-transferase RD27 RD8 BP1669 Lactate dehydrogenase BP1676-BP1677 N/A RD28 RD9 BP1698 N/A RD30 BP1948-BP1966 BP1948 Branched-chain amino acid-binding protein RD33 RD10 L3 RD-4 BP1954 Probable oxidoreductase BP1962 Putative ferrisiderophore receptor BP2088-BP2103 BP2102 lysR family...”
KP13_00216 FMN-dependent L-lactate dehydrogenase LldD from Klebsiella pneumoniae subsp. pneumoniae Kp13
A6TFK0 L-lactate dehydrogenase from Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
KPN_03949 L-lactate dehydrogenase from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
34% identity, 88% coverage
- The polymyxin B-induced transcriptomic response of a clinical, multidrug-resistant Klebsiella pneumoniae involves multiple regulatory elements and intracellular targets
Ramos, BMC genomics 2016 - “...poxB KP13_04234 0.1 D -Lactate DH dld KP13_03193 0.1 L -Lactate DH lctD or lldD KP13_00216 0.2 D -Amino acid DH dad ( dad2) KP13_04669 0.9 Glucose dehydrogenase gcD KP13_32152 0.1 b Succinate DH sdhCDAB KP13_03281-77 0.3, 0.1, 0.1, 0, 0.1 Quinone biosynthesis: Ubiquinone (UQ) ubiA...”
- Disruption of KPC-producing Klebsiella pneumoniae membrane via induction of oxidative stress by cinnamon bark (Cinnamomum verum J. Presl) essential oil
Yang, PloS one 2019 - “...Protein biosynthesis Control 98 Large-conductance mechanosensitive channel mscL B5XNC0 Transport Control 99 L-lactate dehydrogenase lldD A6TFK0 Energy synthesis Control 100 L-threonine 3-dehydrogenase tdh A6TFL2 Protein biosynthesis Control Of the overlapping 232 proteins identified in both treatment groups, only 41 proteins showed significant differences, in terms of...”
- “...Glycerol-3-phosphate acyltransferase Lost A6TDR6 Glycine cleavage system H protein Lost B5XNC0 Large-conductance mechanosensitive channel Lost A6TFK0 L-lactate dehydrogenase Lost A6TEQ3 Malate dehydrogenase Lost B5XXP0 NAD(P)H dehydrogenase (quinone) Lost A6TBX3 NADH-quinone oxidoreductase subunit B Lost A6TBX2 NADH-quinone oxidoreductase subunit C/D Lost A6TC99 Phosphoribosylaminoimidazole-succinocarboxamide synthase Upregulated by 2.52...”
- High Production of 3-Hydroxypropionic Acid in Klebsiella pneumoniae by Systematic Optimization of Glycerol Metabolism
Li, Scientific reports 2016 - “...The deletion of lactic acid and acetic acid synthesis genes ldh1 (GenBank, KPN_01632), ldh2 (GenBank, KPN_03949), and pta (GenBank, KPN_02688) followed the protocol of RecA homologous recombination. The recombinants were confirmed by colony PCR and sequencing. SDS-PAGE analysis The medium used in this study was the...”
6dviD / P21795 Wild-type lactate monooxygenase from mycobacterium smegmatis (see paper)
35% identity, 93% coverage
- Ligand: flavin mononucleotide (6dviD)
2nliB / Q44467 Crystal structure of the complex between l-lactate oxidase and a substrate analogue at 1.59 angstrom resolution (see paper)
32% identity, 92% coverage
- Ligand: flavin mononucleotide (2nliB)
1ldcB / P00175 X-ray structure of two complexes of the y143f flavocytochrome b2 mutant crystallized in the presence of lactate or phenyl-lactate (see paper)
32% identity, 91% coverage
- Ligands: flavin mononucleotide; pyruvic acid (1ldcB)
STY4102 putative L-lactate dehydrogenase from Salmonella enterica subsp. enterica serovar Typhi str. CT18
Q8Z2E5 L-lactate dehydrogenase from Salmonella typhi
35% identity, 86% coverage
SPO0598 alpha-hydroxy acid oxidase from Ruegeria pomeroyi DSS-3
SPO0598, YP_165858 FMN-dependent alpha-hydroxy acid dehydrogenase family protein from Silicibacter pomeroyi DSS-3
35% identity, 88% coverage
- Sulfur metabolites that facilitate oceanic phytoplankton-bacteria carbon flux
Landa, The ISME journal 2019 - “...SPO2934 SPO1914 pta SPO3560 Regulation hpsP slcD SPO0596 SPO0598 cuyR hpsO SPO0595 SPOA0159 hpsN hpsM SPO0593 SPO0594 hpsL SPO0592 DHPS metabolism hpsK SPO0590...”
- An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3
Rivers, Standards in genomic sciences 2014 - “...YP_165856 SPO0596 S or R-dihydroxypropanesulfonate-2-dehydrogenase hpsP Function YP_165857 SPO0597 UspA stress protein hpsQ Function YP_165858 SPO0598 Membrane-bound sulfolactate dehydrogenase slcD Function YP_165912 SPO0657 Metallochaperone, putative naaT Function YP_165913 SPO0658 N-acetyltaurine amidohydrolase naaS Function YP_165914 SPO0659 LysR family transcriptional regulator naaR Function YP_165915 SPO0660 N-acetyltaurine ABC transporter,...”
- An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3
Rivers, Standards in genomic sciences 2014 - “...Function YP_165856 SPO0596 S or R-dihydroxypropanesulfonate-2-dehydrogenase hpsP Function YP_165857 SPO0597 UspA stress protein hpsQ Function YP_165858 SPO0598 Membrane-bound sulfolactate dehydrogenase slcD Function YP_165912 SPO0657 Metallochaperone, putative naaT Function YP_165913 SPO0658 N-acetyltaurine amidohydrolase naaS Function YP_165914 SPO0659 LysR family transcriptional regulator naaR Function YP_165915 SPO0660 N-acetyltaurine ABC...”
SPC_3776 putative L-lactate dehydrogenase from Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
35% identity, 86% coverage
- Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
Liu, Plants (Basel, Switzerland) 2023 - “...subunit SPC_2161 28.095 Respiratory nitrate reductase 2 alpha chain SPC_0939 29.218 Hydroxylamine reductase Pyruvate metabolism SPC_3776 0.04 Putative L-lactate dehydrogenase SPC_1189 0.475 Phosphate acetyltransferase SPC_0937 2.023 Pyruvate dehydrogenase SPC_0998 3.184 YcbL Galactose metabolism SPC_4361 0.009 Alpha-galactosidase SPC_0771 0.051 Galactose-1-phosphate uridylyltransferase SPC_0772 0.087 UDP-galactose 4-epimerase SPC_3916 0.199...”
slcD / A3SN06 sulfolactate dehydrogenase from Roseovarius nubinhibens (strain ATCC BAA-591 / DSM 15170 / ISM) (see paper)
34% identity, 92% coverage
MAP3486 hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
34% identity, 91% coverage
CNAG_05318 L-mandelate dehydrogenase from Cryptococcus neoformans var. grubii H99
33% identity, 65% coverage
MAP2959c hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
36% identity, 90% coverage
B7QEL2 Glycolate oxidase, putative (Fragment) from Ixodes scapularis
42% identity, 71% coverage
NCU11278 hypothetical protein from Neurospora crassa OR74A
34% identity, 79% coverage
- The transcription factor PDR-1 is a multi-functional regulator and key component of pectin deconstruction and catabolism in Neurospora crassa
Thieme, Biotechnology for biofuels 2017 - “...emp - 19 (NCU10106), a glyoxalase (NCU11253), and four hypothetical proteins (NCU01700, NCU01871, NCU08475, and NCU11278). Because all of these genes contain a putative PDR-1-binding site and showed a significantly reduced expression in the pdr - 1 mutant, we conclude that these genes form the core...”
- “...NCU09035 put. rha1 3 C1 NCU10106 emp - 19 2 C1 NCU11253 Glyoxalase 2 C1 NCU11278 Hypothetical protein 2 C1 PDR-1 consensus binding sites (PB sites) with a stringency score of more than 0.6 were used Discussion Pectin is the most complex plant cell wall polysaccharide...”
CCNA_01462 lactate 2-monooxygenase from Caulobacter crescentus NA1000
CC_1396 L-lactate 2-monooxygenase from Caulobacter crescentus CB15
36% identity, 81% coverage
- CspC regulates the expression of the glyoxylate cycle genes at stationary phase in Caulobacter
Santos, BMC genomics 2015 - “...acid metabolism CC_1382 CCNA_01446 LL-diaminopimelate aminotransferase 4.37 CC_1397 CCNA_01463 3-deoxy-7-phosphoheptulonate synthase 10.70 Carbohydrate metabolism CC_1396 CCNA_01462 lactate 2-monooxygenase 7.80 Protein synthesis CC_1870 CCNA_01946 tyrosyl-tRNA synthetase 9.85 Oxydative stress response CC_1871 CCNA_01947 thioredoxin peroxidase 3.99 a Values are fold changes in the expression levels comparing the null...”
- CspC regulates the expression of the glyoxylate cycle genes at stationary phase in Caulobacter
Santos, BMC genomics 2015 - “...Amino acid metabolism CC_1382 CCNA_01446 LL-diaminopimelate aminotransferase 4.37 CC_1397 CCNA_01463 3-deoxy-7-phosphoheptulonate synthase 10.70 Carbohydrate metabolism CC_1396 CCNA_01462 lactate 2-monooxygenase 7.80 Protein synthesis CC_1870 CCNA_01946 tyrosyl-tRNA synthetase 9.85 Oxydative stress response CC_1871 CCNA_01947 thioredoxin peroxidase 3.99 a Values are fold changes in the expression levels comparing the...”
- Regulatory response to carbon starvation in Caulobacter crescentus
Britos, PloS one 2011 - “...regulator 2.18 Yes CC_3219 Two-component sensor histidine kinase 2.54 Yes CC_2644 phoH protein 44.56 Yes CC_1396 Lactate 2-monooxygenase 6.28 Yes CC_1101 Protoporphyrinogen oxidase 2.37 Yes CC_1307 Aspartyl protease perP 3.05 Yes CC_1211 Hypothetical protein 2.01 Yes CC_3291 Hypothetical protein 9.90 Yes CC_1072 Ribonuclease H 3.35 Yes...”
BMAA1565 dehydrogenase, FMN-dependent family from Burkholderia mallei ATCC 23344
35% identity, 86% coverage
Afu4g07050 L-lactate dehydrogenase from Aspergillus fumigatus Af293
33% identity, 81% coverage
- Transcriptomic analysis of the exit from dormancy of Aspergillus fumigatus conidia
Lamarre, BMC genomics 2008 - “...was repressed (Afu2g13870). Energy Genes coding for alcohol dehydrogenase (Afu5g06240, Afu5g03930, Afu5g00300, Afu7g04530), lactate dehydrogenase (Afu4g07050), pyruvate decarboxylase (Afu6g00750) and phosphoenol pyruvate synthase (Afu5g14790) were down-regulated. In contrast, genes that function in TCA cycle were up-regulated. Similarly, 28 mitochondrial genes were up-regulated whereas only one was...”
AO090023000884 No description from Aspergillus oryzae RIB40
32% identity, 74% coverage
CNAG_03663 L-lactate dehydrogenase from Cryptococcus neoformans var. grubii H99
31% identity, 58% coverage
CNB01620 L-lactate dehydrogenase (cytochrome) from Cryptococcus neoformans var. neoformans JEC21
31% identity, 58% coverage
R1E6X7 Putative fmn-dependent dehydrogenase protein from Botryosphaeria parva (strain UCR-NP2)
35% identity, 85% coverage
B7FUG8 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Phaeodactylum tricornutum (see paper)
31% identity, 77% coverage
SPO1172 alpha-hydroxy acid oxidase from Ruegeria pomeroyi DSS-3
35% identity, 89% coverage
- An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3
Rivers, Standards in genomic sciences 2014 - “...Clp protease, ATP-binding subunit ClpX clpX ORF position YP_166357 SPO1106 Hypothetical protein ORF position YP_166419 SPO1172 FMN-dependent alpha-hydroxy acid dehydrogenase family protein ORF position YP_166421 SPO1174 DNA helicase II, putative ORF position YP_166518 SPO1273 Thymidylate synthase, flavin-dependent thyX ORF position YP_166577 SPO1334 Hypothetical protein ORF position...”
CYB2_TALSN / B8MKR3 L-lactate dehydrogenase (cytochrome); EC 1.1.2.3 from Talaromyces stipitatus (strain ATCC 10500 / CBS 375.48 / QM 6759 / NRRL 1006) (Penicillium stipitatum) (see paper)
33% identity, 70% coverage
- function: Catalyzes the oxidation of (S)-lactate (L-lactate) to pyruvate with subsequent transfer of electrons to cytochrome c. Also displays oxidase activity in vitro, catalyzing the oxidation of a broad range of 2-hydroxyacids, such as glycolate, (S)-lactate, 2- hydroxyoctanoate, (S)-2-hydroxyglutarate and to a lesser extent mandelate, to the corresponding 2-oxoacids, with a reduction of O2 to H2O2 (PubMed:34555022). However, the physiological activity of this enzyme is most likely to function as an L-lactate dehydrogenase. May be involved in the utilization of (S)-lactate as a sole source of carbon for growth (Probable).
catalytic activity: (S)-lactate + 2 Fe(III)-[cytochrome c] = 2 Fe(II)-[cytochrome c] + 2 H(+) + pyruvate (RHEA:19909)
catalytic activity: a (2S)-2-hydroxycarboxylate + O2 = a 2-oxocarboxylate + H2O2 (RHEA:16789)
catalytic activity: glycolate + O2 = glyoxylate + H2O2 (RHEA:25311)
catalytic activity: (S)-lactate + O2 = H2O2 + pyruvate (RHEA:55868)
catalytic activity: 2-hydroxyoctanoate + O2 = 2-oxooctanoate + H2O2 (RHEA:67940)
catalytic activity: (S)-2-hydroxyglutarate + O2 = 2-oxoglutarate + H2O2 (RHEA:27662)
catalytic activity: mandelate + O2 = H2O2 + phenylglyoxylate (RHEA:68968)
cofactor: FMN
cofactor: heme b (Binds 1 heme b (iron(II)-protoporphyrin IX) group non-covalently per subunit.)
subunit: Homotetramer. - Experimental and computational investigation of enzyme functional annotations uncovers misannotation in the EC 1.1.3.15 enzyme class
Rembeza, PLoS computational biology 2021 - “...other family members in our selection ( Fig 2C ). Two of the screened proteins (B8MKR3 and B8MMC0 from Talaromyces stipitatus ) contain a heme binding domain (PF00173) characteristic for flavocytochrome b2 L-lactate dehydrogenase (EC 1.1.2.3) [ 29 ] (Figs 2A and S6 ). These two...”
- “...to reduce cytochrome c, a physiological electron acceptor of flavocytochrome b2 L-lactate dehydrogenase. Indeed, the B8MKR3 protein displayed cytochrome b2 L-lactate dehydrogenase activity ( S7 Fig ). Additionally, four other proteins (E6SCX5 from Intrasporangium calvum , C9Y9E7 from a Curvibacter species and W6W585 from Rhizobium sp...”
SPO1172, YP_166419 FMN-dependent alpha-hydroxy acid dehydrogenase family protein from Silicibacter pomeroyi DSS-3
35% identity, 90% coverage
- An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3
Rivers, Standards in genomic sciences 2014 - “...Clp protease, ATP-binding subunit ClpX clpX ORF position YP_166357 SPO1106 Hypothetical protein ORF position YP_166419 SPO1172 FMN-dependent alpha-hydroxy acid dehydrogenase family protein ORF position YP_166421 SPO1174 DNA helicase II, putative ORF position YP_166518 SPO1273 Thymidylate synthase, flavin-dependent thyX ORF position YP_166577 SPO1334 Hypothetical protein ORF position...”
- “...ATP-dependent Clp protease, ATP-binding subunit ClpX clpX ORF position YP_166357 SPO1106 Hypothetical protein ORF position YP_166419 SPO1172 FMN-dependent alpha-hydroxy acid dehydrogenase family protein ORF position YP_166421 SPO1174 DNA helicase II, putative ORF position YP_166518 SPO1273 Thymidylate synthase, flavin-dependent thyX ORF position YP_166577 SPO1334 Hypothetical protein ORF...”
FGSG_01531 hypothetical protein from Fusarium graminearum PH-1
33% identity, 86% coverage
- Comparison of Fusarium graminearum Transcriptomes on Living or Dead Wheat Differentiates Substrate-Responsive and Defense-Responsive Genes
Boedi, Frontiers in microbiology 2016 - “...sugar degrading enzymes, a putative monosaccharide transporter (FGSG_10921) or a probable CYB2lactate dehydrogenase cytochrome b2 (FGSG_01531; Table 4 ), predicted to contribute to C-2 compound and organic acid metabolism as well as lactate fermentation (register tab APup_PPup_in_planta_6 of Table S3 ). Taken together, using the described...”
- “...as in planta expressed genes . FGSG_number Description FGSG_00028 Probable metalloprotease MEP1 FGSG_01468 Uncharacterized protein FGSG_01531 Probable CYB2lactate dehydrogenase cytochrome b2 FGSG_05296 Uncharacterized protein FGSG_10921 Related to monosaccharide transporter FGSG_11027 Related to N6-hydroxylysine acetyl transferase Additionally, we could identify within our experiment 30 new genes within...”
Afu8g06000 FMN dependent dehydrogenase, putative from Aspergillus fumigatus Af293
35% identity, 88% coverage
A0A1P8B993 Aldolase-type TIM barrel family protein from Arabidopsis thaliana
37% identity, 61% coverage
Afu4g07020 mitochondrial cytochrome b2-like, putative from Aspergillus fumigatus Af293
32% identity, 66% coverage
CYBL_RHOGR / P32953 (S)-mandelate dehydrogenase, mitochondrial; Flavocytochrome b; L(+)-mandelate dehydrogenase; L-MDH; EC 1.1.99.31 from Rhodotorula graminis (Yeast) (see 2 papers)
CAA04758.1 L-mandelate dehydrogenase from Rhodotorula graminis (see paper)
32% identity, 61% coverage
- function: Catalyzes the oxidation of (S)-mandelate to benzoylformate and enables utilization of mandelate as substrate for growth.
catalytic activity: (S)-mandelate + A = AH2 + phenylglyoxylate (RHEA:15749)
cofactor: FMN (Binds 1 FMN per subunit.)
cofactor: heme b (Binds 1 heme b group per subunit.)
subunit: Homotetramer.
mftD / A0PM50 pre-mycofactocin synthase (EC 1.4.3.26) from Mycobacterium ulcerans (strain Agy99) (see paper)
MFTD_MYCUA / A0PM50 Pre-mycofactocin synthase; PMFT synthase; EC 1.4.3.26 from Mycobacterium ulcerans (strain Agy99) (see paper)
A0PM50 pre-mycofactocin synthase (EC 1.4.3.26) from Mycobacterium ulcerans (see paper)
MUL_0774 L-lactate dehydrogenase (cytochrome) LldD1 from Mycobacterium ulcerans Agy99
33% identity, 87% coverage
- function: Involved in the biosynthesis of the enzyme cofactor mycofactocin (MFT). Catalyzes the oxidative deamination of AHDP (3- amino-5-[(4-hydroxyphenyl)methyl]-4,4-dimethyl-2-pyrrolidin-2-one), forming an alpha-keto amide moiety on the resulting molecule, which is called pre-mycofactocin (PMFT). This reaction occurs via a 5-[(4- hydroxyphenyl)methyl]-3-imino-4,4-dimethylpyrrolidin-2-one intermediate, which converts to PMFT. The alpha-keto amide moiety is the redox-active center for the redox activity of mycofactocin.
catalytic activity: 3-amino-5-[(4-hydroxyphenyl)methyl]-4,4-dimethyl-2-pyrrolidin- 2-one + H2O + O2 = H2O2 + NH4(+) + pre-mycofactocin (RHEA:65508)
cofactor: FMN - MftD Catalyzes the Formation of a Biologically Active Redox Center in the Biosynthesis of the Ribosomally Synthesized and Post-translationally Modified Redox Cofactor Mycofactocin
Ayikpoe, Journal of the American Chemical Society 2019 - “...catalytically-competent, RiPP-derived, redox cofactor. RESULTS MftD is an FMN Binding Protein. The mftD gene ( mul_0774 ) was cloned from M. ulcerans Agy99 and the Mu MftD protein was heterologously expressed in and anaerobically purified from Escherichia coli ( Figure 2A ). Characterization of as-isolated Mu...”
- “...redox cofactor family. METHODS Cloning, Expression, and Purification of MftD from Mycobacterium ulcerans Agy99. The mul_0774 gene sequence encoding for MftD from Mycobacterium ulcerans Agy99 (Uniprot: 0PM50) was cloned into pET28a-TEV using BamHI and XhoI restriction sites. The sequence verified MumftD/pET28a-TEV plasmid was transformed into E....”
VDAG_07114 cytochrome b2 from Verticillium dahliae VdLs.17
33% identity, 85% coverage
RF|XP_001522874.1 putative cytochrome b2, mitochondrial precursor [Cryptococcus neoformans] from Magnaporthe grisea 70-15 (see paper)
33% identity, 85% coverage
MSMEG_1424, MSMEI_1389 pre-mycofactocin synthase MftD from Mycolicibacterium smegmatis MC2 155
32% identity, 86% coverage
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...0.07 0.04 0.28 0.07 A0QYH8 MSMEG_3663, MSMEI_3576 Oxidoreductase 0.06 0.01 A0QSB9 mftD , lldD1 , MSMEG_1424, MSMEI_1389 FMN-dependent dehydrogenase 0.02 0.03 A0R461 MSMEG_5715, MSMEI_5564 Bac_luciferase domain-containing protein 0.39 0.31 A0QRD2 MSMEG_1073, MSMEI_1041 Oxidoreductase, short-chain dehydrogenase/reductase family protein 0.09 0.05 A0QU11 MSMEG_2037, MSMEI_1991 Bac_luciferase domain-containing protein 0.03...”
- “...0.04 0.28 0.07 A0QYH8 MSMEG_3663, MSMEI_3576 Oxidoreductase 0.06 0.01 A0QSB9 mftD , lldD1 , MSMEG_1424, MSMEI_1389 FMN-dependent dehydrogenase 0.02 0.03 A0R461 MSMEG_5715, MSMEI_5564 Bac_luciferase domain-containing protein 0.39 0.31 A0QRD2 MSMEG_1073, MSMEI_1041 Oxidoreductase, short-chain dehydrogenase/reductase family protein 0.09 0.05 A0QU11 MSMEG_2037, MSMEI_1991 Bac_luciferase domain-containing protein 0.03 0.04...”
MFTD_MYCS2 / A0QSB9 Pre-mycofactocin synthase; PMFT synthase; EC 1.4.3.26 from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (Mycobacterium smegmatis) (see 3 papers)
A0QSB9 pre-mycofactocin synthase (EC 1.4.3.26) from Mycolicibacterium smegmatis (see 2 papers)
MSMEG_1424 FMN-dependent dehydrogenase from Mycobacterium smegmatis str. MC2 155
32% identity, 85% coverage
- function: Involved in the biosynthesis of the enzyme cofactor mycofactocin (MFT) (PubMed:33014324). Catalyzes the oxidative deamination of AHDP (3-amino-5-[(4-hydroxyphenyl)methyl]-4,4-dimethyl- 2-pyrrolidin-2-one), forming an alpha-keto amide moiety on the resulting molecule, which is called pre-mycofactocin (PMFT). This reaction occurs via a 5-[(4-hydroxyphenyl)methyl]-3-imino-4,4- dimethylpyrrolidin-2-one intermediate, which converts to PMFT. The alpha-keto amide moiety is the redox-active center for the redox activity of mycofactocin (PubMed:31381312). Is required for the in vivo ethanol assimilation in M.smegmatis (PubMed:31113891).
catalytic activity: 3-amino-5-[(4-hydroxyphenyl)methyl]-4,4-dimethyl-2-pyrrolidin- 2-one + H2O + O2 = H2O2 + NH4(+) + pre-mycofactocin (RHEA:65508)
cofactor: FMN
disruption phenotype: Cells lacking this gene lose the ability to utilize ethanol as the sole growth substrate (PubMed:31113891). They are unable to produce PMFT(H2) and glycosylated (methyl)MFT(H2), and accumulate AHDP and glycosylated AHDP (PubMed:33014324). - Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...0.07 0.04 0.28 0.07 A0QYH8 MSMEG_3663, MSMEI_3576 Oxidoreductase 0.06 0.01 A0QSB9 mftD , lldD1 , MSMEG_1424, MSMEI_1389 FMN-dependent dehydrogenase 0.02 0.03 A0R461 MSMEG_5715, MSMEI_5564 Bac_luciferase domain-containing protein 0.39 0.31 A0QRD2 MSMEG_1073, MSMEI_1041 Oxidoreductase, short-chain dehydrogenase/reductase family protein 0.09 0.05 A0QU11 MSMEG_2037, MSMEI_1991 Bac_luciferase domain-containing protein 0.03...”
- Biochemical and phenotypic characterisation of the Mycobacterium smegmatis transporter UspABC
Karlikowska, Cell surface (Amsterdam, Netherlands) 2021 - “...respiration 1.9 MSMEG_5634 Rv0910 conserved hypothetical Conserved hypothetical 1.2 MSMEG_0366 hypothetical protein Conserved hypotheticals 2.4 MSMEG_1424 Rv0694 FMN-dependent dehydrogenase, possible L-lactate dehydrogenase Intermediary metabolism and respiration 2.2 MSMEG_1594 enoyl-CoA hydratase Lipid metabolism 1.8 MSMEG_2433 Rv2911 ( dacB2 ) D-alanyl-D-alanine carboxypeptidase Cell wall and cell processes 1.8...”
- MftD Catalyzes the Formation of a Biologically Active Redox Center in the Biosynthesis of the Ribosomally Synthesized and Post-translationally Modified Redox Cofactor Mycofactocin
Ayikpoe, Journal of the American Chemical Society 2019 - “...S2C ). To ensure that this activity was not unique to Mu MftD, the gene msmeg_1424 , encoding for Ms MftD, was cloned from M. smegmatis mc 2 155, the protein was purified from E. coli ( Figure 2A ), and reactions with AHDP were prepared...”
- “...purification step as described below. Cloning, Expression and Purification of MftD from Mycobacterium smegmatis. The msmeg_1424 gene encoding for MftD from Mycobacterium smegmatis mc 2 155 (Uniprot: A0QSB) was cloned into pET28a vector using NdeI and XhoI restriction sites. The sequence verified msmeg_1424/pET28a plasmid was transformed...”
- Mycofactocin Is Associated with Ethanol Metabolism in Mycobacteria
Krishnamoorthy, mBio 2019 - “...MftA chaperone; mftC , Rv0693 / MSMEG_1423 , radical S-adenosylmethionine maturase; mftD , Rv0694 / MSMEG_1424 , flavin/heme dehydrogenase; mftE , Rv0695 / MSMEG_1425 , creatinine aminohydrolase family protein; mftF , Rv0696 / MSMEG_1426 , glycosyltransferase. mftB , mftC , mftD , mftE , and mftF...”
- The MprB extracytoplasmic domain negatively regulates activation of the Mycobacterium tuberculosis MprAB two-component system
Bretl, Journal of bacteriology 2014 - “...3 2 2 MSMEG_4263 MSMEG_0030 MSMEG_6080 MSMEG_1401 MSMEG_1424 MSMEG_6069 MSMEG_3155 MSMEG_0006 MSMEG_5415 MSMEG_0392 MSMEG_4671 rpoA rpoB ask mprB ndh kasA dnaJ...”
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...0.03 A0R2L3 MSMEG_5155, MSMEI_5022 Nitroreductase 0.07 0.04 0.28 0.07 A0QYH8 MSMEG_3663, MSMEI_3576 Oxidoreductase 0.06 0.01 A0QSB9 mftD , lldD1 , MSMEG_1424, MSMEI_1389 FMN-dependent dehydrogenase 0.02 0.03 A0R461 MSMEG_5715, MSMEI_5564 Bac_luciferase domain-containing protein 0.39 0.31 A0QRD2 MSMEG_1073, MSMEI_1041 Oxidoreductase, short-chain dehydrogenase/reductase family protein 0.09 0.05 A0QU11 MSMEG_2037,...”
MAP_RS21325 pre-mycofactocin synthase MftD from Mycobacterium avium subsp. paratuberculosis K-10
MAP4154 LldD1 from Mycobacterium avium subsp. paratuberculosis str. k10
32% identity, 86% coverage
MT0721 FMN-dependent alpha-hydroxy acid dehydrogenase family protein from Mycobacterium tuberculosis CDC1551
32% identity, 84% coverage
P9WND7 pre-mycofactocin synthase (EC 1.4.3.26) from Mycobacterium tuberculosis (see paper)
BCG_0743 putative L-lactate dehydrogenase (cytochrome) lldD1 from Mycobacterium bovis BCG str. Pasteur 1173P2
Rv0694 POSSIBLE L-LACTATE DEHYDROGENASE (CYTOCHROME) LLDD1 from Mycobacterium tuberculosis H37Rv
Mb0713 POSSIBLE L-LACTATE DEHYDROGENASE (CYTOCHROME) LLDD1 from Mycobacterium bovis AF2122/97
33% identity, 86% coverage
- InbR, a TetR family regulator, binds with isoniazid and influences multidrug resistance in Mycobacterium bovis BCG
Yang, Scientific reports 2015 - “...1.36 Rv0692 hypothetical protein BCG_0742 1.84 2.06 Rv0693 pqqE coenzyme PQQ synthesis protein E pqqE BCG_0743 2.18 2.25 Rv0694 lldD1 L-lactate dehydrogenase (cytochrome) lldD1 NA BCG_0744 1.09 1.25 Rv0695 hypothetical protein BCG_0745 1.25 1.43 Rv0696 membrane sugar transferase 8 BCG_0755 1.24 1.42 Rv0705 rpsS 30S ribosomal...”
- Genome-wide screen identifies host loci that modulate Mycobacterium tuberculosis fitness in immunodivergent mice
Meade, G3 (Bethesda, Md.) 2023 - “...39.978 4.00 38.651 42.427 3.83E02 hp135 Rv3540c ltp2 X 101.772 4.43 80.056 115.391 3.14E03 hp136 Rv0694 lldD1 X 115.365 3.91 102.867 167.395 3.70E02 hp137 Rv1791 PE19 X 119.825 4.38 115.497 128.620 2.38E02 hp138 Rv2733c Rv2733c X 133.591 3.40 115.471 138.012 3.90E02 hp139 Rv0182c sigG X 136.470...”
- Shotgun proteomic profiling of dormant, 'non-culturable' Mycobacterium tuberculosis
Nikitushkin, PloS one 2022 - “...2 ( Rv1872c , p < 0.05, log 2 FC = 1.04) and LldD1 ( Rv0694 , p < 0.05, log 2 FC = 2.67); however, lactate dehydrogenase activity was confirmed for LldD2 only [ 59 ]. On the other hand, upregulation of Rv0694 was observed...”
- Biochemical and phenotypic characterisation of the Mycobacterium smegmatis transporter UspABC
Karlikowska, Cell surface (Amsterdam, Netherlands) 2021 - “...1.9 MSMEG_5634 Rv0910 conserved hypothetical Conserved hypothetical 1.2 MSMEG_0366 hypothetical protein Conserved hypotheticals 2.4 MSMEG_1424 Rv0694 FMN-dependent dehydrogenase, possible L-lactate dehydrogenase Intermediary metabolism and respiration 2.2 MSMEG_1594 enoyl-CoA hydratase Lipid metabolism 1.8 MSMEG_2433 Rv2911 ( dacB2 ) D-alanyl-D-alanine carboxypeptidase Cell wall and cell processes 1.8 MSMEG_0889...”
- Increased whiB7 expression and antibiotic resistance in Mycobacterium chelonae carrying two prophages
Cushman, BMC microbiology 2021 - “...ferro-lyase) Rv1485 ferrochelatase BB28_RS19235 alpha-hydroxy-acid oxidizing enzyme -2.1 2.9E-35 MAB_3834c Possible L-lactate dehydrogenase (cytochrome) LldD1 Rv0694 mycofactocin system heme/flavin oxidoreductase MftD BB28_RS08645 epoxide hydrolase -2.2 2.4E-07 MAB_1628c hypothetical protein NA NA BB28_RS13295 beta-ketoacyl-ACP reductase -2.3 3.4E-56 MAB_2723c 3-oxoacyl- Rv1483 3-oxoacyl-ACP reductase FabG BB28_RS13290 enoyl-acyl-carrier-protein reductase FabI...”
- Role of Premycofactocin Synthase in Growth, Microaerophilic Adaptation, and Metabolism of Mycobacterium tuberculosis
Krishnamoorthy, mBio 2021 - “...speculated to provide another means of membrane energization through reoxidation of reduced nicotinamide cofactors. MftD (Rv0694, LldD1) is annotated as a putative lactate dehydrogenase sharing 33% sequence homology with Rv1872c (LldD2), but only the latter has been identified as a bona fide enzyme essential for M....”
- Lineage-Specific Proteomic Signatures in the Mycobacterium tuberculosis Complex Reveal Differential Abundance of Proteins Involved in Virulence, DNA Repair, CRISPR-Cas, Bioenergetics and Lipid Metabolism
Yimer, Frontiers in microbiology 2020 - “...dehydrogenase AdhA adhA Rv1862 3, 4, 5 7 Possible L -lactate dehydrogenase (cytochrome) LldD1 LldD1 Rv0694 3, 4, 5 7 Putative citrate synthase II CitA citA Rv0889c 7 3, 4, 5 Isocitrate lyase Icl Icl1 Rv0467 4, 7 3, 5 6-Phosphogluconate dehydrogenase Gnd1 gnD1 Rv1844c 5,...”
- Activity-Based Protein Profiling Reveals That Cephalosporins Selectively Active on Non-replicating Mycobacterium tuberculosis Bind Multiple Protein Families and Spare Peptidoglycan Transpeptidases
Lopez, Frontiers in microbiology 2020 - “...gtlA2 Yes PP: citrate synthase 1 P0A590 Rv2220 glnA1 Yes PP: glutamine synthetase 1 P95143 Rv0694 lldD No PP: putative L -lactate dehydrogenase P65682 Rv2607 pdxH No SF: pyridoxine/pyridoxamine 5-phosphate oxidase Unknown function O53291 Rv3044 fecB No SF: probable Fe(III) - dicitrate binding lipoprotein O53672 Rv0250c...”
- Occurrence, function, and biosynthesis of mycofactocin
Ayikpoe, Applied microbiology and biotechnology 2019 - “...2008 ; Brzostek et al. 2009 ), TnSeq data indicated that the genes Rv0693 , Rv0694 , Rv0695 , and Rv0696 ( mftC, mftD, mftE, and mftF , respectively) are essential ( Griffin et al. 2011 ). Tn-seq data targeting mftA was not available and data...”
- More
- Microsatellite polymorphism across the M. tuberculosis and M. bovis genomes: implications on genome evolution and plasticity
Sreenu, BMC genomics 2006 - “...Hypothetical protein *Rv0607 (128) MT0636 (147) Mb0623 (128) G3 2 lldD1 *Rv0694 (396) MT0721 (419) Mb0713 (396) C4 5 NusB *Rv2533c(156) MT2608 (290) Mb2562c (156 extra aa) G3 2 transport proteins *Rv3239c (1048) MT3337(1065) Mb3267c (1048) GC4 5 Hypothetical protein *Rv0739 (268) MT0764 (268) Mb0760 (282)...”
- Characterization of a Corynebacterium glutamicum lactate utilization operon induced during temperature-triggered glutamate production
Stansen, Applied and environmental microbiology 2005 - “...M. avium subsp. paratuberculosis MAP4154, and M. bovis Mb0713) and higher than those to LldD from E. coli (34%) and L-lactate ferricytochrome c reductase...”
MAB_3834c Possible L-lactate dehydrogenase (cytochrome) LldD1 from Mycobacterium abscessus ATCC 19977
32% identity, 87% coverage
- Increased whiB7 expression and antibiotic resistance in Mycobacterium chelonae carrying two prophages
Cushman, BMC microbiology 2021 - “...ferrochelatase -2.1 4.5E-40 MAB_2721c Ferrochelatase (Protoheme ferro-lyase) Rv1485 ferrochelatase BB28_RS19235 alpha-hydroxy-acid oxidizing enzyme -2.1 2.9E-35 MAB_3834c Possible L-lactate dehydrogenase (cytochrome) LldD1 Rv0694 mycofactocin system heme/flavin oxidoreductase MftD BB28_RS08645 epoxide hydrolase -2.2 2.4E-07 MAB_1628c hypothetical protein NA NA BB28_RS13295 beta-ketoacyl-ACP reductase -2.3 3.4E-56 MAB_2723c 3-oxoacyl- Rv1483 3-oxoacyl-ACP...”
M4EEX7 FMN hydroxy acid dehydrogenase domain-containing protein from Brassica campestris
31% identity, 51% coverage
CD1263 putative FMN-dependent dehydrogenase from Clostridium difficile 630
31% identity, 80% coverage
- Integration of metabolism and virulence by Clostridium difficile CodY
Dineen, Journal of bacteriology 2010 - “...CD0444 CD0445-CD0447 CD0849 (abgB2) CD0882-CD0886 (glgCDAP) CD1263 CD1389 CD1612 CD2158 (gabT) CD2164 (ldh) CD2344-CD2340 CD2819 CD2859 Oxidoreductase...”
- “...57.1 89.5 21.6 CD2822 CD2426 CD0445 abgB glgCD CD1263 CD2158 CD2164 CD2344 CD2189 CD2859 211.6 103.8 4.46 51.7-174.8 CD0440 tcdR, tcdB Continued on following...”
LOC114303062 peroxisomal (S)-2-hydroxy-acid oxidase GLO4-like from Camellia sinensis
35% identity, 56% coverage
Dret_0157 FMN-dependent alpha-hydroxy acid dehydrogenase from Desulfohalobium retbaense DSM 5692
47% identity, 36% coverage
- Complete genome sequence of Desulfohalobium retbaense type strain (HR(100))
Spring, Standards in genomic sciences 2010 - “...the gene Dret_1039. Following transport, lactate is oxidized to pyruvate by a putative L-lactate dehydrogenase (Dret_0157). Pyruvate is then oxidatively decarboxylated by a pyruvate ferredoxin oxidoreductase to acetyl-CoA. Interestingly, the gene Dret_1036 encoding a homodimeric pyruvate ferredoxin oxidoreductase is located in close proximity to the lactate...”
Dde_0750 L-lactate dehydrogenase (lldD) from Desulfovibrio desulfuricans G20
52% identity, 32% coverage
DVU2784 dehydrogenase, FMN-dependent family from Desulfovibrio vulgaris Hildenborough
49% identity, 32% coverage
- LurR is a regulator of the central lactate oxidation pathway in sulfate-reducing Desulfovibrio species
Rajeev, PloS one 2019 - “...genes in the same operon (DVU2874-3) [ 36 ]. The L-lactate dehydrogenase genes DVU1781-83 and DVU2784 are expressed at similar levels to DVU3032-3033. Expression of some of the alternate D- and L-lactate dehydrogenase genes were variably altered in response to deletions of either dld-II or lldFG...”
- Proteomic and Isotopic Response of Desulfovibrio vulgaris to DsrC Perturbation
Leavitt, Frontiers in microbiology 2019 - “...energy metabolism but less directly involved in sulfate respiration were also identified. Lactate dehydrogenase LldD (DVU2784, 0.45 0.19), was less abundant in IPFG07. Unlike the lactate dehydrogenases discussed above, this enzyme does not belong to the list of putative partners of DsrC ( Venceslau et al.,...”
- The primary pathway for lactate oxidation in Desulfovibrio vulgaris
Vita, Frontiers in microbiology 2015 - “...oxidation ( Figure 2 ). An ortholog of L -lactate dehydrogenase from Escherichia coli , DVU2784, was identified, and it exhibited 32% sequence identity. This protein contained the HGGR motif for FMN binding and essential residue for enzymatic catalysis ( Dong et al., 1993 ). In...”
- “...DVU1781-83 Conserved hypothetical protein (1781) Iron-sulfur cluster-binding protein (1782) Cysteine-rich domain protein (1783) L -LdD DVU2784 Dehydrogenase, FMN-dependent family Fermentative LDHs DVU0600 L -lactate dehydrogenase D -LdhA DVU1412 D -isomer specific 2-hydroxyacid dehydrogenase family protein To obtain information on the functional role of LDH orthologs, expression...”
- Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough
Zhou, Applied and environmental microbiology 2012 - “...0.46 (0.62) 2.00 (2.98) Energy production and conversion DVU3171 DVU2784 N/A lldD 0.63 (0.64) 0.63 (0.97) 1.26 (1.30) 1.36 (2.32) 0.88 (0.93) 1.07 (1.90) 1.45...”
- Temporal transcriptomic analysis as Desulfovibrio vulgaris Hildenborough transitions into stationary phase during electron donor depletion
Clark, Applied and environmental microbiology 2006 - “...ORFs were annotated as putative lactate dehydrogenase genes (DVU0600, DVU2784, and DVU0253) in the D. vulgaris genome. The levels of two of these genes were...”
- “...29 h (data not shown). The level of ORF DVU2784 remained mostly unchanged. The expression of the putative dsrA and dvsB genes (encoding dissimilatory sulfite...”
CACET_c16820 alpha-hydroxy-acid oxidizing protein from Clostridium aceticum
49% identity, 36% coverage
WP_005721074 FMN-dependent dehydrogenase from Lactobacillus crispatus
26% identity, 83% coverage
AF0807 L-lactate dehydrogenase, cytochrome-type (lldD) from Archaeoglobus fulgidus DSM 4304
41% identity, 36% coverage
- Physiological and Genomic Characterization of a Hyperthermophilic Archaeon Archaeoglobus neptunius sp. nov. Isolated From a Deep-Sea Hydrothermal Vent Warrants the Reclassification of the Genus Archaeoglobus
Slobodkina, Frontiers in microbiology 2021 - “...sulfate. The genes for D-lactate and L-lactate dehydrogenases ( dld , AF0394 and lldD , AF0807) were annotated in the genome of the type strain A. fulgidus ( Klenk et al., 1997 ). The transcriptomic study proposed that lldD (AF0807) is part of a cluster and...”
- Identification of key components in the energy metabolism of the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus by transcriptome analyses
Hocking, Frontiers in microbiology 2014 - “...lactate permease and 5 putative lactate dehydrogenase (LDH) genes ( lctp ; AF0806, lldD ; AF0807, dld ; AF0808 and lldEFG ; AF0809-AF0811, Table 1E , Figures 3 , 5 ). The genes AF0809-AF0811 may encode an oligomeric LDH ( lldEFG ) based on the presence...”
AF_0807 alpha-hydroxy acid oxidase from Archaeoglobus fulgidus DSM 4304
41% identity, 37% coverage
- A novel methoxydotrophic metabolism discovered in the hyperthermophilic archaeon Archaeoglobus fulgidus
Welte, Environmental microbiology 2021 - “...and Act14 (AF_0117, AF_0918, AF_1330, AF_2278), Dlactate dehydrogenase Dld (AF_0394 & AF_0808), Llactate dehydrogenase LldD (AF_0807) and LldEFG (AF_0809AF_0811), lactate permease lctP (AF_0806), pyruvate carboxylase PycA (AF_0220) and oxaloacetate decarboxylase Oad (AF_1252), malate dehydrogenase MdhA (AF_0855) and malate oxidoreductase Mae (AF_1727), fumarate hydratase Fum1/2 (AF_1098/9), succinate...”
TP0291 T. pallidum predicted coding region TP0291 from Treponema pallidum subsp. pallidum str. Nichols
TPASS_0291 hypothetical protein from Treponema pallidum subsp. pallidum SS14
37% identity, 29% coverage
mgsC / D7R621 N-methyl-L-glutamate synthase γ subunit (EC 2.1.1.21) from Methyloversatilis universalis (see 2 papers)
33% identity, 25% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 784,739 different protein sequences to 1,253,012 scientific articles. Searches against EuropePMC were last performed on November 25 2024.
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