The Enzyme Database

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EC 1.1.1.11     
Accepted name: D-arabinitol 4-dehydrogenase
Reaction: D-arabinitol + NAD+ = D-xylulose + NADH + H+
Other name(s): D-arabitol dehydrogenase; arabitol dehydrogenase
Systematic name: D-arabinitol:NAD+ 4-oxidoreductase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9028-18-6
References:
1.  Lin, E.C.C. An inducible D-arabitol dehydrogenase from Aerobacter aerogenes. J. Biol. Chem. 236 (1961) 31–36. [PMID: 13762204]
2.  Wood, W.A., McDonough, M.J. and Jacobs, L.B. Ribitol and D-arabitol utilization by Aerobacter aerogenes. J. Biol. Chem. 236 (1961) 2190–2195. [PMID: 13786517]
[EC 1.1.1.11 created 1961]
 
 
EC 1.1.1.56     
Accepted name: ribitol 2-dehydrogenase
Reaction: ribitol + NAD+ = D-ribulose + NADH + H+
Other name(s): adonitol dehydrogenase; ribitol dehydrogenase A (wild type); ribitol dehydrogenase B (mutant enzyme with different properties); ribitol dehydrogenase D (mutant enzyme with different properties)
Systematic name: ribitol:NAD+ 2-oxidoreductase
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9014-23-7
References:
1.  Hollmann, S. and Touster, O. The L-xylulose-xylitol enzyme and other polyol dehydrogenases of guinea pig liver mitochondria. J. Biol. Chem. 225 (1957) 87–102. [PMID: 13416220]
2.  Nordlie, R.C. and Fromm, H.J. Ribitol dehydrogenase. II. Studies on the reaction mechanism. J. Biol. Chem. 234 (1959) 2523–2531. [PMID: 14427582]
3.  Wood, W.A., McDonough, M.J. and Jacobs, L.B. Ribitol and D-arabitol utilization by Aerobacter aerogenes. J. Biol. Chem. 236 (1961) 2190–2195. [PMID: 13786517]
[EC 1.1.1.56 created 1965]
 
 
EC 1.1.1.95     
Accepted name: phosphoglycerate dehydrogenase
Reaction: 3-phospho-D-glycerate + NAD+ = 3-phosphooxypyruvate + NADH + H+
For diagram of serine biosynthesis, click here
Other name(s): PHGDH (gene name); D-3-phosphoglycerate:NAD+ oxidoreductase; α-phosphoglycerate dehydrogenase; 3-phosphoglycerate dehydrogenase; 3-phosphoglyceric acid dehydrogenase; D-3-phosphoglycerate dehydrogenase; glycerate 3-phosphate dehydrogenase; glycerate-1,3-phosphate dehydrogenase; phosphoglycerate oxidoreductase; phosphoglyceric acid dehydrogenase; SerA; 3-phosphoglycerate:NAD+ 2-oxidoreductase; SerA 3PG dehydrogenase; 3PHP reductase
Systematic name: 3-phospho-D-glycerate:NAD+ 2-oxidoreductase
Comments: This enzyme catalyses the first committed and rate-limiting step in the phosphoserine pathway of serine biosynthesis. The reaction occurs predominantly in the direction of reduction. The enzyme from the bacterium Escherichia coli also catalyses the activity of EC 1.1.1.399, 2-oxoglutarate reductase [6].
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9075-29-0
References:
1.  Pizer, L.I. The pathway and control of serine biosynthesis in Escherichia coli. J. Biol. Chem. 238 (1963) 3934–3944. [PMID: 14086727]
2.  Walsh, D.A. and Sallach, H.J. Purification and properties of chicken liver D-3-phosphoglycerate dehydrogenase. Biochemistry 4 (1965) 1076–1085. [PMID: 4378782]
3.  Slaughter, J.C. and Davies, D.D. The isolation and characterization of 3-phosphoglycerate dehydrogenase from peas. Biochem. J. 109 (1968) 743–748. [PMID: 4386930]
4.  Sugimoto, E. and Pizer, L.I. The mechanism of end product inhibition of serine biosynthesis. I. Purification and kinetics of phosphoglycerate dehydrogenase. J. Biol. Chem. 243 (1968) 2081. [PMID: 4384871]
5.  Schuller, D.J., Grant, G.A. and Banaszak, L.J. The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase. Nat. Struct. Biol. 2 (1995) 69–76. [PMID: 7719856]
6.  Zhao, G. and Winkler, M.E. A novel α-ketoglutarate reductase activity of the serA-encoded 3-phosphoglycerate dehydrogenase of Escherichia coli K-12 and its possible implications for human 2-hydroxyglutaric aciduria. J. Bacteriol. 178 (1996) 232–239. [DOI] [PMID: 8550422]
7.  Achouri, Y., Rider, M.H., Schaftingen, E.V. and Robbi, M. Cloning, sequencing and expression of rat liver 3-phosphoglycerate dehydrogenase. Biochem. J. 323 (1997) 365–370. [PMID: 9163325]
8.  Dey, S., Grant, G.A. and Sacchettini, J.C. Crystal structure of Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase: extreme asymmetry in a tetramer of identical subunits. J. Biol. Chem. 280 (2005) 14892–14899. [DOI] [PMID: 15668249]
[EC 1.1.1.95 created 1972, modified 2006, modified 2016]
 
 
EC 1.1.1.266     
Accepted name: dTDP-4-dehydro-6-deoxyglucose reductase
Reaction: dTDP-α-D-fucopyranose + NAD(P)+ = dTDP-4-dehydro-6-deoxy-α-D-glucose + NAD(P)H + H+
For diagram of dTDP-6-deoxyhexose biosynthesis, click here
Glossary: dTDP-4-dehydro-6-deoxy-α-D-glucose = dTDP-6-deoxy-α-D-xylo-hexopyranos-4-ulose = thymidine 5′-[3-(6-deoxy--D-xylo-hexopyranosyl-4-ulose) diphosphate]
Other name(s): dTDP-4-keto-6-deoxyglucose reductase; dTDP-D-fucose:NADP+ oxidoreductase; Fcf1; dTDP-6-deoxy-D-xylo-hex-4-ulopyranose reductase
Systematic name: dTDP-α-D-fucopyranose:NAD(P)+ oxidoreductase
Comments: The enzymes from the Gram-negative bacteria Aggregatibacter actinomycetemcomitans and Escherichia coli O52 are involved in activation of fucose for incorporation into capsular polysaccharide O-antigens [1,3]. The enzyme from the Gram-positive bacterium Anoxybacillus tepidamans (Geobacillus tepidamans) is involved in activation of fucose for incorporation into the organism’s S-layer [2]. The enzyme from Escherichia coli O52 has a higher catalytic efficiency with NADH than with NADPH [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Yoshida, Y., Nakano, Y., Nezu, T., Yamashita, Y. and Koga, T. A novel NDP-6-deoxyhexosyl-4-ulose reductase in the pathway for the synthesis of thymidine diphosphate-D-fucose. J. Biol. Chem. 274 (1999) 16933–16939. [DOI] [PMID: 10358040]
2.  Zayni, S., Steiner, K., Pfostl, A., Hofinger, A., Kosma, P., Schaffer, C. and Messner, P. The dTDP-4-dehydro-6-deoxyglucose reductase encoding fcd gene is part of the surface layer glycoprotein glycosylation gene cluster of Geobacillus tepidamans GS5-97T. Glycobiology 17 (2007) 433–443. [DOI] [PMID: 17202151]
3.  Wang, Q., Ding, P., Perepelov, A.V., Xu, Y., Wang, Y., Knirel, Y.A., Wang, L. and Feng, L. Characterization of the dTDP-D-fucofuranose biosynthetic pathway in Escherichia coli O52. Mol. Microbiol. 70 (2008) 1358–1367. [DOI] [PMID: 19019146]
[EC 1.1.1.266 created 2001, modified 2013]
 
 
EC 1.1.1.271     
Accepted name: GDP-L-fucose synthase
Reaction: GDP-β-L-fucose + NADP+ = GDP-4-dehydro-α-D-rhamnose + NADPH + H+
For diagram of GDP-L-Fucose and GDP-mannose biosynthesis, click here
Glossary: GDP-4-dehydro-α-D-rhamnose = GDP-4-dehydro-6-deoxy-α-D-mannose
Other name(s): GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4-reductase; GDP-L-fucose:NADP+ 4-oxidoreductase (3,5-epimerizing)
Systematic name: GDP-β-L-fucose:NADP+ 4-oxidoreductase (3,5-epimerizing)
Comments: Both human and Escherichia coli enzymes can use NADH in place of NADPH to a slight extent.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 113756-18-6
References:
1.  Chang, S., Duerr, B. and Serif, G. An epimerase-reductase in L-fucose synthesis. J. Biol. Chem. 263 (1988) 1693–1697. [PMID: 3338988]
2.  Mattila, P., Räbinä, J, Hortling, S., Jelin, J. and Renkonen, R. Functional expression of Escherichia coli enzymes synthesizing GDP-L-fucose from inherent GDP-D-mannose in Saccharomyces cerevisiae. Glycobiology 10 (2000) 1041–1047. [DOI] [PMID: 11030750]
3.  Menon, S., Stahl, M., Kumar, R., Xu, G.-Y. and Sullivan, F. Stereochemical course and steady state mechanism of the reaction catalyzed by the GDP-fucose synthetase from Escherichia coli. J. Biol. Chem. 274 (1999) 26743–26750. [DOI] [PMID: 10480878]
4.  Somers, W.S., Stahl, M.L. and Sullivan, F.X. GDP-fucose synthetase from Escherichia coli: Structure of a unique member of the short-chain dehydrogenase/reductase family that catalyzes two distinct reactions at the same active site. Structure 6 (1998) 1601–1612. [DOI] [PMID: 9862812]
[EC 1.1.1.271 created 2002, modified 2003]
 
 
EC 1.1.1.306     
Accepted name: S-(hydroxymethyl)mycothiol dehydrogenase
Reaction: S-(hydroxymethyl)mycothiol + NAD+ = S-formylmycothiol + NADH + H+
Glossary: mycothiol = 1-O-[2-(N2-acetyl-L-cysteinamido)-2-deoxy-α-D-glucopyranosyl]-1D-myo-inositol
Other name(s): NAD/factor-dependent formaldehyde dehydrogenase; mycothiol-dependent formaldehyde dehydrogenase
Systematic name: S-(hydroxymethyl)mycothiol:NAD+ oxidoreductase
Comments: S-hydroxymethylmycothiol is believed to form spontaneously from formaldehyde and mycothiol. This enzyme oxidizes the product of this spontaneous reaction to S-formylmycothiol, in a reaction that is analogous to EC 1.1.1.284, S-(hydroxymethyl)glutathione dehydrogenase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 192140-85-5
References:
1.  Misset-Smits, M., Van Ophem, P.W., Sakuda, S. and Duine, J.A. Mycothiol, 1-O-(2′-[N-acetyl-L-cysteinyl]amido-2′-deoxy-α-D-glucopyranosyl)-D-myo-inositol, is the factor of NAD/factor-dependent formaldehyde dehydrogenase. FEBS Lett. 409 (1997) 221–222. [DOI] [PMID: 9202149]
2.  Norin, A., Van Ophem, P.W., Piersma, S.R., Person, B., Duine, J.A. and Jornvall, H. Mycothiol-dependent formaldehyde dehydrogenase, a prokaryotic medium-chain dehydrogenase/reductase, phylogenetically links different eukaryotic alcohol dehydrogenase's - primary structure, conformational modelling and functional correlations. Eur. J. Biochem. 248 (1997) 282–289. [DOI] [PMID: 9346279]
3.  Vogt, R.N., Steenkamp, D.J., Zheng, R. and Blanchard, J.S. The metabolism of nitrosothiols in the Mycobacteria: identification and characterization of S-nitrosomycothiol reductase. Biochem. J. 374 (2003) 657–666. [DOI] [PMID: 12809551]
4.  Rawat, M. and Av-Gay, Y. Mycothiol-dependent proteins in actinomycetes. FEMS Microbiol. Rev. 31 (2007) 278–292. [DOI] [PMID: 17286835]
[EC 1.1.1.306 created 2010 as EC 1.2.1.66, transferred 2010 to EC 1.1.1.306]
 
 
EC 1.1.1.333     
Accepted name: decaprenylphospho-β-D-erythro-pentofuranosid-2-ulose 2-reductase
Reaction: trans,octacis-decaprenylphospho-β-D-arabinofuranose + NAD+ = trans,octacis-decaprenylphospho-β-D-erythro-pentofuranosid-2-ulose + NADH + H+
For diagram of decaprenylphosphoarabinofuranose biosynthesis, click here
Other name(s): decaprenylphospho-β-D-ribofuranose 2′-epimerase; Rv3791; DprE2
Systematic name: trans,octacis-decaprenylphospho-β-D-arabinofuranose:NAD+ 2-oxidoreductase
Comments: The reaction is catalysed in the reverse direction. The enzyme, isolated from the bacterium Mycobacterium smegmatis, is involved, along with EC 1.1.98.3, decaprenylphospho-β-D-ribofuranose 2-oxidase, in the epimerization of trans,octacis-decaprenylphospho-β-D-ribofuranose to trans,octacis-decaprenylphospho-β-D-arabinoofuranose, the arabinosyl donor for the biosynthesis of mycobacterial cell wall arabinan polymers.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Trefzer, C., Škovierová, H., Buroni, S., Bobovská, A., Nenci, S., Molteni, E., Pojer, F., Pasca, M.R., Makarov, V., Cole, S.T., Riccardi, G., Mikušová, K. and Johnsson, K. Benzothiazinones are suicide inhibitors of mycobacterial decaprenylphosphoryl-β-D-ribofuranose 2′-oxidase DprE1. J. Am. Chem. Soc. 134 (2012) 912–915. [DOI] [PMID: 22188377]
[EC 1.1.1.333 created 2012]
 
 
EC 1.1.1.364     
Accepted name: dTDP-4-dehydro-6-deoxy-α-D-gulose 4-ketoreductase
Reaction: dTDP-6-deoxy-α-D-allose + NAD(P)+ = dTDP-4-dehydro-6-deoxy-α-D-gulose + NAD(P)H + H+
For diagram of dTDP-6-deoxy-α-D-allose biosynthesis, click here and for diagram of dTDP-6-deoxyhexose biosynthesis, click here
Glossary: dTDP-4-dehydro-6-deoxy-α-D-gulose = dTDP-4-dehydro-6-deoxy-α-D-allose
Other name(s): dTDP-4-dehydro-6-deoxygulose reductase; tylD (gene name); gerKI (gene name); chmD (gene name); mydI (gene name)
Systematic name: dTDP-6-deoxy-α-D-allose:NAD(P)+ oxidoreductase
Comments: The enzyme forms an activated deoxy-α-D-allose, which is converted to mycinose after attachment to the aglycones of several macrolide antibiotics, including tylosin, chalcomycin, dihydrochalcomycin, and mycinamicin II.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Bate, N. and Cundliffe, E. The mycinose-biosynthetic genes of Streptomyces fradiae, producer of tylosin. J Ind Microbiol Biotechnol 23 (1999) 118–122. [PMID: 10510490]
2.  Anzai, Y., Saito, N., Tanaka, M., Kinoshita, K., Koyama, Y. and Kato, F. Organization of the biosynthetic gene cluster for the polyketide macrolide mycinamicin in Micromonospora griseorubida. FEMS Microbiol. Lett. 218 (2003) 135–141. [DOI] [PMID: 12583909]
3.  Thuy, T.T., Liou, K., Oh, T.J., Kim, D.H., Nam, D.H., Yoo, J.C. and Sohng, J.K. Biosynthesis of dTDP-6-deoxy-β-D-allose, biochemical characterization of dTDP-4-keto-6-deoxyglucose reductase (GerKI) from Streptomyces sp. KCTC 0041BP. Glycobiology 17 (2007) 119–126. [DOI] [PMID: 17053005]
4.  Kubiak, R.L., Phillips, R.K., Zmudka, M.W., Ahn, M.R., Maka, E.M., Pyeatt, G.L., Roggensack, S.J. and Holden, H.M. Structural and functional studies on a 3′-epimerase involved in the biosynthesis of dTDP-6-deoxy-D-allose. Biochemistry 51 (2012) 9375–9383. [DOI] [PMID: 23116432]
[EC 1.1.1.364 created 2013]
 
 
EC 1.1.1.400     
Accepted name: 2-methyl-1,2-propanediol dehydrogenase
Reaction: 2-methylpropane-1,2-diol + NAD+ = 2-hydroxy-2-methylpropanal + NADH + H+
Other name(s): mpdB (gene name)
Systematic name: 2-methylpropane-1,2-diol:NAD+ 1-oxidoreductase
Comments: This bacterial enzyme is involved in the degradation pathways of the alkene 2-methylpropene and the fuel additive tert-butyl methyl ether (MTBE), a widely occurring groundwater contaminant.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Lopes Ferreira, N., Labbe, D., Monot, F., Fayolle-Guichard, F. and Greer, C.W. Genes involved in the methyl tert-butyl ether (MTBE) metabolic pathway of Mycobacterium austroafricanum IFP 2012. Microbiology 152 (2006) 1361–1374. [DOI] [PMID: 16622053]
2.  Kottegoda, S., Waligora, E. and Hyman, M. Metabolism of 2-methylpropene (isobutylene) by the aerobic bacterium Mycobacterium sp. strain ELW1. Appl. Environ. Microbiol. 81 (2015) 1966–1976. [DOI] [PMID: 25576605]
[EC 1.1.1.400 created 2016]
 
 
EC 1.1.1.403     
Accepted name: D-threitol dehydrogenase (NAD+)
Reaction: D-threitol + NAD+ = D-erythrulose + NADH + H+
Other name(s): dthD (gene name)
Systematic name: D-threitol:NAD+ oxidoreductase
Comments: The enzyme, characterized from the bacterium Mycobacterium smegmatis, participates in the degradation of D-threitol.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Huang, H., Carter, M.S., Vetting, M.W., Al-Obaidi, N., Patskovsky, Y., Almo, S.C. and Gerlt, J.A. A general strategy for the discovery of metabolic pathways: D-threitol, L-threitol, and erythritol utilization in Mycobacterium smegmatis. J. Am. Chem. Soc. 137 (2015) 14570–14573. [DOI] [PMID: 26560079]
[EC 1.1.1.403 created 2016]
 
 
EC 1.1.1.408     
Accepted name: 4-phospho-D-threonate 3-dehydrogenase
Reaction: 4-phospho-D-threonate + NAD+ = glycerone phosphate + CO2 + NADH + H+ (overall reaction)
(1a) 4-phospho-D-threonate + NAD+ = 3-dehydro-4-phospho-D-erythronate + NADH + H+
(1b) 3-dehydro-4-phospho-D-erythronate = glycerone phosphate + CO2 (spontaneous)
For diagram of erythronate and threonate catabolism, click here
Glossary: D-threonate = (2S,3R)-2,3,4-trihydroxybutanoate
glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): pdxA2 (gene name) (ambiguous)
Systematic name: 4-phospho-D-threonate:NAD+ 3-oxidoreductase
Comments: The enzyme, characterized from bacteria, is involved in a pathway for D-threonate catabolism.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Zhang, X., Carter, M.S., Vetting, M.W., San Francisco, B., Zhao, S., Al-Obaidi, N.F., Solbiati, J.O., Thiaville, J.J., de Crecy-Lagard, V., Jacobson, M.P., Almo, S.C. and Gerlt, J.A. Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Proc. Natl. Acad. Sci. USA 113 (2016) E4161–E4169. [DOI] [PMID: 27402745]
[EC 1.1.1.408 created 2017]
 
 
EC 1.1.1.409     
Accepted name: 4-phospho-D-erythronate 3-dehydrogenase
Reaction: 4-phospho-D-erythronate + NAD+ = glycerone phosphate + CO2 + NADH + H+ (overall reaction)
(1a) 4-phospho-D-erythronate + NAD+ = 3-dehydro-4-phospho-L-threonate + NADH + H+
(1b) 3-dehydro-4-phospho-L-threonate = glycerone phosphate + CO2 (spontaneous)
For diagram of erythronate and threonate catabolism, click here
Glossary: D-erythronate = (2R,3R)-2,3,4-trihydroxybutanoate
Other name(s): pdxA2 (gene name) (ambiguous)
Systematic name: 4-phospho-D-erythronate:NAD+ 3-oxidoreductase
Comments: The enzyme, characterized from bacteria, is involved in a pathway for D-erythronate catabolism.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Zhang, X., Carter, M.S., Vetting, M.W., San Francisco, B., Zhao, S., Al-Obaidi, N.F., Solbiati, J.O., Thiaville, J.J., de Crecy-Lagard, V., Jacobson, M.P., Almo, S.C. and Gerlt, J.A. Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Proc. Natl. Acad. Sci. USA 113 (2016) E4161–E4169. [DOI] [PMID: 27402745]
[EC 1.1.1.409 created 2017]
 
 
EC 1.1.1.410     
Accepted name: D-erythronate 2-dehydrogenase
Reaction: D-erythronate + NAD+ = 2-dehydro-D-erythronate + NADH + H+
For diagram of erythronate and threonate catabolism, click here
Glossary: D-erythronate = (2R,3R)-2,3,4-trihydroxybutanoate
2-dehydro-D-erythronate = (3R)-3,4-dihydroxy-2-oxobutanoate
Other name(s): denD (gene name)
Systematic name: D-erythronate:NAD+ 2-oxidoreductase
Comments: The enzyme, characterized from bacteria, is involved in D-erythronate catabolism.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Zhang, X., Carter, M.S., Vetting, M.W., San Francisco, B., Zhao, S., Al-Obaidi, N.F., Solbiati, J.O., Thiaville, J.J., de Crecy-Lagard, V., Jacobson, M.P., Almo, S.C. and Gerlt, J.A. Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Proc. Natl. Acad. Sci. USA 113 (2016) E4161–E4169. [DOI] [PMID: 27402745]
[EC 1.1.1.410 created 2017]
 
 
EC 1.1.1.411     
Accepted name: L-threonate 2-dehydrogenase
Reaction: L-threonate + NAD+ = 2-dehydro-L-erythronate + NADH + H+
For diagram of erythronate and threonate catabolism, click here
Glossary: L-threonate = (2R,3S)-2,3,4-trihydroxybutanoate
2-dehydro-L-erythronate = (3R)-3,4-dihydroxy-2-oxobutanoate
Other name(s): ltnD (gene name)
Systematic name: L-threonate:NAD+ 2-oxidoreductase
Comments: The enzyme, characterized from bacteria, is involved in L-threonate catabolism.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Zhang, X., Carter, M.S., Vetting, M.W., San Francisco, B., Zhao, S., Al-Obaidi, N.F., Solbiati, J.O., Thiaville, J.J., de Crecy-Lagard, V., Jacobson, M.P., Almo, S.C. and Gerlt, J.A. Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Proc. Natl. Acad. Sci. USA 113 (2016) E4161–E4169. [DOI] [PMID: 27402745]
[EC 1.1.1.411 created 2017]
 
 
EC 1.1.5.4     
Accepted name: malate dehydrogenase (quinone)
Reaction: (S)-malate + a quinone = oxaloacetate + reduced quinone
Other name(s): FAD-dependent malate-vitamin K reductase; malate-vitamin K reductase; (S)-malate:(acceptor) oxidoreductase; L-malate-quinone oxidoreductase; malate:quinone oxidoreductase; malate quinone oxidoreductase; MQO; malate:quinone reductase; malate dehydrogenase (acceptor); FAD-dependent malate dehydrogenase
Systematic name: (S)-malate:quinone oxidoreductase
Comments: A flavoprotein (FAD). Vitamin K and several other quinones can act as acceptors. Different from EC 1.1.1.37 (malate dehydrogenase (NAD+)), EC 1.1.1.82 (malate dehydrogenase (NADP+)) and EC 1.1.1.299 (malate dehydrogenase [NAD(P)+]).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Imai, D. and Brodie, A.F. A phospholipid-requiring enzyme, malate-vitamin K reductase. J. Biol. Chem. 248 (1973) 7487–7494.
2.  Imai, T. FAD-dependent malate dehydrogenase, a phospholipid-requiring enzyme from Mycobacterium sp. strain Takeo. Purification and some properties. Biochim. Biophys. Acta 523 (1978) 37–46. [DOI] [PMID: 629992]
3.  Reddy, T.L.P., Suryanarayana, P.M. and Venkitasubramanian, T.A. Variations in the pathways of malate oxidation and phosphorylation in different species of Mycobacteria. Biochim. Biophys. Acta 376 (1975) 210–218. [DOI] [PMID: 234747]
4.  Molenaar, D., van der Rest, M.E. and Petrovic, S. Biochemical and genetic characterization of the membrane-associated malate dehydrogenase (acceptor) from Corynebacterium glutamicum. Eur. J. Biochem. 254 (1998) 395–403. [DOI] [PMID: 9660197]
5.  Kather, B., Stingl, K., van der Rest, M.E., Altendorf, K. and Molenaar, D. Another unusual type of citric acid cycle enzyme in Helicobacter pylori: the malate:quinone oxidoreductase. J. Bacteriol. 182 (2000) 3204–3209. [DOI] [PMID: 10809701]
[EC 1.1.5.4 created 1978 as EC 1.1.99.16, transferred 2009 to EC 1.1.5.4]
 
 
EC 1.1.98.2     
Accepted name: glucose-6-phosphate dehydrogenase (coenzyme-F420)
Reaction: D-glucose 6-phosphate + oxidized coenzyme F420 = 6-phospho-D-glucono-1,5-lactone + reduced coenzyme F420
Other name(s): coenzyme F420-dependent glucose-6-phosphate dehydrogenase; F420-dependent glucose-6-phosphate dehydrogenase; FGD1; Rv0407; F420-dependent glucose-6-phosphate dehydrogenase 1
Systematic name: D-glucose-6-phosphate:F420 1-oxidoreductase
Comments: The enzyme is very specific for D-glucose 6-phosphate. No activity with NAD+, NADP+, FAD and FMN [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Purwantini, E. and Daniels, L. Purification of a novel coenzyme F420-dependent glucose-6-phosphate dehydrogenase from Mycobacterium smegmatis. J. Bacteriol. 178 (1996) 2861–2866. [DOI] [PMID: 8631674]
2.  Bashiri, G., Squire, C.J., Baker, E.N. and Moreland, N.J. Expression, purification and crystallization of native and selenomethionine labeled Mycobacterium tuberculosis FGD1 (Rv0407) using a Mycobacterium smegmatis expression system. Protein Expr. Purif. 54 (2007) 38–44. [DOI] [PMID: 17376702]
3.  Purwantini, E., Gillis, T.P. and Daniels, L. Presence of F420-dependent glucose-6-phosphate dehydrogenase in Mycobacterium and Nocardia species, but absence from Streptomyces and Corynebacterium species and methanogenic Archaea. FEMS Microbiol. Lett. 146 (1997) 129–134. [DOI] [PMID: 8997717]
[EC 1.1.98.2 created 2010 as EC 1.1.99.34, transferred 2011 to EC 1.1.98.2]
 
 
EC 1.1.98.3     
Accepted name: decaprenylphospho-β-D-ribofuranose 2-dehydrogenase
Reaction: trans,octacis-decaprenylphospho-β-D-ribofuranose + FAD = trans,octacis-decaprenylphospho-β-D-erythro-pentofuranosid-2-ulose + FADH2
For diagram of decaprenylphosphoarabinofuranose biosynthesis, click here
Other name(s): decaprenylphosphoryl-β-D-ribofuranose 2′-epimerase; Rv3790; DprE1; decaprenylphospho-β-D-ribofuranose 2-oxidase
Systematic name: trans,octacis-decaprenylphospho-β-D-ribofuranose:FAD 2-oxidoreductase
Comments: The enzyme, isolated from the bacterium Mycobacterium smegmatis, is involved, along with EC 1.1.1.333, decaprenylphospho-D-erythro-pentofuranosid-2-ulose 2-reductase, in the epimerization of trans,octacis-decaprenylphospho-β-D-ribofuranose to trans,octacis-decaprenylphospho-β-D-arabinofuranose, the arabinosyl donor for the biosynthesis of mycobacterial cell wall arabinan polymers.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Ribeiro, A.L., Degiacomi, G., Ewann, F., Buroni, S., Incandela, M.L., Chiarelli, L.R., Mori, G., Kim, J., Contreras-Dominguez, M., Park, Y.S., Han, S.J., Brodin, P., Valentini, G., Rizzi, M., Riccardi, G. and Pasca, M.R. Analogous mechanisms of resistance to benzothiazinones and dinitrobenzamides in Mycobacterium smegmatis. PLoS One 6:e26675 (2011). [DOI] [PMID: 22069462]
2.  Trefzer, C., Škovierová, H., Buroni, S., Bobovská, A., Nenci, S., Molteni, E., Pojer, F., Pasca, M.R., Makarov, V., Cole, S.T., Riccardi, G., Mikušová, K. and Johnsson, K. Benzothiazinones are suicide inhibitors of mycobacterial decaprenylphosphoryl-β-D-ribofuranose 2′-oxidase DprE1. J. Am. Chem. Soc. 134 (2012) 912–915. [DOI] [PMID: 22188377]
[EC 1.1.98.3 created 2012, modified 2014]
 
 
EC 1.1.99.16      
Transferred entry: malate dehydrogenase (acceptor). As the acceptor is now known, the enzyme has been transferred to EC 1.1.5.4, malate dehydrogenase (quinone).
[EC 1.1.99.16 created 1978, deleted 2009]
 
 
EC 1.1.99.34      
Transferred entry: glucose-6-phosphate dehydrogenase (coenzyme-F420). As the acceptor is now known, the enzyme has been transferred to EC 1.1.98.2, glucose-6-phosphate dehydrogenase (coenzyme-F420)
[EC 1.1.99.34 created 2010, deleted 2011]
 
 
EC 1.1.99.37     
Accepted name: methanol dehydrogenase (nicotinoprotein)
Reaction: methanol + acceptor = formaldehyde + reduced acceptor
Other name(s): NDMA-dependent methanol dehydrogenase; nicotinoprotein methanol dehydrogenase; methanol:N,N-dimethyl-4-nitrosoaniline oxidoreductase
Systematic name: methanol:acceptor oxidoreductase
Comments: Contains Zn2+ and Mg2+. Nicotinoprotein methanol dehydrogenases have a tightly bound NADP+/NADPH cofactor that does not dissociate during the catalytic process. Instead, the cofactor is regenerated by a second substrate or electron carrier. While the in vivo electron acceptor is not known, N,N-dimethyl-4-nitrosoaniline (NDMA), which is reduced to 4-(hydroxylamino)-N,N-dimethylaniline, can serve this function in vitro. The enzyme has been detected in several Gram-positive methylotrophic bacteria, including Amycolatopsis methanolica, Rhodococcus rhodochrous and Rhodococcus erythropolis [1-3]. These enzymes are decameric, and possess a 5-fold symmetry [4]. Some of the enzymes can also dismutate formaldehyde to methanol and formate [5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Vonck, J., Arfman, N., De Vries, G.E., Van Beeumen, J., Van Bruggen, E.F. and Dijkhuizen, L. Electron microscopic analysis and biochemical characterization of a novel methanol dehydrogenase from the thermotolerant Bacillus sp. C1. J. Biol. Chem. 266 (1991) 3949–3954. [PMID: 1995642]
2.  Van Ophem, P.W., Van Beeumen, J. and Duine, J.A. Nicotinoprotein [NAD(P)-containing] alcohol/aldehyde oxidoreductases. Purification and characterization of a novel type from Amycolatopsis methanolica. Eur. J. Biochem. 212 (1993) 819–826. [DOI] [PMID: 8385013]
3.  Bystrykh, L.V., Vonck, J., van Bruggen, E.F., van Beeumen, J., Samyn, B., Govorukhina, N.I., Arfman, N., Duine, J.A. and Dijkhuizen, L. Electron microscopic analysis and structural characterization of novel NADP(H)-containing methanol: N,N′-dimethyl-4-nitrosoaniline oxidoreductases from the gram-positive methylotrophic bacteria Amycolatopsis methanolica and Mycobacterium gastri MB19. J. Bacteriol. 175 (1993) 1814–1822. [DOI] [PMID: 8449887]
4.  Hektor, H.J., Kloosterman, H. and Dijkhuizen, L. Identification of a magnesium-dependent NAD(P)(H)-binding domain in the nicotinoprotein methanol dehydrogenase from Bacillus methanolicus. J. Biol. Chem. 277 (2002) 46966–46973. [DOI] [PMID: 12351635]
5.  Park, H., Lee, H., Ro, Y.T. and Kim, Y.M. Identification and functional characterization of a gene for the methanol : N,N′-dimethyl-4-nitrosoaniline oxidoreductase from Mycobacterium sp. strain JC1 (DSM 3803). Microbiology 156 (2010) 463–471. [DOI] [PMID: 19875438]
[EC 1.1.99.37 created 2010]
 
 
EC 1.2.1.98     
Accepted name: 2-hydroxy-2-methylpropanal dehydrogenase
Reaction: 2-hydroxy-2-methylpropanal + NAD+ + H2O = 2-hydroxy-2-methylpropanoate + NADH + H+
Other name(s): mpdC (gene name)
Systematic name: 2-hydroxy-2-methylpropanal:NAD+ oxidoreductase
Comments: This bacterial enzyme is involved in the degradation pathways of the alkene 2-methylpropene and the fuel additive tert-butyl methyl ether (MTBE), a widely occurring groundwater contaminant.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Lopes Ferreira, N., Labbe, D., Monot, F., Fayolle-Guichard, F. and Greer, C.W. Genes involved in the methyl tert-butyl ether (MTBE) metabolic pathway of Mycobacterium austroafricanum IFP 2012. Microbiology 152 (2006) 1361–1374. [DOI] [PMID: 16622053]
[EC 1.2.1.98 created 2016]
 
 
EC 1.2.2.4      
Deleted entry: carbon-monoxide dehydrogenase (cytochrome b-561). Now classified as EC 1.2.5.3, aerobic carbon monoxide dehydrogenase
[EC 1.2.2.4 created 1999 (EC 1.2.3.10 created 1990, incorporated 2003), modified 2003, deleted 2020]
 
 
EC 1.2.7.12     
Accepted name: formylmethanofuran dehydrogenase
Reaction: a formylmethanofuran + H2O + 2 oxidized ferredoxin [iron-sulfur] cluster = CO2 + a methanofuran + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+
For diagram of methane biosynthesis, click here
Glossary: methanofuran a = 4-[4-(2-{[(4R*,5S*)-4,5,7-tricarboxyheptanoyl]-γ-L-glutamyl-γ-L-glutamylamino}ethyl)phenoxymethyl]furan-2-ylmethanamine
Other name(s): formylmethanofuran:acceptor oxidoreductase
Systematic name: formylmethanofuran:ferredoxin oxidoreductase
Comments: Contains a molybdopterin cofactor and numerous [4Fe-4S] clusters. In some organisms an additional subunit enables the incorporation of tungsten when molybdenum availability is low. The enzyme catalyses a reversible reaction in methanogenic archaea, and is involved in methanogenesis from CO2 as well as the oxidation of coenzyme M to CO2. The reaction is endergonic, and is driven by coupling with the soluble CoB-CoM heterodisulfide reductase via electron bifurcation.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 119940-12-4
References:
1.  Karrasch, M., Börner, G., Enssle, M. and Thauer, R.K. The molybdoenzyme formylmethanofuran dehydrogenase from Methanosarcina barkeri contains a pterin cofactor. Eur. J. Biochem. 194 (1990) 367–372. [DOI] [PMID: 2125267]
2.  Bertram, P.A., Schmitz, R.A., Linder, D. and Thauer, R.K. Tungstate can substitute for molybdate in sustaining growth of Methanobacterium thermoautotrophicum. Identification and characterization of a tungsten isoenzyme of formylmethanofuran dehydrogenase. Arch. Microbiol. 161 (1994) 220–228. [PMID: 8161283]
3.  Bertram, P.A., Karrasch, M., Schmitz, R.A., Bocher, R., Albracht, S.P. and Thauer, R.K. Formylmethanofuran dehydrogenases from methanogenic Archaea. Substrate specificity, EPR properties and reversible inactivation by cyanide of the molybdenum or tungsten iron-sulfur proteins. Eur. J. Biochem. 220 (1994) 477–484. [DOI] [PMID: 8125106]
4.  Vorholt, J.A. and Thauer, R.K. The active species of ’CO2’ utilized by formylmethanofuran dehydrogenase from methanogenic Archaea. Eur. J. Biochem. 248 (1997) 919–924. [DOI] [PMID: 9342247]
5.  Meuer, J., Kuettner, H.C., Zhang, J.K., Hedderich, R. and Metcalf, W.W. Genetic analysis of the archaeon Methanosarcina barkeri Fusaro reveals a central role for Ech hydrogenase and ferredoxin in methanogenesis and carbon fixation. Proc. Natl. Acad. Sci. USA 99 (2002) 5632–5637. [DOI] [PMID: 11929975]
6.  Kaster, A.K., Moll, J., Parey, K. and Thauer, R.K. Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic archaea. Proc. Natl. Acad. Sci. USA 108 (2011) 2981–2986. [DOI] [PMID: 21262829]
7.  Wagner, T., Ermler, U. and Shima, S. The methanogenic CO2 reducing-and-fixing enzyme is bifunctional and contains 46 [4Fe-4S] clusters. Science 354 (2016) 114–117. [PMID: 27846502]
[EC 1.2.7.12 created 1992 as EC 1.2.99.5, transferred 2017 to EC 1.2.7.12]
 
 
EC 1.2.98.1     
Accepted name: formaldehyde dismutase
Reaction: 2 formaldehyde + H2O = formate + methanol
Other name(s): aldehyde dismutase; cannizzanase; nicotinoprotein aldehyde dismutase
Systematic name: formaldehyde:formaldehyde oxidoreductase
Comments: The enzyme contains a tightly but noncovalently bound NADP(H) cofactor, as well as Zn2+ and Mg2+. Enzyme-bound NADPH formed by oxidation of formaldehyde to formate is oxidized back to NADP+ by reaction with a second formaldehyde, yielding methanol. The enzyme from the bacterium Mycobacterium sp. DSM 3803 also catalyses the reactions of EC 1.1.99.36, alcohol dehydrogenase (nicotinoprotein) and EC 1.1.99.37, methanol dehydrogenase (nicotinoprotein) [3]. Formaldehyde and acetaldehyde can act as donors; formaldehyde, acetaldehyde and propanal can act as acceptors [1,2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 85204-94-0
References:
1.  Kato, N., Shirakawa, K., Kobayashi, H. and Sakazawa, C. The dismutation of aldehydes by a bacterial enzyme. Agric. Biol. Chem. 47 (1983) 39–46.
2.  Kato, N., Yamagami, T., Shimao, M. and Sakazawa, C. Formaldehyde dismutase, a novel NAD-binding oxidoreductase from Pseudomonas putida F61. Eur. J. Biochem. 156 (1986) 59–64. [DOI] [PMID: 3514215]
3.  Park, H., Lee, H., Ro, Y.T. and Kim, Y.M. Identification and functional characterization of a gene for the methanol : N,N′-dimethyl-4-nitrosoaniline oxidoreductase from Mycobacterium sp. strain JC1 (DSM 3803). Microbiology 156 (2010) 463–471. [DOI] [PMID: 19875438]
[EC 1.2.98.1 created 1986 as EC 1.2.99.4, modified 2012, transferred 2015 to EC 1.2.98.1]
 
 
EC 1.2.99.4      
Transferred entry: formaldehyde dismutase. Now EC 1.2.98.1, formaldehyde dismutase.
[EC 1.2.99.4 created 1986, modified 2012, deleted 2015]
 
 
EC 1.3.1.9     
Accepted name: enoyl-[acyl-carrier-protein] reductase (NADH)
Reaction: an acyl-[acyl-carrier protein] + NAD+ = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH + H+
Other name(s): enoyl-[acyl carrier protein] reductase; enoyl-ACP reductase; NADH-enoyl acyl carrier protein reductase; NADH-specific enoyl-ACP reductase; acyl-[acyl-carrier-protein]:NAD+ oxidoreductase; fabI (gene name)
Systematic name: acyl-[acyl-carrier protein]:NAD+ oxidoreductase
Comments: The enzyme catalyses an essential step in fatty acid biosynthesis, the reduction of the 2,3-double bond in enoyl-acyl-[acyl-carrier-protein] derivatives of the elongating fatty acid moiety. The enzyme from the bacterium Escherichia coli accepts substrates with carbon chain length from 4 to 18 [3]. The FAS-I enzyme from the bacterium Mycobacterium tuberculosis prefers substrates with carbon chain length from 12 to 24 carbons.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37251-08-4
References:
1.  Shimakata, T. and Stumpf, P.K. Purification and characterizations of β-ketoacyl-[acyl-carrier-protein] reductase, β-hydroxyacyl-[acylcarrier-protein] dehydrase, and enoyl-[acyl-carrier-protein] reductase from Spinacia oleracea leaves. Arch. Biochem. Biophys. 218 (1982) 77–91. [DOI] [PMID: 6756317]
2.  Weeks, G. and Wakil, S.J. Studies on the mechanism of fatty acid synthesis. 18. Preparation and general properties of the enoyl acyl carrier protein reductases from Escherichia coli. J. Biol. Chem. 243 (1968) 1180–1189. [PMID: 4384650]
3.  Yu, X., Liu, T., Zhu, F. and Khosla, C. In vitro reconstitution and steady-state analysis of the fatty acid synthase from Escherichia coli. Proc. Natl. Acad. Sci. USA 108 (2011) 18643–18648. [DOI] [PMID: 22042840]
[EC 1.3.1.9 created 1972, modified 2013]
 
 
EC 1.3.1.54     
Accepted name: precorrin-6A reductase
Reaction: precorrin-6B + NADP+ = precorrin-6A + NADPH + H+
For diagram of corrin biosynthesis (part 3), click here
Other name(s): precorrin-6X reductase; precorrin-6Y:NADP+ oxidoreductase; CobK
Systematic name: precorrin-6B:NADP+ oxidoreductase
Comments: The enzyme, which participates in the aerobic (late cobalt insertion) pathway of adenosylcobalamin biosynthesis, catalyses the reduction of the double bond between C-18 and C-19 of precorrin-6A. See EC 1.3.1.106, cobalt-precorrin-6A reductase, for the corresponding enzyme that participates in the anaerobic cobalamin biosynthesis pathway.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 137573-72-9
References:
1.  Blanche, F., Thibaut, D., Famechon, A., Debussche, L., Cameron, B. and Crouzet, J. Precorrin-6X reductase from Pseudomonas denitrificans: purification and characterization of the enzyme and identification of the structural gene. J. Bacteriol. 174 (1992) 1036–1042. [DOI] [PMID: 1732193]
2.  Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390–412. [PMID: 12195810]
[EC 1.3.1.54 created 1999, modified 2004]
 
 
EC 1.3.1.76     
Accepted name: precorrin-2 dehydrogenase
Reaction: precorrin-2 + NAD+ = sirohydrochlorin + NADH + H+
For diagram of corrin and siroheme biosynthesis (part 2), click here
Other name(s): Met8p; SirC; CysG
Systematic name: precorrin-2:NAD+ oxidoreductase
Comments: This enzyme catalyses the second of three steps leading to the formation of siroheme from uroporphyrinogen III. The first step involves the donation of two S-adenosyl-L-methionine-derived methyl groups to carbons 2 and 7 of uroporphyrinogen III to form precorrin-2 (EC 2.1.1.107, uroporphyrin-III C-methyltransferase) and the third step involves the chelation of ferrous iron to sirohydrochlorin to form siroheme (EC 4.99.1.4, sirohydrochlorin ferrochelatase). In Saccharomyces cerevisiae, the last two steps are carried out by a single bifunctional enzyme, Met8p. In some bacteria, steps 1-3 are catalysed by a single multifunctional protein called CysG, whereas in Bacillus megaterium, three separate enzymes carry out each of the steps, with SirC being responsible for the above reaction.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 227184-47-6
References:
1.  Schubert, H.L., Raux, E., Brindley, A.A., Leech, H.K., Wilson, K.S., Hill, C.P. and Warren, M.J. The structure of Saccharomyces cerevisiae Met8p, a bifunctional dehydrogenase and ferrochelatase. EMBO J. 21 (2002) 2068–2075. [DOI] [PMID: 11980703]
2.  Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390–412. [PMID: 12195810]
[EC 1.3.1.76 created 2004]
 
 
EC 1.3.1.106     
Accepted name: cobalt-precorrin-6A reductase
Reaction: cobalt-precorrin-6B + NAD+ = cobalt-precorrin-6A + NADH + H+
For diagram of anaerobic corrin biosynthesis (part 2), click here
Other name(s): cbiJ (gene name)
Systematic name: cobalt-precorrin-6B:NAD+ oxidoreductase
Comments: The enzyme, which participates in the anaerobic (early cobalt insertion) pathway of adenosylcobalamin biosynthesis, catalyses the reduction of the double bond between C-18 and C-19 of cobalt-precorrin-6A. The enzyme from the bacterium Bacillus megaterium has no activity with NADPH. See EC 1.3.1.54, precorrin-6A reductase, for the corresponding enzyme that participates in the aerobic cobalamin biosynthesis pathway.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kim, W., Major, T.A. and Whitman, W.B. Role of the precorrin 6-X reductase gene in cobamide biosynthesis in Methanococcus maripaludis. Archaea 1 (2005) 375–384. [PMID: 16243778]
2.  Moore, S.J., Lawrence, A.D., Biedendieck, R., Deery, E., Frank, S., Howard, M.J., Rigby, S.E. and Warren, M.J. Elucidation of the anaerobic pathway for the corrin component of cobalamin (vitamin B12). Proc. Natl. Acad. Sci. USA 110 (2013) 14906–14911. [DOI] [PMID: 23922391]
[EC 1.3.1.106 created 2014]
 
 
EC 1.3.1.118     
Accepted name: meromycolic acid enoyl-[acyl-carrier-protein] reductase
Reaction: a meromycolyl-[acyl-carrier protein] + NAD+ = a trans2-meromycolyl-[acyl-carrier protein] + NADH + H+
Glossary: meromycolic acids are one of the two precursors of the mycolic acids produced by Mycobacteria. They consist of a long chain typically of 50–60 carbons, which is functionalized by different groups.
Other name(s): inhA (gene name)
Systematic name: meromycolyl-[acyl-carrier protein]:NAD+ oxidoreductase
Comments: InhA is a component of the fatty acid synthase (FAS) II system of Mycobacterium tuberculosis, catalysing an enoyl-[acyl-carrier-protein] reductase step. The enzyme acts on very long and unsaturated fatty acids that form the meromycolic component of mycolic acids. It extends FASI-derived C20 fatty acids to form C60 to C90 mycolic acids. The enzyme, which forms a homotetramer, is the target of the preferred antitubercular drug isoniazid.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Quemard, A., Sacchettini, J.C., Dessen, A., Vilcheze, C., Bittman, R., Jacobs, W.R., Jr. and Blanchard, J.S. Enzymatic characterization of the target for isoniazid in Mycobacterium tuberculosis. Biochemistry 34 (1995) 8235–8241. [PMID: 7599116]
2.  Rozwarski, D.A., Vilcheze, C., Sugantino, M., Bittman, R. and Sacchettini, J.C. Crystal structure of the Mycobacterium tuberculosis enoyl-ACP reductase, InhA, in complex with NAD+ and a C16 fatty acyl substrate. J. Biol. Chem. 274 (1999) 15582–15589. [PMID: 10336454]
3.  Marrakchi, H., Laneelle, G. and Quemard, A. InhA, a target of the antituberculous drug isoniazid, is involved in a mycobacterial fatty acid elongation system, FAS-II. Microbiology 146 (2000) 289–296. [PMID: 10708367]
4.  Vilcheze, C., Morbidoni, H.R., Weisbrod, T.R., Iwamoto, H., Kuo, M., Sacchettini, J.C. and Jacobs, W.R., Jr. Inactivation of the inhA-encoded fatty acid synthase II (FASII) enoyl-acyl carrier protein reductase induces accumulation of the FASI end products and cell lysis of Mycobacterium smegmatis. J. Bacteriol. 182 (2000) 4059–4067. [PMID: 10869086]
5.  Gurvitz, A., Hiltunen, J.K. and Kastaniotis, A.J. Function of heterologous Mycobacterium tuberculosis InhA, a type 2 fatty acid synthase enzyme involved in extending C20 fatty acids to C60-to-C90 mycolic acids, during de novo lipoic acid synthesis in Saccharomyces cerevisiae. Appl. Environ. Microbiol. 74 (2008) 5078–5085. [PMID: 18552191]
6.  Chollet, A., Mourey, L., Lherbet, C., Delbot, A., Julien, S., Baltas, M., Bernadou, J., Pratviel, G., Maveyraud, L. and Bernardes-Genisson, V. Crystal structure of the enoyl-ACP reductase of Mycobacterium tuberculosis (InhA) in the apo-form and in complex with the active metabolite of isoniazid pre-formed by a biomimetic approach. J. Struct. Biol. 190 (2015) 328–337. [PMID: 25891098]
[EC 1.3.1.118 created 2018]
 
 
EC 1.3.4.1     
Accepted name: fumarate reductase (CoM/CoB)
Reaction: fumarate + CoM + CoB = succinate + CoM-S-S-CoB
Glossary: CoB = coenzyme B = N-(7-sulfanylheptanoyl)threonine = N-(7-mercaptoheptanoyl)threonine (deprecated)
CoM = coenzyme M = 2-sulfanylethane-1-sulfonate = 2-mercaptoethanesulfonate (deprecated)
Other name(s): thiol:fumarate reductase; Tfr
Systematic name: fumarate CoM:CoB oxidoreductase (succinate-forming)
Comments: The enzyme, isolated from the archaeon Methanobacterium thermoautotrophicum, is very oxygen sensitive. It cannot use reduced flavins, reduced coenzyme F420, or NAD(P)H as an electron donor. Distinct from EC 1.3.1.6 [fumarate reductase (NADH)], EC 1.3.5.1 [succinate dehydrogenase (ubiquinone)], and EC 1.3.5.4 [fumarate reductase (quinol)].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Khandekar, S.S. and Eirich, L.D. Purification and characterization of an anabolic fumarate reductase from Methanobacterium thermoautotrophicum. Appl. Environ. Microbiol. 55 (1989) 856–861. [PMID: 2499256]
2.  Heim, S., Kunkel, A., Thauer, R.K. and Hedderich, R. Thiol:fumarate reductase (Tfr) from Methanobacterium thermoautotrophicum. Identification of the catalytic sites for fumarate reduction and thiol oxidation. Eur. J. Biochem. 253 (1998) 292–299. [DOI] [PMID: 9578488]
[EC 1.3.4.1 created 2014 as EC 1.3.98.2, transferred 2014 to EC 1.3.4.1]
 
 
EC 1.3.7.5     
Accepted name: phycocyanobilin:ferredoxin oxidoreductase
Reaction: (3Z)-phycocyanobilin + 4 oxidized ferredoxin = biliverdin IXα + 4 reduced ferredoxin
For diagram of biliverdin metabolism, click here
Systematic name: (3Z)-phycocyanobilin:ferredoxin oxidoreductase
Comments: Catalyses the four-electron reduction of biliverdin IXα (2-electron reduction at both the A and D rings). Reaction proceeds via an isolatable 2-electron intermediate, 181,182-dihydrobiliverdin. Flavodoxins can be used instead of ferredoxin. The direct conversion of biliverdin IXα (BV) to (3Z)-phycocyanolbilin (PCB) in the cyanobacteria Synechocystis sp. PCC 6803, Anabaena sp. PCC7120 and Nostoc punctiforme is in contrast to the proposed pathways of PCB biosynthesis in the red alga Cyanidium caldarium, which involves (3Z)-phycoerythrobilin (PEB) as an intermediate [2] and in the green alga Mesotaenium caldariorum, in which PCB is an isolable intermediate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 347401-12-1
References:
1.  Frankenberg, N., Mukougawa, K., Kohchi, T. and Lagarias, J.C. Functional genomic analysis of the HY2 family of ferredoxin-dependent bilin reductases from oxygenic photosynthetic organisms. Plant Cell 13 (2001) 965–978. [PMID: 11283349]
2.  Beale, S.I. Biosynthesis of phycobilins. Chem. Rev. 93 (1993) 785–802.
3.  Wu, S.-H., McDowell, M.T. and Lagarias, J.C. Phycocyanobilin is the natural chromophore precursor of phytochrome from the green alga Mesotaenium caldariorum. J. Biol. Chem. 272 (1997) 25700–25705. [DOI] [PMID: 9325294]
[EC 1.3.7.5 created 2002, modified 2014]
 
 
EC 1.3.98.2      
Transferred entry: fumarate reductase (CoM/CoB). Now EC 1.3.4.1, fumarate reductase (CoM/CoB)
[EC 1.3.98.2 created 2014, deleted 2014]
 
 
EC 1.3.99.38     
Accepted name: menaquinone-9 β-reductase
Reaction: menaquinone-9 + reduced acceptor = β-dihydromenaquinone-9 + acceptor
For diagram of vitamin K biosynthesis, click here
Glossary: β-dihydromenaquinone-9 = MK-9(II-H2) = 2-methyl-3-[(2E,10E,14E,18E,22E,26E,30E,33E)-3,7,11,15,19,23,27,31,35-nonamethylhexatriaconta-2,10,14,18,22,26,30,33-octaen-1-yl]naphthalene-1,4-dione
Other name(s): MenJ
Systematic name: menaquinone-9 oxidoreductase (β-dihydromenaquinone-9-forming)
Comments: The enzyme from the bacterium Mycobacterium tuberculosis reduces the β-isoprene unit of menaquinone-9, forming the predominant form of menaquinone found in mycobacteria. Contains FAD.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Upadhyay, A., Fontes, F.L., Gonzalez-Juarrero, M., McNeil, M.R., Crans, D.C., Jackson, M. and Crick, D.C. Partial saturation of menaquinone in Mycobacterium tuberculosis: function and essentiality of a novel reductase, MenJ. ACS Cent. Sci. 1 (2015) 292–302. [DOI] [PMID: 26436137]
[EC 1.3.99.38 created 2017]
 
 
EC 1.4.1.10     
Accepted name: glycine dehydrogenase
Reaction: glycine + H2O + NAD+ = glyoxylate + NH3 + NADH + H+
Systematic name: glycine:NAD+ oxidoreductase (deaminating)
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number: 37255-40-6
References:
1.  Goldman, D.S. and Wagner, M.J. Enzyme systems in the mycobacteria. XIII. Glycine dehydrogenase and the glyoxylic acid cycle. Biochim. Biophys. Acta 65 (1962) 297–306. [DOI] [PMID: 13948749]
[EC 1.4.1.10 created 1972]
 
 
EC 1.4.3.8     
Accepted name: ethanolamine oxidase
Reaction: ethanolamine + H2O + O2 = glycolaldehyde + NH3 + H2O2
Systematic name: ethanolamine:oxygen oxidoreductase (deaminating)
Comments: A cobamide-protein.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9013-00-7
References:
1.  Narrod, S.A. and Jakoby, W.B. Metabolism of ethanolamine. An ethanolamine oxidase. J. Biol. Chem. 239 (1964) 2189–2193. [PMID: 14209947]
[EC 1.4.3.8 created 1972]
 
 
EC 1.4.5.1     
Accepted name: D-amino acid dehydrogenase (quinone)
Reaction: a D-amino acid + H2O + a quinone = a 2-oxo carboxylate + NH3 + a quinol
Other name(s): DadA
Systematic name: D-amino acid:quinone oxidoreductase (deaminating)
Comments: An iron-sulfur flavoprotein (FAD). The enzyme from the bacterium Helicobacter pylori is highly specific for D-proline, while the enzyme from the bacterium Escherichia coli B is most active with D-alanine, D-phenylalanine and D-methionine. This enzyme may be the same as EC 1.4.99.6.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Olsiewski, P.J., Kaczorowski, G.J. and Walsh, C. Purification and properties of D-amino acid dehydrogenase, an inducible membrane-bound iron-sulfur flavoenzyme from Escherichia coli B. J. Biol. Chem. 255 (1980) 4487–4494. [PMID: 6102989]
2.  Tanigawa, M., Shinohara, T., Saito, M., Nishimura, K., Hasegawa, Y., Wakabayashi, S., Ishizuka, M. and Nagata, Y. D-Amino acid dehydrogenase from Helicobacter pylori NCTC 11637. Amino Acids 38 (2010) 247–255. [DOI] [PMID: 19212808]
[EC 1.4.5.1 created 2010]
 
 
EC 1.5.1.52     
Accepted name: staphylopine dehydrogenase
Reaction: staphylopine + NADP+ + H2O = (2S)-2-amino-4-{[(1R)-1-carboxy-2-(1H-imidazol-4-yl)ethyl]amino}butanoate + pyruvate + NADPH + H+
Glossary: staphylopine = (2S)-4-{[(1R)-1-carboxy-2-(1H-imidazol-4-yl)ethyl]amino}-2-[(1-carboxyethyl)amino]butanoate
Other name(s): cntM (gene name); staphylopine synthase
Systematic name: staphylopine:NADP+ oxidoreductase [(2S)-2-amino-4-{[(1R)-1-carboxy-2-(1H-imidazol-4-yl)ethyl]amino}butanoate]-forming
Comments: The enzyme, characterized from the bacterium Staphylococcus aureus, catalyses the last reaction in the biosynthesis of the metallophore staphylopine, which is involved in the acquisition of nickel, copper, and cobalt.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Ghssein, G., Brutesco, C., Ouerdane, L., Fojcik, C., Izaute, A., Wang, S., Hajjar, C., Lobinski, R., Lemaire, D., Richaud, P., Voulhoux, R., Espaillat, A., Cava, F., Pignol, D., Borezee-Durant, E. and Arnoux, P. Biosynthesis of a broad-spectrum nicotianamine-like metallophore in Staphylococcus aureus. Science 352 (2016) 1105–1109. [PMID: 27230378]
2.  McFarlane, J.S., Davis, C.L. and Lamb, A.L. Staphylopine, pseudopaline, and yersinopine dehydrogenases: A structural and kinetic analysis of a new functional class of opine dehydrogenase. J. Biol. Chem. 293 (2018) 8009–8019. [PMID: 29618515]
[EC 1.5.1.52 created 2018]
 
 
EC 1.5.98.3     
Accepted name: coenzyme F420:methanophenazine dehydrogenase
Reaction: reduced coenzyme F420 + methanophenazine = oxidized coenzyme F420 + dihydromethanophenazine
Glossary: methanophenazine = 2-{[(6E,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl]oxy}phenazine
dihydromethanophenazine = 2-{[(6E,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl]oxy}-5,10-dihydrophenazine
Other name(s): F420H2 dehydrogenase; fpoBCDIF (gene names)
Systematic name: reduced coenzyme F420:methanophenazine oxidoreductase
Comments: The enzyme, found in some methanogenic archaea, is responsible for the reoxidation of coenzyme F420, which is reduced during methanogenesis, and for the reduction of methanophenazine to dihydromethanophenazine, which is required by EC 1.8.98.1, dihydromethanophenazine:CoB-CoM heterodisulfide reductase. The enzyme is membrane-bound, and is coupled to proton translocation across the cytoplasmic membrane, generating a proton motive force that is used for ATP generation.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Brodersen, J., Gottschalk, G. and Deppenmeier, U. Membrane-bound F420H2-dependent heterodisulfide reduction in Methanococcus volta. Arch. Microbiol. 171 (1999) 115–121. [PMID: 9914308]
2.  Baumer, S., Ide, T., Jacobi, C., Johann, A., Gottschalk, G. and Deppenmeier, U. The F420H2 dehydrogenase from Methanosarcina mazei is a Redox-driven proton pump closely related to NADH dehydrogenases. J. Biol. Chem. 275 (2000) 17968–17973. [DOI] [PMID: 10751389]
3.  Deppenmeier, U. The membrane-bound electron transport system of Methanosarcina species. J. Bioenerg. Biomembr. 36 (2004) 55–64. [PMID: 15168610]
4.  Abken H. J. and Deppenmeier, U. Purification and properties of an F420H2 dehydrogenase from Methanosarcina mazei Gö1. FEMS Microbiol. Lett. 154 (2006) 231–237.
[EC 1.5.98.3 created 2017]
 
 
EC 1.5.99.12     
Accepted name: cytokinin dehydrogenase
Reaction: N6-prenyladenine + acceptor + H2O = adenine + 3-methylbut-2-enal + reduced acceptor
Glossary: zeatin = (E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol = (E)-N6-(4-hydroxy-3-methylbut-2-enyl)adenine
N6-prenyladenine = N6-(3-methylbut-2-en-1-yl)purin-6-amine
Other name(s): N6-dimethylallyladenine:(acceptor) oxidoreductase; 6-N-dimethylallyladenine:acceptor oxidoreductase; OsCKX2; CKX; cytokinin oxidase/dehydrogenase; N6-dimethylallyladenine:acceptor oxidoreductase
Systematic name: N6-prenyladenine:acceptor oxidoreductase
Comments: A flavoprotein (FAD). Catalyses the oxidation of cytokinins, a family of N6-substituted adenine derivatives that are plant hormones, where the substituent is a prenyl group. Although this activity was previously thought to be catalysed by a hydrogen-peroxide-forming oxidase, this enzyme does not require oxygen for activity and does not form hydrogen peroxide. 2,6-Dichloroindophenol, methylene blue, nitroblue tetrazolium, phenazine methosulfate and copper(II) in the presence of imidazole can act as acceptors. This enzyme plays a part in regulating rice-grain production, with lower levels of the enzyme resulting in enhanced grain production [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 55326-39-1
References:
1.  Galuszka, P., Frebort, I., Sebela, M., Jacobsen, S. and Pec, P. Cytokinin oxidase or dehydrogenase? Mechanism of cytokinin degradation in plants. Eur. J. Biochem. 268 (2001) 450–461. [DOI] [PMID: 11168382]
2.  Ashikari, M., Sakakibara, H., Lin, S., Yamamoto, T., Takashi, T., Nishimura, A., Angeles, E.R., Qian, Q., Kitano, H. and Matsuoka, M. Cytokinin oxidase regulates rice grain production. Science 309 (2005) 741–745. [DOI] [PMID: 15976269]
[EC 1.5.99.12 created 2001]
 
 
EC 1.6.99.8      
Deleted entry: aquacobalamin reductase. This entry has been deleted since no specific enzyme catalysing this activity has been identified and it has been shown that aquacobalamin is efficiently reduced by free dihydroflavins and by non-specific reduced flavoproteins.
[EC 1.6.99.8 created 1972, deleted 2002]
 
 
EC 1.6.99.9      
Transferred entry: cob(II)alamin reductase. Now EC 1.16.1.4, cob(II)alamin reductase
[EC 1.6.99.9 created 1972, deleted 2002]
 
 
EC 1.6.99.11      
Deleted entry: aquacobalamin reductase (NADPH). This entry has been deleted since the enzyme the entry was based on was later shown to be EC 1.2.1.51, pyruvate dehydrogenase (NADP+). On the other hand, it has been shown that non-enzymatic reduction of cob(III)alamin to cob(II)alamin occurs efficiently in the presence of free dihydroflavins or non-specific reduced flavoproteins.
[EC 1.6.99.11 created 1989, deleted 2002]
 
 
EC 1.6.99.12      
Transferred entry: cyanocobalamin reductase (NADPH, cyanide-eliminating). Now EC 1.16.1.6, cyanocobalamin reductase (cyanide-eliminating)
[EC 1.6.99.12 created 1989, deleted 2002]
 
 
EC 1.8.1.6     
Accepted name: cystine reductase
Reaction: 2 L-cysteine + NAD+ = L-cystine + NADH + H+
Other name(s): cystine reductase (NADH); NADH-dependent cystine reductase; cystine reductase (NADH2); NADH2:L-cystine oxidoreductase
Systematic name: L-cysteine:NAD+ oxidoreductase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9029-18-9
References:
1.  Romano, A.H. and Nickerson, W.J. Cystine reductase of pea seeds and yeast. J. Biol. Chem. 208 (1954) 409–416. [PMID: 13174550]
2.  Carroll, J.E., Kosicki, G.W. and Thibert, R.J. α-Substituted cystines as possible substrates for cystine reductase and L-amino acid oxidase. Biochim. Biophys. Acta 198 (1970) 601–603. [DOI] [PMID: 5436160]
3.  Maresca, B., Jacobson, E., Medoff, G. and Kobayashi, G. Cystine reductase in the dimorphic fungus Histoplasma capsulatum. J. Bacteriol. 135 (1978) 987–992. [PMID: 211119]
[EC 1.8.1.6 created 1961 as EC 1.6.4.1, transferred 2002 to EC 1.8.1.6]
 
 
EC 1.8.1.15     
Accepted name: mycothione reductase
Reaction: 2 mycothiol + NAD(P)+ = mycothione + NAD(P)H + H+
Glossary: mycothiol = 1-O-[2-(N2-acetyl-L-cysteinamido)-2-deoxy--D-glucopyranosyl]-1D-myo-inositol
mycothione = oxidized (disulfide) form of mycothiol
Other name(s): mycothiol-disulfide reductase
Systematic name: mycothiol:NAD(P)+ oxidoreductase
Comments: Contains FAD. No activity with glutathione, trypanothione or coenzyme A as substrate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 252212-92-3
References:
1.  Patel, M.P. and Blanchard, J.S. Expression, purification, and characterization of Mycobacterium tuberculosis mycothione reductase. Biochemistry 38 (1999) 11827–11833. [DOI] [PMID: 10512639]
2.  Patel, M.P. and Blanchard, J.S. Mycobacterium tuberculosis mycothione reductase: pH dependence of the kinetic parameters and kinetic isotope effects. Biochemistry 40 (2001) 5119–5126. [DOI] [PMID: 11318633]
[EC 1.8.1.15 created 2002]
 
 
EC 1.8.4.10     
Accepted name: adenylyl-sulfate reductase (thioredoxin)
Reaction: AMP + sulfite + thioredoxin disulfide = 5′-adenylyl sulfate + thioredoxin
Other name(s): thioredoxin-dependent 5′-adenylylsulfate reductase
Systematic name: AMP,sulfite:thioredoxin-disulfide oxidoreductase (adenosine-5′-phosphosulfate-forming)
Comments: Uses adenylyl sulfate, not phosphoadenylyl sulfate, distinguishing this enzyme from EC 1.8.4.8, phosphoadenylyl-sulfate reductase (thioredoxin). Uses thioredoxin as electron donor, not glutathione or other donors, distinguishing it from EC 1.8.4.9 [adenylyl-sulfate reductase (glutathione)] and EC 1.8.99.2 (adenylyl-sulfate reductase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Bick, J.A., Dennis, J.J., Zylstra, G.J., Nowack, J. and Leustek, T. Identification of a new class of 5-adenylylsulfate (APS) reductase from sulfate-assimilating bacteria. J. Bacteriol. 182 (2000) 135–142. [DOI] [PMID: 10613872]
2.  Abola, A.P., Willits, M.G., Wang, R.C. and Long, S.R. Reduction of adenosine-5′-phosphosulfate instead of 3′-phosphoadenosine-5′-phosphosulfate in cysteine biosynthesis by Rhizobium meliloti and other members of the family Rhizobiaceae. J. Bacteriol. 181 (1999) 5280–5287. [PMID: 10464198]
3.  Williams, S.J., Senaratne, R.H., Mougous, J.D., Riley, L.W. and Bertozzi, C.R. 5′-Adenosinephosphosulfate lies at a metabolic branchpoint in mycobacteria. J. Biol. Chem. 277 (2002) 32606–32615. [DOI] [PMID: 12072441]
4.  Neumann, S., Wynen, A., Truper, H.G. and Dahl, C. Characterization of the cys gene locus from Allochromatium vinosum indicates an unusual sulfate assimilation pathway. Mol. Biol. Rep. 27 (2000) 27–33. [PMID: 10939523]
[EC 1.8.4.10 created 2003]
 
 
EC 1.8.4.11     
Accepted name: peptide-methionine (S)-S-oxide reductase
Reaction: (1) peptide-L-methionine + thioredoxin disulfide + H2O = peptide-L-methionine (S)-S-oxide + thioredoxin
(2) L-methionine + thioredoxin disulfide + H2O = L-methionine (S)-S-oxide + thioredoxin
For diagram of reaction, click here and for mechanism of reaction, click here
Other name(s): MsrA; methionine sulfoxide reductase (ambiguous); methionine sulphoxide reductase A; methionine S-oxide reductase (ambiguous); methionine S-oxide reductase (S-form oxidizing); methionine sulfoxide reductase A; peptide methionine sulfoxide reductase
Systematic name: peptide-L-methionine:thioredoxin-disulfide S-oxidoreductase [L-methionine (S)-S-oxide-forming]
Comments: The reaction occurs in the reverse direction to that shown above. The enzyme exhibits high specificity for the reduction of the S-form of L-methionine S-oxide, acting faster on the residue in a peptide than on the free amino acid [9]. On the free amino acid, it can also reduce D-methionine (S)-S-oxide but more slowly [9]. The enzyme plays a role in preventing oxidative-stress damage caused by reactive oxygen species by reducing the oxidized form of methionine back to methionine and thereby reactivating peptides that had been damaged. In some species, e.g. Neisseria meningitidis, both this enzyme and EC 1.8.4.12, peptide-methionine (R)-S-oxide reductase, are found within the same protein whereas, in other species, they are separate proteins [1,4]. The reaction proceeds via a sulfenic-acid intermediate [5,10].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Moskovitz, J., Singh, V.K., Requena, J., Wilkinson, B.J., Jayaswal, R.K. and Stadtman, E.R. Purification and characterization of methionine sulfoxide reductases from mouse and Staphylococcus aureus and their substrate stereospecificity. Biochem. Biophys. Res. Commun. 290 (2002) 62–65. [DOI] [PMID: 11779133]
2.  Taylor, A.B., Benglis, D.M., Jr., Dhandayuthapani, S. and Hart, P.J. Structure of Mycobacterium tuberculosis methionine sulfoxide reductase A in complex with protein-bound methionine. J. Bacteriol. 185 (2003) 4119–4126. [DOI] [PMID: 12837786]
3.  Singh, V.K. and Moskovitz, J. Multiple methionine sulfoxide reductase genes in Staphylococcus aureus: expression of activity and roles in tolerance of oxidative stress. Microbiology 149 (2003) 2739–2747. [DOI] [PMID: 14523107]
4.  Boschi-Muller, S., Olry, A., Antoine, M. and Branlant, G. The enzymology and biochemistry of methionine sulfoxide reductases. Biochim. Biophys. Acta 1703 (2005) 231–238. [DOI] [PMID: 15680231]
5.  Ezraty, B., Aussel, L. and Barras, F. Methionine sulfoxide reductases in prokaryotes. Biochim. Biophys. Acta 1703 (2005) 221–229. [DOI] [PMID: 15680230]
6.  Weissbach, H., Resnick, L. and Brot, N. Methionine sulfoxide reductases: history and cellular role in protecting against oxidative damage. Biochim. Biophys. Acta 1703 (2005) 203–212. [DOI] [PMID: 15680228]
7.  Kauffmann, B., Aubry, A. and Favier, F. The three-dimensional structures of peptide methionine sulfoxide reductases: current knowledge and open questions. Biochim. Biophys. Acta 1703 (2005) 249–260. [DOI] [PMID: 15680233]
8.  Vougier, S., Mary, J. and Friguet, B. Subcellular localization of methionine sulphoxide reductase A (MsrA): evidence for mitochondrial and cytosolic isoforms in rat liver cells. Biochem. J. 373 (2003) 531–537. [DOI] [PMID: 12693988]
9.  Olry, A., Boschi-Muller, S., Marraud, M., Sanglier-Cianferani, S., Van Dorsselear, A. and Branlant, G. Characterization of the methionine sulfoxide reductase activities of PILB, a probable virulence factor from Neisseria meningitidis. J. Biol. Chem. 277 (2002) 12016–12022. [DOI] [PMID: 11812798]
10.  Brot, N., Weissbach, L., Werth, J. and Weissbach, H. Enzymatic reduction of protein-bound methionine sulfoxide. Proc. Natl. Acad. Sci. USA 78 (1981) 2155–2158. [DOI] [PMID: 7017726]
[EC 1.8.4.11 created 2006]
 
 
EC 1.8.4.12     
Accepted name: peptide-methionine (R)-S-oxide reductase
Reaction: peptide-L-methionine + thioredoxin disulfide + H2O = peptide-L-methionine (R)-S-oxide + thioredoxin
For diagram of reaction, click here and for mechanism of reaction, click here
Other name(s): MsrB; methionine sulfoxide reductase (ambiguous); pMSR; methionine S-oxide reductase (ambiguous); selenoprotein R; methionine S-oxide reductase (R-form oxidizing); methionine sulfoxide reductase B; SelR; SelX; PilB; pRMsr
Systematic name: peptide-methionine:thioredoxin-disulfide S-oxidoreductase [methionine (R)-S-oxide-forming]
Comments: The reaction occurs in the reverse direction to that shown above. The enzyme exhibits high specificity for reduction of the R-form of methionine S-oxide, with higher activity being observed with L-methionine S-oxide than with D-methionine S-oxide [9]. While both free and protein-bound methionine (R)-S-oxide act as substrates, the activity with the peptide-bound form is far greater [10]. The enzyme plays a role in preventing oxidative-stress damage caused by reactive oxygen species by reducing the oxidized form of methionine back to methionine and thereby reactivating peptides that had been damaged. In some species, e.g. Neisseria meningitidis, both this enzyme and EC 1.8.4.11, peptide-methionine (S)-S-oxide reductase, are found within the same protein whereas in other species, they are separate proteins [3,5]. The reaction proceeds via a sulfenic-acid intermediate [5,10]. For MsrB2 and MsrB3, thioredoxin is a poor reducing agent but thionein works well [11]. The enzyme from some species contains selenocysteine and Zn2+.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Moskovitz, J., Singh, V.K., Requena, J., Wilkinson, B.J., Jayaswal, R.K. and Stadtman, E.R. Purification and characterization of methionine sulfoxide reductases from mouse and Staphylococcus aureus and their substrate stereospecificity. Biochem. Biophys. Res. Commun. 290 (2002) 62–65. [DOI] [PMID: 11779133]
2.  Taylor, A.B., Benglis, D.M., Jr., Dhandayuthapani, S. and Hart, P.J. Structure of Mycobacterium tuberculosis methionine sulfoxide reductase A in complex with protein-bound methionine. J. Bacteriol. 185 (2003) 4119–4126. [DOI] [PMID: 12837786]
3.  Singh, V.K. and Moskovitz, J. Multiple methionine sulfoxide reductase genes in Staphylococcus aureus: expression of activity and roles in tolerance of oxidative stress. Microbiology 149 (2003) 2739–2747. [DOI] [PMID: 14523107]
4.  Boschi-Muller, S., Olry, A., Antoine, M. and Branlant, G. The enzymology and biochemistry of methionine sulfoxide reductases. Biochim. Biophys. Acta 1703 (2005) 231–238. [DOI] [PMID: 15680231]
5.  Ezraty, B., Aussel, L. and Barras, F. Methionine sulfoxide reductases in prokaryotes. Biochim. Biophys. Acta 1703 (2005) 221–229. [DOI] [PMID: 15680230]
6.  Weissbach, H., Resnick, L. and Brot, N. Methionine sulfoxide reductases: history and cellular role in protecting against oxidative damage. Biochim. Biophys. Acta 1703 (2005) 203–212. [DOI] [PMID: 15680228]
7.  Kauffmann, B., Aubry, A. and Favier, F. The three-dimensional structures of peptide methionine sulfoxide reductases: current knowledge and open questions. Biochim. Biophys. Acta 1703 (2005) 249–260. [DOI] [PMID: 15680233]
8.  Vougier, S., Mary, J. and Friguet, B. Subcellular localization of methionine sulphoxide reductase A (MsrA): evidence for mitochondrial and cytosolic isoforms in rat liver cells. Biochem. J. 373 (2003) 531–537. [DOI] [PMID: 12693988]
9.  Olry, A., Boschi-Muller, S., Marraud, M., Sanglier-Cianferani, S., Van Dorsselear, A. and Branlant, G. Characterization of the methionine sulfoxide reductase activities of PILB, a probable virulence factor from Neisseria meningitidis. J. Biol. Chem. 277 (2002) 12016–12022. [DOI] [PMID: 11812798]
10.  Sagher, D., Brunell, D., Hejtmancik, J.F., Kantorow, M., Brot, N. and Weissbach, H. Thionein can serve as a reducing agent for the methionine sulfoxide reductases. Proc. Natl. Acad. Sci. USA 103 (2006) 8656–8661. [DOI] [PMID: 16735467]
[EC 1.8.4.12 created 2006]
 
 
EC 1.8.7.3     
Accepted name: ferredoxin:CoB-CoM heterodisulfide reductase
Reaction: 2 oxidized ferredoxin [iron-sulfur] cluster + CoB + CoM = 2 reduced ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB + 2 H+
Glossary: CoB = coenzyme B = N-(7-sulfanylheptanoyl)threonine = N-(7-mercaptoheptanoyl)threonine 3-O-phosphate (deprecated)
CoM = coenzyme M = 2-sulfanylethane-1-sulfonate = 2-mercaptoethanesulfonate (deprecated)
CoM-S-S-CoB = CoB-CoM heterodisulfide = N-{7-[(2-sulfoethyl)dithio]heptanoyl}-O3-phospho-L-threonine =
O3-phospho-N-{7-[2-(2-sulfoethyl)disulfan-1-yl]heptanoyl}-L-threonine
Other name(s): hdrABC (gene names); hdrA1B1C1 (gene names); hdrA2B2C2 (gene names)
Systematic name: CoB,CoM:ferredoxin oxidoreductase
Comments: HdrABC is an enzyme complex that is found in most methanogens and catalyses the reduction of the CoB-CoM heterodisulfide back to CoB and CoM. HdrA contains a FAD cofactor that acts as the entry point for electrons, which are transferred via HdrC to the HdrB catalytic subunit. One form of the enzyme from Methanosarcina acetivorans (HdrA2B2C2) can also catalyse EC 1.8.98.4, coenzyme F420:CoB-CoM heterodisulfide,ferredoxin reductase. cf. EC 1.8.98.5, H2:CoB-CoM heterodisulfide,ferredoxin reductase, EC 1.8.98.6, formate:CoB-CoM heterodisulfide,ferredoxin reductase, and EC 1.8.98.1, dihydromethanophenazine:CoB-CoM heterodisulfide reductase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Buan, N.R. and Metcalf, W.W. Methanogenesis by Methanosarcina acetivorans involves two structurally and functionally distinct classes of heterodisulfide reductase. Mol. Microbiol. 75 (2010) 843–853. [DOI] [PMID: 19968794]
2.  Yan, Z., Wang, M. and Ferry, J.G. A ferredoxin- and F420H2-dependent, electron-bifurcating, heterodisulfide reductase with homologs in the domains Bacteria and Archaea. mBio 8 (2017) e02285-16. [DOI] [PMID: 28174314]
[EC 1.8.7.3 created 2017]
 
 


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