The Enzyme Database

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EC 1.5.3.22     Relevance: 100%
Accepted name: coenzyme F420H2 oxidase
Reaction: 2 reduced coenzyme F420 + O2 = 2 oxidized coenzyme F420 + 2 H2O
For diagram of coenzyme F420 biosynthesis, click here
Glossary: oxidized coenzyme F420 = N-(N-{O-[5-(8-hydroxy-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinolin-10-yl)-5-deoxy-L-ribityl-1-phospho]-(S)-lactyl}-γ-L-glutamyl)-L-glutamate
Other name(s): FprA
Systematic name: reduced coenzyme F420:oxygen oxidoreductase
Comments: The enzyme contains FMN and a binuclear iron center. The enzyme from the archaeon Methanothermobacter marburgensis is Si-face specific with respect to C-5 of coenzyme F420 [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Seedorf, H., Dreisbach, A., Hedderich, R., Shima, S. and Thauer, R.K. F420H2 oxidase (FprA) from Methanobrevibacter arboriphilus, a coenzyme F420-dependent enzyme involved in O2 detoxification. Arch. Microbiol. 182 (2004) 126–137. [DOI] [PMID: 15340796]
2.  Seedorf, H., Kahnt, J., Pierik, A.J. and Thauer, R.K. Si-face stereospecificity at C5 of coenzyme F420 for F420H2 oxidase from methanogenic Archaea as determined by mass spectrometry. FEBS J. 272 (2005) 5337–5342. [DOI] [PMID: 16218963]
3.  Seedorf, H., Hagemeier, C.H., Shima, S., Thauer, R.K., Warkentin, E. and Ermler, U. Structure of coenzyme F420H2 oxidase (FprA), a di-iron flavoprotein from methanogenic Archaea catalyzing the reduction of O2 to H2O. FEBS J. 274 (2007) 1588–1599. [DOI] [PMID: 17480207]
[EC 1.5.3.22 created 2013]
 
 
EC 1.3.8.17     Relevance: 99.5%
Accepted name: dehydro coenzyme F420 reductase
Reaction: oxidized coenzyme F420-0 + FMN = dehydro coenzyme F420-0 + FMNH2
Glossary: dehydro coenzyme F420-0 = 2-{[5-deoxy-5-(8-hydroxy-2,4-dioxopyrimidino[4,5-b]quinolin-10(2H)-yl)-L-ribityloxy]hydroxyphosphoryloxy}prop-2-enoate
Other name(s): fbiB (gene name)
Systematic name: oxidized coenzyme F420-0:FMN oxidoreductase
Comments: This enzyme is involved in the biosynthesis of factor 420 (coenzyme F420), a redox-active compound found in all methanogenic archaea, as well as some eubacteria. In some eubacteria the enzyme is multifunctional, also catalysing the activities of EC 6.3.2.31, coenzyme F420-0:L-glutamate ligase, and EC 6.3.2.34, coenzyme F420-1:γ-L-glutamate ligase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Bashiri, G., Antoney, J., Jirgis, E.NM., Shah, M.V., Ney, B., Copp, J., Stuteley, S.M., Sreebhavan, S., Palmer, B., Middleditch, M., Tokuriki, N., Greening, C., Scott, C., Baker, E.N. and Jackson, C.J. A revised biosynthetic pathway for the cofactor F420 in prokaryotes. Nat. Commun. 10:1558 (2019). [DOI] [PMID: 30952857]
[EC 1.3.8.17 created 2021]
 
 
EC 1.17.98.3     Relevance: 95.1%
Accepted name: formate dehydrogenase (coenzyme F420)
Reaction: formate + oxidized coenzyme F420 = CO2 + reduced coenzyme F420
Other name(s): coenzyme F420 reducing formate dehydrogenase; coenzyme F420-dependent formate dehydrogenase
Systematic name: formate:coenzyme-F420 oxidoreductase
Comments: The enzyme, characterized from methanogenic archaea, is involved in formate-dependent H2 production. It contains noncovalently bound FAD [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Schauer, N.L. and Ferry, J.G. FAD requirement for the reduction of coenzyme F420 by formate dehydrogenase from Methanobacterium formicicum. J. Bacteriol. 155 (1983) 467–472. [PMID: 6874636]
2.  Schauer, N.L. and Ferry, J.G. Composition of the coenzyme F420-dependent formate dehydrogenase from Methanobacterium formicicum. J. Bacteriol. 165 (1986) 405–411. [DOI] [PMID: 3944055]
3.  Lupa, B., Hendrickson, E.L., Leigh, J.A. and Whitman, W.B. Formate-dependent H2 production by the mesophilic methanogen Methanococcus maripaludis. Appl. Environ. Microbiol. 74 (2008) 6584–6590. [DOI] [PMID: 18791018]
[EC 1.17.98.3 created 2014 as EC 1.2.99.9, transferred 2017 to EC 1.17.98.3]
 
 
EC 1.2.99.9      
Transferred entry: formate dehydrogenase (coenzyme F420). Now EC 1.17.98.3, formate dehydrogenase (coenzyme F420)
[EC 1.2.99.9 created 2014, deleted 2017]
 
 
EC 3.6.1.77     Relevance: 92.9%
Accepted name: coenzyme A diphosphatase
Reaction: coenzyme A + H2O = adenosine 3′,5′-bisphosphate + 4′-phosphopantetheine
Other name(s): CoA pyrophosphatase; coenzyme A pyrophosphatase; CoA diphosphohydrolase; Nudt19; Nudt7; thnR (gene name)
Systematic name: coenzyme A 4′-phosphopantetheine phosphohydrolase
Comments: The enzyme belongs to the Nudix hydrolase family. It has been reported from bacteria, yeast, and mammals. Activity is higher with oxidized disulfide CoA than with reduced CoA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Xu, W., Shen, J., Dunn, C.A., Desai, S. and Bessman, M.J. The Nudix hydrolases of Deinococcus radiodurans. Mol. Microbiol. 39 (2001) 286–290. [DOI] [PMID: 11136450]
2.  Gasmi, L. and McLennan, A.G. The mouse Nudt7 gene encodes a peroxisomal nudix hydrolase specific for coenzyme A and its derivatives. Biochem. J. 357 (2001) 33–38. [DOI] [PMID: 11415433]
3.  Kang, L.W., Gabelli, S.B., Bianchet, M.A., Xu, W.L., Bessman, M.J. and Amzel, L.M. Structure of a coenzyme A pyrophosphatase from Deinococcus radiodurans: a member of the Nudix family. J. Bacteriol. 185 (2003) 4110–4118. [DOI] [PMID: 12837785]
4.  Freeman, M.F., Moshos, K.A., Bodner, M.J., Li, R. and Townsend, C.A. Four enzymes define the incorporation of coenzyme A in thienamycin biosynthesis. Proc. Natl. Acad. Sci. USA 105 (2008) 11128–11133. [DOI] [PMID: 18678912]
5.  Shumar, S.A., Kerr, E.W., Geldenhuys, W.J., Montgomery, G.E., Fagone, P., Thirawatananond, P., Saavedra, H., Gabelli, S.B. and Leonardi, R. Nudt19 is a renal CoA diphosphohydrolase with biochemical and regulatory properties that are distinct from the hepatic Nudt7 isoform. J. Biol. Chem. 293 (2018) 4134–4148. [DOI] [PMID: 29378847]
[EC 3.6.1.77 created 2024]
 
 
EC 1.12.98.1     Relevance: 91.2%
Accepted name: coenzyme F420 hydrogenase
Reaction: H2 + oxidized coenzyme F420 = reduced coenzyme F420
For diagram of reaction, click here
Glossary: coenzyme F420 = N-(N-{O-[5-(8-hydroxy-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinolin-10-yl)-5-deoxy-L-ribityl-1-phospho]-(S)-lactyl}-γ-L-glutamyl)-L-glutamate
Other name(s): 8-hydroxy-5-deazaflavin-reducing hydrogenase; F420-reducing hydrogenase; coenzyme F420-dependent hydrogenase
Systematic name: hydrogen:coenzyme F420 oxidoreductase
Comments: An iron-sulfur flavoprotein (FAD) containing nickel. The enzyme from some sources contains selenocysteine. The enzyme also reduces the riboflavin analogue of F420, flavins and methyl viologen, but to a lesser extent. The hydrogen acceptor coenzyme F420 is a deazaflavin derivative.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9027-05-8
References:
1.  Adams, M.W.W., Mortenson, L.E. and Chen, J.-S. Hydrogenase. Biochim. Biophys. Acta 594 (1981) 105–176. [PMID: 6786341]
2.  Yamazaki, S. A selenium-containing hydrogenase from Methanococcus vannielii. Identification of the selenium moiety as a selenocysteine residue. J. Biol. Chem. 257 (1982) 7926–7929. [PMID: 6211447]
3.  Fox, J.A., Livingston, D.J., Orme-Johnson, W.H. and Walsh, C.T. 8-Hydroxy-5-deazaflavin-reducing hydrogenase from Methanobacterium thermoautotrophicum: 1. Purification and characterization. Biochemistry 26 (1987) 4219–4228. [PMID: 3663585]
4.  Muth, E., Morschel, E. and Klein, A. Purification and characterization of an 8-hydroxy-5-deazaflavin-reducing hydrogenase from the archaebacterium Methanococcus voltae. Eur. J. Biochem. 169 (1987) 571–577. [DOI] [PMID: 3121317]
5.  Baron, S.F. and Ferry, J.G. Purification and properties of the membrane-associated coenzyme F420-reducing hydrogenase from Methanobacterium formicicum. J. Bacteriol. 171 (1989) 3846–3853. [DOI] [PMID: 2738024]
[EC 1.12.98.1 created 1989 as EC 1.12.99.1, transferred 2002 to EC 1.12.98.1]
 
 
EC 6.3.2.31     Relevance: 91.1%
Accepted name: coenzyme F420-0:L-glutamate ligase
Reaction: GTP + coenzyme F420-0 + L-glutamate = GDP + phosphate + coenzyme F420-1
For diagram of coenzyme F420 biosynthesis, click here
Glossary: coenzyme F420 = N-(N-{O-[5-(8-hydroxy-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinolin-10-yl)-5-deoxy-L-ribityl-1-phospho]-(S)-lactyl}-γ-L-glutamyl)-L-glutamate
Other name(s): CofE-AF; MJ0768; CofE
Systematic name: L-glutamate:coenzyme F420-0 ligase (GDP-forming)
Comments: This protein catalyses the successive addition of two glutamate residues to factor F420 (coenzyme F420) by two distinct and independent reactions. In the reaction described here the enzyme attaches a glutamate via its α-amine group to F420-0. In the second reaction (EC 6.3.2.34, coenzyme F420-1:γ-L-glutamate ligase) it catalyses the addition of a second L-glutamate residue to the γ-carboxyl of the first glutamate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Li, H., Graupner, M., Xu, H. and White, R.H. CofE catalyzes the addition of two glutamates to F420-0 in F420 coenzyme biosynthesis in Methanococcus jannaschii. Biochemistry 42 (2003) 9771–9778. [DOI] [PMID: 12911320]
2.  Nocek, B., Evdokimova, E., Proudfoot, M., Kudritska, M., Grochowski, L.L., White, R.H., Savchenko, A., Yakunin, A.F., Edwards, A. and Joachimiak, A. Structure of an amide bond forming F420:γ-glutamyl ligase from Archaeoglobus fulgidus — a member of a new family of non-ribosomal peptide synthases. J. Mol. Biol. 372 (2007) 456–469. [DOI] [PMID: 17669425]
[EC 6.3.2.31 created 2010]
 
 
EC 1.8.98.3     Relevance: 90.7%
Accepted name: sulfite reductase (coenzyme F420)
Reaction: hydrogen sulfide + 3 oxidized coenzyme F420 + 3 H2O = sulfite + 3 reduced coenzyme F420
Other name(s): coenzyme F420-dependent sulfite reductase; Fsr
Systematic name: hydrogen sulfide:coenzyme F420 oxidoreductase
Comments: The enzyme, isolated from the archaeon Methanocaldococcus jannaschii, is involved in sulfite detoxification and assimilation.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Johnson, E.F. and Mukhopadhyay, B. A new type of sulfite reductase, a novel coenzyme F420-dependent enzyme, from the methanarchaeon Methanocaldococcus jannaschii. J. Biol. Chem. 280 (2005) 38776–38786. [DOI] [PMID: 16048999]
2.  Johnson, E.F. and Mukhopadhyay, B. Coenzyme F420-dependent sulfite reductase-enabled sulfite detoxification and use of sulfite as a sole sulfur source by Methanococcus maripaludis. Appl. Environ. Microbiol. 74 (2008) 3591–3595. [DOI] [PMID: 18378657]
[EC 1.8.98.3 created 2014]
 
 
EC 6.4.1.9     Relevance: 90%
Accepted name: coenzyme F430 synthetase
Reaction: ATP + 15,173-seco-F430-173-acid = ADP + phosphate + coenzyme F430
Other name(s): cfbE (gene name)
Systematic name: 15,173-seco-F430-173-acid cyclo-ligase (ADP-forming)
Comments: The enzyme, studied from the methanogenic archaeon Methanosarcina acetivorans, catalyses the last step in the biosynthesis of the nickel-containing tetrapyrrole cofactor coenzyme F430, which is required by EC 2.8.4.1, coenzyme-B sulfoethylthiotransferase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Zheng, K., Ngo, P.D., Owens, V.L., Yang, X.P. and Mansoorabadi, S.O. The biosynthetic pathway of coenzyme F430 in methanogenic and methanotrophic archaea. Science 354 (2016) 339–342. [DOI] [PMID: 27846569]
[EC 6.4.1.9 created 2017]
 
 
EC 6.3.2.32     Relevance: 89.9%
Accepted name: coenzyme γ-F420-2:α-L-glutamate ligase
Reaction: ATP + coenzyme γ-F420-2 + L-glutamate = ADP + phosphate + coenzyme α-F420-3
For diagram of coenzyme F420 biosynthesis, click here
Other name(s): MJ1001; CofF protein; γ-F420-2:α-L-glutamate ligase
Systematic name: L-glutamate:coenzyme γ-F420-2 (ADP-forming)
Comments: The enzyme caps the γ-glutamyl tail of the hydride carrier coenzyme F420 [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Li, H., Xu, H., Graham, D.E. and White, R.H. Glutathione synthetase homologs encode α-L-glutamate ligases for methanogenic coenzyme F420 and tetrahydrosarcinapterin biosyntheses. Proc. Natl. Acad. Sci. USA 100 (2003) 9785–9790. [DOI] [PMID: 12909715]
[EC 6.3.2.32 created 2010]
 
 
EC 6.3.2.34     Relevance: 87.6%
Accepted name: coenzyme F420-1:γ-L-glutamate ligase
Reaction: GTP + coenzyme F420-1 + L-glutamate = GDP + phosphate + coenzyme γ-F420-2
For diagram of coenzyme F420 biosynthesis, click here
Glossary: coenzyme F420 = N-(N-{O-[5-(8-hydroxy-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinolin-10-yl)-5-deoxy-L-ribityl-1-phospho]-(S)-lactyl}-γ-L-glutamyl)-L-glutamate
Other name(s): F420:γ-glutamyl ligase; CofE-AF; MJ0768; CofE
Systematic name: L-glutamate:coenzyme F420-1 ligase (GDP-forming)
Comments: This protein catalyses the successive addition of two glutamate residues to factor 420 (coenzyme F420) by two distinct and independent reactions. In the first reaction (EC 6.3.2.31, coenzyme F420-0:L-glutamate ligase) the enzyme attaches a glutamate via its α-amine group to F420-0. In the second reaction, which is described here, the enzyme catalyses the addition of a second L-glutamate residue to the γ-carboxyl of the first glutamate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Li, H., Graupner, M., Xu, H. and White, R.H. CofE catalyzes the addition of two glutamates to F420-0 in F420 coenzyme biosynthesis in Methanococcus jannaschii. Biochemistry 42 (2003) 9771–9778. [DOI] [PMID: 12911320]
2.  Nocek, B., Evdokimova, E., Proudfoot, M., Kudritska, M., Grochowski, L.L., White, R.H., Savchenko, A., Yakunin, A.F., Edwards, A. and Joachimiak, A. Structure of an amide bond forming F420:γ-glutamyl ligase from Archaeoglobus fulgidus — a member of a new family of non-ribosomal peptide synthases. J. Mol. Biol. 372 (2007) 456–469. [DOI] [PMID: 17669425]
[EC 6.3.2.34 created 2010, modified 2023]
 
 
EC 1.5.98.2     Relevance: 86.7%
Accepted name: 5,10-methylenetetrahydromethanopterin reductase
Reaction: 5-methyltetrahydromethanopterin + oxidized coenzyme F420 = 5,10-methylenetetrahydromethanopterin + reduced coenzyme F420
For diagram of methane biosynthesis, click here
Other name(s): 5,10-methylenetetrahydromethanopterin cyclohydrolase; N5,N10-methylenetetrahydromethanopterin reductase; methylene-H4MPT reductase; coenzyme F420-dependent N5,N10-methenyltetrahydromethanopterin reductase; N5,N10-methylenetetrahydromethanopterin:coenzyme-F420 oxidoreductase
Systematic name: 5-methyltetrahydromethanopterin:coenzyme-F420 oxidoreductase
Comments: Catalyses an intermediate step in methanogenesis from CO2 and H2 in methanogenic archaea.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Ma, K. and Thauer, R.K. Purification and properties of N5,N10-methylenetetrahydromethanopterin reductase from Methanobacterium thermoautotrophicum (strain Marburg). Eur. J. Biochem. 191 (1990) 187–193. [DOI] [PMID: 2379499]
2.  te Brömmelstroet, B.W., Geerts, W.J., Keltjens, J.T., van der Drift, C. and Vogels, G.D. Purification and properties of 5,10-methylenetetrahydromethanopterin dehydrogenase and 5,10-methylenetetrahydromethanopterin reductase, two coenzyme F420-dependent enzymes, from Methanosarcina barkeri. Biochim. Biophys. Acta 1079 (1991) 293–302. [DOI] [PMID: 1911853]
3.  Ma, K. and Thauer, R.K. Single step purification of methylenetetrahydromethanopterin reductase from Methanobacterium thermoautotrophicum by specific binding to blue sepharose CL-6B. FEBS Lett. 268 (1990) 59–62. [DOI] [PMID: 1696553]
4.  te Brömmelstroet, B.W., Hensgens, C.M., Keltjens, J.T., van der Drift, C. and Vogels, G.D. Purification and properties of 5,10-methylenetetrahydromethanopterin reductase, a coenzyme F420-dependent enzyme, from Methanobacterium thermoautotrophicum strain ΔH*. J. Biol. Chem. 265 (1990) 1852–1857. [PMID: 2298726]
5.  te Brömmelstroet, B.W., Hensgens, C.M., Geerts, W.J., Keltjens, J.T., van der Drift, C. and Vogels, G.D. Purification and properties of 5,10-methenyltetrahydromethanopterin cyclohydrolase from Methanosarcina barkeri. J. Bacteriol. 172 (1990) 564–571. [DOI] [PMID: 2298699]
[EC 1.5.98.2 created 2000 as EC 1.5.99.11, modified 2004, transferred to EC 1.5.98.2 2014]
 
 
EC 1.5.99.11      
Transferred entry: methylenetetrahydromethanopterin dehydrogenase. As the acceptor is known the enzyme has been transferred to EC 1.5.98.2, 5,10-methylenetetrahydromethanopterin reductase
[EC 1.5.99.11 created 2000, modified 2004, deleted 2014]
 
 
EC 1.5.7.2     Relevance: 86.5%
Accepted name: coenzyme F420 oxidoreductase (ferredoxin)
Reaction: reduced coenzyme F420 + 2 oxidized ferredoxin = oxidized coenzyme F420 + 2 reduced ferredoxin + 2 H+
Glossary: oxidized coenzyme F420 = N-(N-{O-[5-(8-hydroxy-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinolin-10-yl)-5-deoxy-L-ribityl-1-phospho]-(S)-lactyl}-γ-L-glutamyl)-L-glutamate
Other name(s): Fd:F420 oxidoreductase; FpoF protein; ferredoxin:F420 oxidoreductase
Systematic name: coenzyme F420:ferredoxin oxidoreductase
Comments: The enzyme from the archaeon Methanosarcina mazei contains iron-sulfur centres and FAD.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Welte, C. and Deppenmeier, U. Re-evaluation of the function of the F420 dehydrogenase in electron transport of Methanosarcina mazei. FEBS J. 278 (2011) 1277–1287. [DOI] [PMID: 21306561]
[EC 1.5.7.2 created 2013]
 
 
EC 2.8.4.1     Relevance: 83.7%
Accepted name: coenzyme-B sulfoethylthiotransferase
Reaction: methyl-CoM + CoB = CoM-S-S-CoB + methane
For diagram of methane biosynthesis, click here
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)
Other name(s): methyl-CoM reductase; methyl coenzyme M reductase
Systematic name: methyl-CoM:CoB S-(2-sulfoethyl)thiotransferase
Comments: This enzyme catalyses the final step in methanogenesis, the biological production of methane. This important anaerobic process is carried out only by methanogenic archaea. The enzyme can also function in reverse, for anaerobic oxidation of methane.The enzyme requires the hydroporphinoid nickel complex coenzyme F430. Highly specific for coenzyme B with a heptanoyl chain; ethyl CoM and difluoromethyl CoM are poor substrates. The sulfide sulfur can be replaced by selenium but not by oxygen.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Bobik, T.A., Olson, K.D., Noll, K.M. and Wolfe, R.S. Evidence that the heterodisulfide of coenzyme-M and 7-mercaptanoylthreonine phosphate is a product of the methylreductase reaction in Methanobacterium. Biochem. Biophys. Res. Commun. 149 (1987) 455–460. [DOI] [PMID: 3122735]
2.  Ellermann, J., Hedderich, R., Boecher, R. and Thauer, R.K. The final step in methane formation: investigations with highly purified methyl coenzyme M reductase component C from Methanobacterium thermoautotrophicum (strain Marburg). Eur. J. Biochem. 184 (1988) 63–68.
3.  Ermler, U., Grabarse, W., Shima, S., Goubeaud, M. and Thauer, R.K. Crystal structure of methyl coenzyme M reductase: The key enzyme of biological methane formation. Science 278 (1997) 1457–1462. [DOI] [PMID: 9367957]
4.  Signor, L., Knuppe, C., Hug, R., Schweizer, B., Pfaltz, A. and Jaun, B. Methane formation by reaction of a methyl thioether with a photo-excited nickel thiolate — a process mimicking methanogenesis in Archaea. Chemistry 6 (2000) 3508–3516. [PMID: 11072815]
5.  Scheller, S., Goenrich, M., Boecher, R., Thauer, R.K. and Jaun, B. The key nickel enzyme of methanogenesis catalyses the anaerobic oxidation of methane. Nature 465 (2010) 606–608. [DOI] [PMID: 20520712]
[EC 2.8.4.1 created 2001, modified 2011]
 
 
EC 2.8.3.5     Relevance: 83.6%
Accepted name: 3-oxoacid CoA-transferase
Reaction: succinyl-CoA + a 3-oxo acid = succinate + a 3-oxoacyl-CoA
Other name(s): 3-oxoacid coenzyme A-transferase; 3-ketoacid CoA-transferase; 3-ketoacid coenzyme A transferase; 3-oxo-CoA transferase; 3-oxoacid CoA dehydrogenase; acetoacetate succinyl-CoA transferase; acetoacetyl coenzyme A-succinic thiophorase; succinyl coenzyme A-acetoacetyl coenzyme A-transferase; succinyl-CoA transferase
Systematic name: succinyl-CoA:3-oxo-acid CoA-transferase
Comments: Acetoacetate and, more slowly, 3-oxopropanoate, 3-oxopentanoate, 3-oxo-4-methylpentanoate or 3-oxohexanoate can act as acceptors; malonyl-CoA can act instead of succinyl-CoA.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9027-43-4
References:
1.  Hersh, L.B. and Jencks, W.P. Coenzyme A transferase. Kinetics and exchange reactions. J. Biol. Chem. 242 (1967) 3468–3480.
2.  Lynen, F. and Ochoa, S. Enzymes of fatty acid metabolism. Biochim. Biophys. Acta 12 (1953) 299–314. [DOI] [PMID: 13115439]
3.  Menon, G.K.K. and Stern, J.R. Enzymic synthesis and metabolism of malonyl coenzyme A and glutaryl coenzyme A. J. Biol. Chem. 235 (1960) 3393–3398. [PMID: 13769479]
4.  Stern, J.R., Coon, M.J., del Campillo, A. and Schneider, M.C. Enzymes of fatty acid metabolism. IV. Preparation and properties of coenzyme A transferase. J. Biol. Chem. 221 (1956) 15–31. [PMID: 13345795]
[EC 2.8.3.5 created 1961, modified 1980]
 
 
EC 1.5.99.9      
Transferred entry: methylenetetrahydromethanopterin dehydrogenase. As the acceptor is known the enzyme has been transferred to EC 1.5.98.1, methylenetetrahydromethanopterin dehydrogenase
[EC 1.5.99.9 created 1989, modified 2004, deleted 2014]
 
 
EC 2.3.3.10     Relevance: 83.2%
Accepted name: hydroxymethylglutaryl-CoA synthase
Reaction: acetyl-CoA + H2O + acetoacetyl-CoA = (S)-3-hydroxy-3-methylglutaryl-CoA + CoA
For diagram of the mevalonate-biosynthesis pathway, click here
Other name(s): (S)-3-hydroxy-3-methylglutaryl-CoA acetoacetyl-CoA-lyase (CoA-acetylating); 3-hydroxy-3-methylglutaryl CoA synthetase; 3-hydroxy-3-methylglutaryl coenzyme A synthase; 3-hydroxy-3-methylglutaryl coenzyme A synthetase; 3-hydroxy-3-methylglutaryl-CoA synthase; 3-hydroxy-3-methylglutaryl-coenzyme A synthase; β-hydroxy-β-methylglutaryl-CoA synthase; HMG-CoA synthase; acetoacetyl coenzyme A transacetase; hydroxymethylglutaryl coenzyme A synthase; hydroxymethylglutaryl coenzyme A-condensing enzyme
Systematic name: acetyl-CoA:acetoacetyl-CoA C-acetyltransferase (thioester-hydrolysing, carboxymethyl-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9027-44-5
References:
1.  Rudney, H. The biosynthesis of β-hydroxy-β-methylglutaric acid. J. Biol. Chem. 227 (1957) 363–377. [PMID: 13449080]
[EC 2.3.3.10 created 1961 as EC 4.1.3.5, transferred 2002 to EC 2.3.3.10]
 
 
EC 1.5.98.1     Relevance: 82.8%
Accepted name: methylenetetrahydromethanopterin dehydrogenase
Reaction: 5,10-methylenetetrahydromethanopterin + oxidized coenzyme F420 = 5,10-methenyltetrahydromethanopterin + reduced coenzyme F420
For diagram of methane biosynthesis, click here
Other name(s): N5,N10-methylenetetrahydromethanopterin dehydrogenase; 5,10-methylenetetrahydromethanopterin dehydrogenase
Systematic name: 5,10-methylenetetrahydromethanopterin:coenzyme-F420 oxidoreductase
Comments: Coenzyme F420 is a 7,8-didemethyl-8-hydroxy-5-deazariboflavin derivative; methanopterin is a pterin analogue. The enzyme is involved in the formation of methane from CO2 in the methanogen Methanothermobacter thermautotrophicus.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 100357-01-5
References:
1.  Hartzell, P.L., Zvilius, G., Escalante-Semerena, J.C. and Donnelly, M.I. Coenzyme F420 dependence of the methylenetetrahydromethanopterin dehydrogenase of Methanobacterium thermoautotrophicum. Biochem. Biophys. Res. Commun. 133 (1985) 884–890. [DOI] [PMID: 4084309]
2.  te Brömmelstroet, B.W., Geerts, W.J., Keltjens, J.T., van der Drift, C. and Vogels, G.D. Purification and properties of 5,10-methylenetetrahydromethanopterin dehydrogenase and 5,10-methylenetetrahydromethanopterin reductase, two coenzyme F420-dependent enzymes, from Methanosarcina barkeri. Biochim. Biophys. Acta 1079 (1991) 293–302. [DOI] [PMID: 1911853]
[EC 1.5.98.1 created 1989 as EC 1.5.99.9, modified 2004, transferred to EC 1.5.98.1 2014]
 
 
EC 6.2.1.12     Relevance: 82.7%
Accepted name: 4-coumarate—CoA ligase
Reaction: ATP + 4-coumarate + CoA = AMP + diphosphate + 4-coumaroyl-CoA
For diagram of chalcone and stilbene biosynthesis, click here
Glossary: 4-coumarate = 3-(4-hydroxyphenyl)prop-2-enoate
Other name(s): 4-coumaroyl-CoA synthetase; p-coumaroyl CoA ligase; p-coumaryl coenzyme A synthetase; p-coumaryl-CoA synthetase; p-coumaryl-CoA ligase; feruloyl CoA ligase; hydroxycinnamoyl CoA synthetase; 4-coumarate:coenzyme A ligase; caffeolyl coenzyme A synthetase; p-hydroxycinnamoyl coenzyme A synthetase; feruloyl coenzyme A synthetase; sinapoyl coenzyme A synthetase; 4-coumaryl-CoA synthetase; hydroxycinnamate:CoA ligase; p-coumaryl-CoA ligase; p-hydroxycinnamic acid:CoA ligase; 4CL
Systematic name: 4-coumarate:CoA ligase (AMP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37332-51-7
References:
1.  Gross, G.G. and Zenk, M.H. Isolation and properties of hydroxycinnamate: CoA ligase from lignifying tissue of Forsythia. Eur. J. Biochem. 42 (1974) 453–459. [DOI] [PMID: 4364250]
2.  Lindl, T., Kreuzaler, F. and Hahlbrock, F. Synthesis of p-coumaroyl coenzyme A with a partially purified p-coumarate:CoA ligase from cell suspension cultures of soybean (Glycine max). Biochim. Biophys. Acta 302 (1973) 457–464. [DOI] [PMID: 4699252]
[EC 6.2.1.12 created 1976]
 
 
EC 1.1.98.4     Relevance: 82.5%
Accepted name: F420H2:quinone oxidoreductase
Reaction: a quinol + oxidized coenzyme F420 = a quinone + reduced coenzyme F420
Glossary: oxidized coenzyme F420 = N-(N-{O-[5-(8-hydroxy-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinolin-10-yl)-5-deoxy-L-ribityl-1-phospho]-(S)-lactyl}-γ-L-glutamyl)-L-glutamate
Other name(s): FqoF protein
Systematic name: quinol:coenzyme-F420 oxidoreductase
Comments: An enzyme complex that contains FAD and iron-sulfur clusters. The enzyme has been described in the archaea Methanosarcina mazei and Archaeoglobus fulgidus.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Bruggemann, H., Falinski, F. and Deppenmeier, U. Structure of the F420H2:quinone oxidoreductase of Archaeoglobus fulgidus identification and overproduction of the F420H2-oxidizing subunit. Eur. J. Biochem. 267 (2000) 5810–5814. [DOI] [PMID: 10971593]
2.  Kunow, J., Linder, D., Stetter, K.O. and Thauer, R.K. F420H2: quinone oxidoreductase from Archaeoglobus fulgidus. Characterization of a membrane-bound multisubunit complex containing FAD and iron-sulfur clusters. Eur. J. Biochem. 223 (1994) 503–511. [DOI] [PMID: 8055920]
3.  Abken, H.-J. and Deppenmeier, U. Purification and properties of an F420H2 dehydrogenase from Methanosarcina mazei Gö1. FEMS Microbiol. Lett. 154 (1997) 231–237.
[EC 1.1.98.4 created 2013]
 
 
EC 1.1.98.5     Relevance: 82%
Accepted name: secondary-alcohol dehydrogenase (coenzyme-F420)
Reaction: R-CHOH-R′ + oxidized coenzyme F420 = R-CO-R′ + reduced coenzyme F420
Glossary: oxidized coenzyme F420 = N-(N-{O-[5-(8-hydroxy-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinolin-10-yl)-5-deoxy-L-ribityl-1-phospho]-(S)-lactyl}-γ-L-glutamyl)-L-glutamate
Other name(s): F420-dependent alcohol dehydrogenase; secondary alcohol:F420 oxidoreductase; F420-dependent secondary alcohol dehydrogenase
Systematic name: secondary-alcohol:coenzyme F420 oxidoreductase
Comments: The enzyme isolated from the methanogenic archaea Methanogenium liminatans catalyses the reversible oxidation of various secondary and cyclic alcohols to the corresponding ketones.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Bleicher, K. and Winter, J. Purification and properties of F420- and NADP+-dependent alcohol dehydrogenases of Methanogenium liminatans and Methanobacterium palustre, specific for secondary alcohols. Eur. J. Biochem. 200 (1991) 43–51. [DOI] [PMID: 1879431]
2.  Aufhammer, S.W., Warkentin, E., Berk, H., Shima, S., Thauer, R.K. and Ermler, U. Coenzyme binding in F420-dependent secondary alcohol dehydrogenase, a member of the bacterial luciferase family. Structure 12 (2004) 361–370. [DOI] [PMID: 15016352]
[EC 1.1.98.5 created 2013]
 
 
EC 4.2.1.17     Relevance: 80.3%
Accepted name: enoyl-CoA hydratase
Reaction: (3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H2O
For diagram of aerobic phenylacetate catabolism, click here
Other name(s): enoyl hydrase; unsaturated acyl-CoA hydratase; β-hydroxyacyl-CoA dehydrase; β-hydroxyacid dehydrase; acyl coenzyme A hydrase; crotonase; crotonyl hydrase; 2-octenoyl coenzyme A hydrase; enoyl coenzyme A hydratase; 2-enoyl-CoA hydratase; short-chain enoyl-CoA hydratase; ECH; trans-2-enoyl-CoA hydratase; enoyl coenzyme A hydrase (D); enoyl coenzyme A hydrase (L); short chain enoyl coenzyme A hydratase; D-3-hydroxyacyl-CoA dehydratase; enol-CoA hydratase
Systematic name: (3S)-3-hydroxyacyl-CoA hydro-lyase
Comments: Acts in the reverse direction. With cis-compounds, yields (3R)-3-hydroxyacyl-CoA. cf. EC 4.2.1.74 long-chain-enoyl-CoA hydratase.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9027-13-8
References:
1.  Moskowitz, G.J. and Merrick, J.M. Metabolism of poly-β-hydroxybutyrate. II. Enzymatic synthesis of D-(-)-β-hydroxybutyryl coenzyme A by an enoyl hydrase from Rhodospirillum rubrum. Biochemistry 8 (1969) 2748–2755. [PMID: 5808333]
2.  Stern, J.R. Thioltranscrotylase and β-hydroxybutyryl CoA racemase activities of crystalline crotonase. Biochim. Biophys. Acta 26 (1957) 641–643. [DOI] [PMID: 13499425]
[EC 4.2.1.17 created 1961]
 
 
EC 1.2.1.44     Relevance: 79.3%
Accepted name: cinnamoyl-CoA reductase
Reaction: cinnamaldehyde + CoA + NADP+ = cinnamoyl-CoA + NADPH + H+
Other name(s): feruloyl-CoA reductase; cinnamoyl-coenzyme A reductase; ferulyl-CoA reductase; feruloyl coenzyme A reductase; p-hydroxycinnamoyl coenzyme A reductase; cinnamoyl-CoA:NADPH reductase
Systematic name: cinnamaldehyde:NADP+ oxidoreductase (CoA-cinnamoylating)
Comments: Acts also on a number of substituted cinnamoyl esters of coenzyme A.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 59929-39-4
References:
1.  Gross, G.G. and Kreiten, W. Reduction of coenzyme A thioesters of cinnamic acids with an enzyme preparation from lignifying tissue of Forsythia. FEBS Lett. 54 (1975) 259–262. [DOI] [PMID: 236926]
2.  Sarni, F., Grand, C. and Baudet, A.M. Purification and properties of cinnamoyl-CoA reductase and cinnamyl alcohol dehydrogenase from poplar stems (Populus X euramericana). Eur. J. Biochem. 139 (1984) 259–265. [DOI] [PMID: 6365550]
3.  Wengenmayer, H., Ebel, J. and Grisebach, H. Enzymic synthesis of lignin precursors. Purification and properties of a cinnamoyl-CoA: NADPH reductase from cell suspension cultures of soybean (Glycinemax). Eur. J. Biochem. 65 (1976) 529–536. [DOI] [PMID: 7454]
[EC 1.2.1.44 created 1978]
 
 
EC 1.5.98.3     Relevance: 79%
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 1.5.1.40     Relevance: 78.7%
Accepted name: 8-hydroxy-5-deazaflavin:NADPH oxidoreductase
Reaction: reduced coenzyme F420 + NADP+ = oxidized coenzyme F420 + NADPH + H+
For diagram of coenzyme F420 biosynthesis, click here
Other name(s): 8-OH-5dFl:NADPH oxidoreductase
Systematic name: reduced coenzyme F420:NADP+ oxidoreductase
Comments: The enzyme has an absolute requirement for both the 5-deazaflavin structure and the presence of an 8-hydroxy group in the substrate [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Eker, A.P., Hessels, J.K. and Meerwaldt, R. Characterization of an 8-hydroxy-5-deazaflavin:NADPH oxidoreductase from Streptomyces griseus. Biochim. Biophys. Acta 990 (1989) 80–86. [DOI] [PMID: 2492438]
[EC 1.5.1.40 created 2011]
 
 
EC 1.1.1.35     Relevance: 77.7%
Accepted name: 3-hydroxyacyl-CoA dehydrogenase
Reaction: (S)-3-hydroxyacyl-CoA + NAD+ = 3-oxoacyl-CoA + NADH + H+
Other name(s): β-hydroxyacyl dehydrogenase; β-keto-reductase; 3-keto reductase; 3-hydroxyacyl coenzyme A dehydrogenase; β-hydroxyacyl-coenzyme A synthetase; β-hydroxyacylcoenzyme A dehydrogenase; β-hydroxybutyrylcoenzyme A dehydrogenase; 3-hydroxyacetyl-coenzyme A dehydrogenase; L-3-hydroxyacyl coenzyme A dehydrogenase; L-3-hydroxyacyl CoA dehydrogenase; β-hydroxyacyl CoA dehydrogenase; 3β-hydroxyacyl coenzyme A dehydrogenase; 3-hydroxybutyryl-CoA dehydrogenase; β-ketoacyl-CoA reductase; β-hydroxy acid dehydrogenase; 3-L-hydroxyacyl-CoA dehydrogenase; 3-hydroxyisobutyryl-CoA dehydrogenase; 1-specific DPN-linked β-hydroxybutyric dehydrogenase
Systematic name: (S)-3-hydroxyacyl-CoA:NAD+ oxidoreductase
Comments: Also oxidizes S-3-hydroxyacyl-N-acylthioethanolamine and S-3-hydroxyacyl-hydrolipoate. Some enzymes act, more slowly, with NADP+. Broad specificity to acyl chain-length (cf. EC 1.1.1.211 [long-chain-3-hydroxyacyl-CoA dehydrogenase]).
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9028-40-4
References:
1.  Hillmer, P. and Gottschalk, G. Solubilization and partial characterisation of particulate dehydrogenases from Clostridium kluyveri. Biochim. Biophys. Acta 334 (1974) 12–23.
2.  Lehninger, A.L. and Greville, G.D. The enzymatic oxidation of d- and l-β-hydroxybutyrate. Biochim. Biophys. Acta 12 (1953) 188–202. [DOI] [PMID: 13115428]
3.  Stern, J.R. Crystalline β-hydroxybutyrate dehydrogenase from pig heart. Biochim. Biophys. Acta 26 (1957) 448–449. [DOI] [PMID: 13499396]
4.  Wakil, S.J., Green, D.E., Mii, S. and Mahler, H.R. Studies on the fatty acid oxidizing system of animal tissues. VI. β-Hydroxyacyl coenzyme A dehydrogenase. J. Biol. Chem. 207 (1954) 631–638. [PMID: 13163047]
[EC 1.1.1.35 created 1961]
 
 
EC 5.4.99.2     Relevance: 76.1%
Accepted name: methylmalonyl-CoA mutase
Reaction: (R)-methylmalonyl-CoA = succinyl-CoA
For diagram of the 3-hydroxypropanoate cycle, click here
Other name(s): methylmalonyl-CoA CoA-carbonyl mutase; methylmalonyl coenzyme A mutase; methylmalonyl coenzyme A carbonylmutase; (S)-methylmalonyl-CoA mutase; (R)-2-methyl-3-oxopropanoyl-CoA CoA-carbonylmutase [incorrect]
Systematic name: (R)-methylmalonyl-CoA CoA-carbonylmutase
Comments: Requires a cobamide coenzyme.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9023-90-9
References:
1.  Barker, H.A. Coenzyme B12-dependent mutases causing carbon chain rearrangements. In: Boyer, P.D. (Ed.), The Enzymes, 3rd edn, vol. 6, Academic Press, New York, 1972, pp. 509–537.
[EC 5.4.99.2 created 1961, modified 1983]
 
 
EC 1.8.4.3     Relevance: 75.5%
Accepted name: glutathione—CoA-glutathione transhydrogenase
Reaction: CoA + glutathione disulfide = CoA-glutathione + glutathione
Other name(s): glutathione-coenzyme A glutathione disulfide transhydrogenase; glutathione-coenzyme A glutathione disulfide transhydrogenase; glutathione coenzyme A-glutathione transhydrogenase; glutathione:coenzyme A-glutathione transhydrogenase; coenzyme A:oxidized-glutathione oxidoreductase; coenzyme A:glutathione-disulfide oxidoreductase
Systematic name: CoA:glutathione-disulfide oxidoreductase
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number: 37256-48-7
References:
1.  Chang, S.H. and Wilken, D.R. Participation of the unsymmetrical disulfide of coenzyme A and glutathione in an enzymatic sulfhydryl-disulfide interchange. I. Partial purification and properties of the bovine kidney enzyme. J. Biol. Chem. 241 (1966) 4251–4260. [PMID: 5924646]
[EC 1.8.4.3 created 1972]
 
 
EC 2.1.1.379     Relevance: 75.4%
Accepted name: [methyl coenzyme M reductase]-L-arginine C-5-methyltransferase
Reaction: 2 S-adenosyl-L-methionine + a [methyl coenzyme-M reductase]-L-arginine + reduced acceptor = S-adenosyl-L-homocysteine + L-methionine + 5′-deoxyadenosine + a [methyl coenzyme-M reductase]-(5S)-C-methyl-L-arginine + acceptor
Other name(s): methanogenesis marker protein 10; Mmp10
Systematic name: S-adenosyl-L-methionine:[methyl coenzyme M reductase]-L-arginine C-5-(S)-methyltransferase
Comments: The enzyme, present in methanogenic archaea, catalyses a modification of an L-arginine residue at the active site of EC 2.8.4.1, coenzyme-B sulfoethylthiotransferase (better known as methyl-coenzyme M reductase), which catalyses the last and methane-releasing step of methanogenesis. The enzyme is a radical AdoMet (radical SAM) enzyme and contains a [4Fe-4S] cluster and a Coα-[α-(5-hydroxybenzimidazolyl)]-cobamide cofactor. The methyl group, which is derived from S-adenosyl-L-methionine, is transferred to the cob(I)amide cofactor, forming methylcob(III)amide as an intermediate carrier, before being transferred to the arginine residue.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Deobald, D., Adrian, L., Schone, C., Rother, M. and Layer, G. Identification of a unique radical SAM methyltransferase required for the sp3-C-methylation of an arginine residue of methyl-coenzyme M reductase. Sci. Rep. 8:7404 (2018). [DOI] [PMID: 29743535]
2.  Radle, M.I., Miller, D.V., Laremore, T.N. and Booker, S.J. Methanogenesis marker protein 10 (Mmp10) from Methanosarcina acetivorans is a radical S-adenosylmethionine methylase that unexpectedly requires cobalamin. J. Biol. Chem. 294 (2019) 11712–11725. [DOI] [PMID: 31113866]
3.  Lyu, Z., Shao, N., Chou, C.W., Shi, H., Patel, R., Duin, E.C. and Whitman, W.B. Posttranslational methylation of arginine in methyl coenzyme M reductase has a profound impact on both methanogenesis and growth of Methanococcus maripaludis. J. Bacteriol. 202 (2020) . [DOI] [PMID: 31740491]
[EC 2.1.1.379 created 2021]
 
 
EC 1.1.98.2     Relevance: 74.8%
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 1.1.99.34      
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 4.99.1.11     Relevance: 74.1%
Accepted name: sirohydrochlorin nickelchelatase
Reaction: Ni-sirohydrochlorin + 2 H+ = sirohydrochlorin + Ni2+
Other name(s): cfbA (gene name)
Systematic name: Ni-sirohydrochlorin nickel-lyase (sirohydrochlorin-forming)
Comments: The enzyme, studied from the methanogenic archaeon Methanosarcina acetivorans, participates in the biosynthesis of the nickel-containing tetrapyrrole cofactor coenzyme F430, which is required by EC 2.8.4.1, coenzyme-B sulfoethylthiotransferase. It catalyses the insertion of the nickel ion into sirohydrochlorin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Zheng, K., Ngo, P.D., Owens, V.L., Yang, X.P. and Mansoorabadi, S.O. The biosynthetic pathway of coenzyme F430 in methanogenic and methanotrophic archaea. Science 354 (2016) 339–342. [DOI] [PMID: 27846569]
[EC 4.99.1.11 created 2017]
 
 
EC 1.8.98.1     Relevance: 73.8%
Accepted name: dihydromethanophenazine:CoB-CoM heterodisulfide reductase
Reaction: CoB + CoM + methanophenazine = CoM-S-S-CoB + dihydromethanophenazine
For diagram of methane biosynthesis, click here
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)
methanophenazine = 2-{[(6E,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl]oxy}phenazine
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): hdrDE (gene names); CoB—CoM heterodisulfide reductase (ambiguous); heterodisulfide reductase (ambiguous); coenzyme B:coenzyme M:methanophenazine oxidoreductase
Systematic name: CoB:CoM:methanophenazine oxidoreductase
Comments: This enzyme, found in methanogenic archaea that belong to the Methanosarcinales order, regenerates CoM and CoB after the action of EC 2.8.4.1, coenzyme-B sulfoethylthiotransferase. It is a membrane-bound enzyme that contains (per heterodimeric unit) two distinct b-type hemes and two [4Fe-4S] clusters. cf. EC 1.8.7.3, ferredoxin:CoB-CoM heterodisulfide reductase, EC 1.8.98.5, H2:CoB-CoM heterodisulfide,ferredoxin reductase, EC 1.8.98.6, formate:CoB-CoM heterodisulfide,ferredoxin reductase and EC 1.8.98.4, coenzyme F420:CoB-CoM heterodisulfide,ferredoxin reductase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Hedderich, R., Berkessel, A. and Thauer, R.K. Purification and properties of heterodisulfide reductase from Methanobacterium thermoautotrophicum (strain Marburg). Eur. J. Biochem. 193 (1990) 255–261. [DOI] [PMID: 2121478]
2.  Abken, H.J., Tietze, M., Brodersen, J., Bäumer, S., Beifuss, U. and Deppenmeier, U. Isolation and characterization of methanophenazine and function of phenazines in membrane-bound electron transport of Methanosarcina mazei gol. J. Bacteriol. 180 (1998) 2027–2032. [PMID: 9555882]
3.  Simianu, M., Murakami, E., Brewer, J.M. and Ragsdale, S.W. Purification and properties of the heme- and iron-sulfur-containing heterodisulfide reductase from Methanosarcina thermophila. Biochemistry 37 (1998) 10027–10039. [DOI] [PMID: 9665708]
4.  Murakami, E., Deppenmeier, U. and Ragsdale, S.W. Characterization of the intramolecular electron transfer pathway from 2-hydroxyphenazine to the heterodisulfide reductase from Methanosarcina thermophila. J. Biol. Chem. 276 (2001) 2432–2439. [DOI] [PMID: 11034998]
[EC 1.8.98.1 created 2003, modified 2017]
 
 
EC 6.3.5.12     Relevance: 73.6%
Accepted name: Ni-sirohydrochlorin a,c-diamide synthase
Reaction: 2 ATP + Ni-sirohydrochlorin + 2 L-glutamine + 2 H2O = 2 ADP + 2 phosphate + Ni-sirohydrochlorin a,c-diamide + 2 L-glutamate
Other name(s): cfbB (gene name)
Systematic name: Ni-sirohydrochlorin:L-glutamine amido-ligase (ADP-forming)
Comments: The enzyme, studied from the methanogenic archaeon Methanosarcina acetivorans, participates in the biosynthesis of the nickel-containing tetrapyrrole cofactor coenzyme F430, which is required by EC 2.8.4.1, coenzyme-B sulfoethylthiotransferase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Zheng, K., Ngo, P.D., Owens, V.L., Yang, X.P. and Mansoorabadi, S.O. The biosynthetic pathway of coenzyme F430 in methanogenic and methanotrophic archaea. Science 354 (2016) 339–342. [DOI] [PMID: 27846569]
[EC 6.3.5.12 created 2017]
 
 
EC 4.2.1.54     Relevance: 73.4%
Accepted name: lactoyl-CoA dehydratase
Reaction: (R)-lactoyl-CoA = acryloyl-CoA + H2O
Other name(s): lactoyl coenzyme A dehydratase; lactyl-coenzyme A dehydrase; lactyl CoA dehydratase; acrylyl coenzyme A hydratase; lactoyl-CoA hydro-lyase
Systematic name: (R)-lactoyl-CoA hydro-lyase (acryloyl-CoA-forming)
Comments: A bacterial enzyme that is involved in propanoate fermentation (also known as the acrylate pathway).
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, CAS registry number: 9031-12-3
References:
1.  Baldwin, R.L., Wood, W.A. and Emery, R.S. Lactate metabolism by Peptostreptococcus elsdenii: evidence for lactyl coenzyme a dehydrase. Biochim. Biophys. Acta 97 (1965) 202–213. [DOI] [PMID: 14292829]
2.  Schweiger, G. and Buckel, W. On the dehydration of (R)-lactate in the fermentation of alanine to propionate by Clostridium propionicum. FEBS Lett. 171 (1984) 79–84. [DOI] [PMID: 6586495]
3.  Kuchta, R.D. and Abeles, R.H. Lactate reduction in Clostridium propionicum. Purification and properties of lactyl-CoA dehydratase. J. Biol. Chem. 260 (1985) 13181–13189. [PMID: 4055736]
4.  Kuchta, R.D., Hanson, G.R., Holmquist, B. and Abeles, R.H. Fe-S centers in lactyl-CoA dehydratase. Biochemistry 25 (1986) 7301–7307. [PMID: 3026450]
5.  Hofmeister, A.E. and Buckel, W. (R)-Lactyl-CoA dehydratase from Clostridium propionicum. Stereochemistry of the dehydration of (R)-2-hydroxybutyryl-CoA to crotonyl-CoA. Eur. J. Biochem. 206 (1992) 547–552. [DOI] [PMID: 1597194]
[EC 4.2.1.54 created 1972, modified 2012]
 
 
EC 1.6.5.9     Relevance: 73.2%
Accepted name: NADH:quinone reductase (non-electrogenic)
Reaction: NADH + H+ + a quinone = NAD+ + a quinol
Other name(s): type II NAD(P)H:quinone oxidoreductase; NDE2 (gene name); ndh (gene name); NDH-II; NDH-2; NADH dehydrogenase (quinone) (ambiguous); ubiquinone reductase (ambiguous); coenzyme Q reductase (ambiguous); dihydronicotinamide adenine dinucleotide-coenzyme Q reductase (ambiguous); DPNH-coenzyme Q reductase (ambiguous); DPNH-ubiquinone reductase (ambiguous); NADH-coenzyme Q oxidoreductase (ambiguous); NADH-coenzyme Q reductase (ambiguous); NADH-CoQ oxidoreductase (ambiguous); NADH-CoQ reductase (ambiguous); NADH-ubiquinone reductase (ambiguous); NADH-ubiquinone oxidoreductase (ambiguous); reduced nicotinamide adenine dinucleotide-coenzyme Q reductase (ambiguous); NADH-Q6 oxidoreductase (ambiguous); NADH2 dehydrogenase (ubiquinone) (ambiguous); NADH:ubiquinone oxidoreductase; NADH:ubiquinone reductase (non-electrogenic)
Systematic name: NADH:quinone oxidoreductase
Comments: A flavoprotein (FAD or FMN). Occurs in mitochondria of yeast and plants, and in aerobic bacteria. Has low activity with NADPH. Unlike EC 7.1.1.2, NADH:ubiquinone reductase (H+-translocating), this enzyme does not pump proteons of sodium ions across the membrane. It is also not sensitive to rotenone.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9028-04-0
References:
1.  Bergsma, J., Strijker, R., Alkema, J.Y., Seijen, H.G. and Konings, W.N. NADH dehydrogenase and NADH oxidation in membrane vesicle from Bacillus subtilis. Eur. J. Biochem. 120 (1981) 599–606. [PMID: 6800784]
2.  Møller, I.M, and Palmer, J.M. Direct evidence for the presence of a rotenone-resistant NADH dehydrogenase on the inner surface of plant mitochondria. Physiol. Plant. 54 (1982) 267–274. [DOI]
3.  de Vries, S. and Grivell, L.A. Purification and characterization of a rotenone-insensitive NADH:Q6 oxidoreductase from mitochondria of Saccharomyces cerevisiae. Eur. J. Biochem. 176 (1988) 377–384. [DOI] [PMID: 3138118]
4.  Kerscher, S.J., Okun, J.G. and Brandt, U. A single external enzyme confers alternative NADH:ubiquinone oxidoreductase activity in Yarrowia lipolytica. J. Cell Sci. 112 ( Pt 14) (1999) 2347–2354. [PMID: 10381390]
5.  Rasmusson, A.G., Soole, K.L. and Elthon, T.E. Alternative NAD(P)H dehydrogenases of plant mitochondria. Annu. Rev. Plant Biol. 55 (2004) 23–39. [DOI] [PMID: 15725055]
6.  Melo, A.M., Bandeiras, T.M. and Teixeira, M. New insights into type II NAD(P)H:quinone oxidoreductases. Microbiol. Mol. Biol. Rev. 68 (2004) 603–616. [PMID: 15590775]
[EC 1.6.5.9 created 2011 (EC 1.6.5.11 created 1972 as EC 1.6.99.5, transferred 2015 to EC 1.6.5.11, incorporated 2019), modified 2019]
 
 
EC 3.1.2.5     Relevance: 72.7%
Accepted name: hydroxymethylglutaryl-CoA hydrolase
Reaction: (S)-3-hydroxy-3-methylglutaryl-CoA + H2O = CoA + 3-hydroxy-3-methylglutarate
For diagram of the mevalonate-biosynthesis pathway, click here
Other name(s): β-hydroxy-β-methylglutaryl coenzyme A hydrolase; β-hydroxy-β-methylglutaryl coenzyme A deacylase; hydroxymethylglutaryl coenzyme A hydrolase; hydroxymethylglutaryl coenzyme A deacylase; 3-hydroxy-3-methylglutaryl-CoA hydrolase
Systematic name: (S)-3-hydroxy-3-methylglutaryl-CoA hydrolase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9025-89-2
References:
1.  Dekker, E.E., Schlesinger, M.J. and Coon, M.J. β-Hydroxy-β-methylglutaryl coenzyme A deacetylase. J. Biol. Chem. 233 (1958) 434–438. [PMID: 13563516]
[EC 3.1.2.5 created 1961]
 
 
EC 3.1.2.1     Relevance: 70.8%
Accepted name: acetyl-CoA hydrolase
Reaction: acetyl-CoA + H2O = CoA + acetate
Other name(s): acetyl-CoA deacylase; acetyl-CoA acylase; acetyl coenzyme A hydrolase; acetyl coenzyme A deacylase; acetyl coenzyme A acylase; acetyl-CoA thiol esterase
Systematic name: acetyl-CoA hydrolase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9027-54-7
References:
1.  Gergely, J., Hele, P. and Ramakrishnan, C.V. Succinyl and acetyl coenzyme A deacylases. J. Biol. Chem. 198 (1952) 323–334. [PMID: 12999747]
[EC 3.1.2.1 created 1961]
 
 
EC 1.8.98.4     Relevance: 70.8%
Accepted name: coenzyme F420:CoB-CoM heterodisulfide,ferredoxin reductase
Reaction: 2 oxidized coenzyme F420 + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+ = 2 reduced coenzyme F420 + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
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): hdrA2B2C2 (gene names)
Systematic name: CoB,CoM,ferredoxin:coenzyme F420 oxidoreductase
Comments: The enzyme, characterized from the archaeon Methanosarcina acetivorans, catalyses the reduction of CoB-CoM heterodisulfide back to CoB and CoM. The enzyme consists of three components, HdrA, HdrB and HdrC, all of which contain [4Fe-4S] clusters. Electrons enter at HdrA, which also contains FAD, and are transferred via HdrC to the catalytic component, HdrB. During methanogenesis from acetate the enzyme catalyses the activity of EC 1.8.7.3, ferredoxin:CoB-CoM heterodisulfide reductase. However, it can also use electron bifurcation to direct electron pairs from reduced coenzyme F420 towards the reduction of both ferredoxin and CoB-CoM heterodisulfide. This activity is proposed to take place during Fe(III)-dependent anaerobic methane oxidation. 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.  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 1.8.98.4 created 2017]
 
 
EC 1.8.98.6     Relevance: 70.5%
Accepted name: formate:CoB-CoM heterodisulfide,ferredoxin reductase
Reaction: 2 CO2 + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+ = 2 formate + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
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
Systematic name: coenzyme B,coenzyme M,ferredoxin:formate oxidoreductase
Comments: The enzyme is found in formate-oxidizing CO2-reducing methanogenic archaea such as Methanococcus maripaludis. It consists of a cytoplasmic complex of HdrABC reductase and formate dehydrogenase. Electron pairs donated by formate dehydrogenase are transferred to the HdrA subunit of the reductase, where they are bifurcated, reducing both ferredoxin and CoB-CoM heterodisulfide. cf. EC 1.8.7.3, ferredoxin:CoB-CoM heterodisulfide reductase, EC 1.8.98.4, coenzyme F420:CoB-CoM heterodisulfide,ferredoxin reductase, EC 1.8.98.5, H2: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.  Costa, K.C., Wong, P.M., Wang, T., Lie, T.J., Dodsworth, J.A., Swanson, I., Burn, J.A., Hackett, M. and Leigh, J.A. Protein complexing in a methanogen suggests electron bifurcation and electron delivery from formate to heterodisulfide reductase. Proc. Natl. Acad. Sci. USA 107 (2010) 11050–11055. [DOI] [PMID: 20534465]
2.  Costa, K.C., Lie, T.J., Xia, Q. and Leigh, J.A. VhuD facilitates electron flow from H2 or formate to heterodisulfide reductase in Methanococcus maripaludis. J. Bacteriol. 195 (2013) 5160–5165. [DOI] [PMID: 24039260]
[EC 1.8.98.6 created 2017]
 
 
EC 1.3.4.1     Relevance: 70.4%
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 1.6.5.3      
Transferred entry: NADH:ubiquinone reductase (H+-translocating). Now EC 7.1.1.2, NADH:ubiquinone reductase (H+-translocating)
[EC 1.6.5.3 created 1961, deleted 1965, reinstated 1983, modified 2011, modified 2013, deleted 2018]
 
 
EC 6.2.1.32     Relevance: 70.1%
Accepted name: anthranilate—CoA ligase
Reaction: ATP + anthranilate + CoA = AMP + diphosphate + anthraniloyl-CoA
For diagram of acridone alkaloid biosynthesis, click here
Glossary: anthraniloyl-CoA = 2-aminobenzoyl-CoA
Other name(s): anthraniloyl coenzyme A synthetase; 2-aminobenzoate—CoA ligase; 2-aminobenzoate—coenzyme A ligase; 2-aminobenzoate coenzyme A ligase
Systematic name: anthranilate:CoA ligase (AMP-forming)
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 112692-58-7
References:
1.  Altenschmidt, U., Eckerskorn, C. and Fuchs, G. Evidence that enzymes of a novel aerobic 2-amino-benzoate metabolism in denitrifying Pseudomonas are coded on a small plasmid. Eur. J. Biochem. 194 (1990) 647–653. [DOI] [PMID: 2176602]
[EC 6.2.1.32 created 1992]
 
 
EC 6.2.1.3     Relevance: 69.2%
Accepted name: long-chain-fatty-acid—CoA ligase
Reaction: ATP + a long-chain fatty acid + CoA = AMP + diphosphate + an acyl-CoA
Glossary: a long-chain-fatty acid = a fatty acid with an aliphatic chain of 13-22 carbons.
Other name(s): acyl-CoA synthetase; fatty acid thiokinase (long chain); acyl-activating enzyme; palmitoyl-CoA synthase; lignoceroyl-CoA synthase; arachidonyl-CoA synthetase; acyl coenzyme A synthetase; acyl-CoA ligase; palmitoyl coenzyme A synthetase; thiokinase; palmitoyl-CoA ligase; acyl-coenzyme A ligase; fatty acid CoA ligase; long-chain fatty acyl coenzyme A synthetase; oleoyl-CoA synthetase; stearoyl-CoA synthetase; long chain fatty acyl-CoA synthetase; long-chain acyl CoA synthetase; fatty acid elongase; LCFA synthetase; pristanoyl-CoA synthetase; ACS3; long-chain acyl-CoA synthetase I; long-chain acyl-CoA synthetase II; fatty acyl-coenzyme A synthetase; long-chain acyl-coenzyme A synthetase; FAA1
Systematic name: long-chain fatty acid:CoA ligase (AMP-forming)
Comments: Acts on a wide range of long-chain saturated and unsaturated fatty acids, but the enzymes from different tissues show some variation in specificity. The liver enzyme acts on acids from C6 to C20; that from brain shows high activity up to C24.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9013-18-7
References:
1.  Bakken, A.M. and Farstad, M. Identical subcellular distribution of palmitoyl-CoA and arachidonoyl-CoA synthetase activities in human blood platelets. Biochem. J. 261 (1989) 71–76. [PMID: 2528345]
2.  Hosaka, K., Mishima, M., Tanaka, T., Kamiryo, T. and Numa, S. Acyl-coenzyme-A synthetase I from Candida lipolytica. Purification, properties and immunochemical studies. Eur. J. Biochem. 93 (1979) 197–203. [DOI] [PMID: 108099]
3.  Nagamatsu, K., Soeda, S., Mori, M. and Kishimoto, Y. Lignoceroyl-coenzyme A synthetase from developing rat brain: partial purification, characterization and comparison with palmitoyl-coenzyme A synthetase activity and liver enzyme. Biochim. Biophys. Acta 836 (1985) 80–88. [DOI] [PMID: 3161545]
4.  Tanaka, T., Hosaka, K., Hoshimaru, M. and Numa, S. Purification and properties of long-chain acyl-coenzyme-A synthetase from rat liver. Eur. J. Biochem. 98 (1979) 165–172. [DOI] [PMID: 467438]
[EC 6.2.1.3 created 1961, modified 1989, modified 2011]
 
 
EC 1.3.98.4     Relevance: 69.2%
Accepted name: 5a,11a-dehydrotetracycline reductase
Reaction: tetracycline + oxidized coenzyme F420 = 5a,11a-dehydrotetracycline + reduced coenzyme F420
For diagram of tetracycline biosynthesis, click here
Other name(s): oxyR (gene name); 12-dehydrotetracycline dehydrogenase; dehydrooxytetracycline dehydrogenase; 12-dehydrotetracycline reductase
Systematic name: tetracycline:coenzyme F420 dehydrogenase
Comments: The enzyme, characterized from the bacteria Streptomyces aureofaciens and Streptomyces rimosus, catalyses the last step in the biosynthesis of the tetracycline antibiotics tetracycline and oxytetracycline.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  McCormick, J.R.D., Hirsch, U., Sjolander, N.O. and Doerschuk, A.P. Cosynthesis of tetracyclines by pairs of Streptomyces aureofaciens mutants. J. Am. Chem. Soc. 82 (1960) 5006–5007.
2.  Miller, P.A., Sjolander, N.O., Nalesnyk, S., Arnold, N., Johnson, S., Doerschuk, A.P. and McCormick, J.R.D. Cosynthetic factor I, a factor involved in hydrogen-transfer in Streptomyces aureofaciens. J. Am. Chem. Soc. 82 (1960) 5002–5003.
3.  McCormick, J.R.D. and Morton, G.O. Identity of cosynthetic factor I of Streptomyces aureofaciens and fragment FO from coenzyme F420 of Methanobacterium species. J. Am. Chem. Soc. 104 (1982) 4014–4015.
4.  Wang, P., Bashiri, G., Gao, X., Sawaya, M.R. and Tang, Y. Uncovering the enzymes that catalyze the final steps in oxytetracycline biosynthesis. J. Am. Chem. Soc. 135 (2013) 7138–7141. [DOI] [PMID: 23621493]
[EC 1.3.98.4 created 2016]
 
 
EC 7.1.1.2     Relevance: 67.7%
Accepted name: NADH:ubiquinone reductase (H+-translocating)
Reaction: NADH + H+ + an ubiquinone + 4 H+[side 1] = NAD+ + an ubiquinol + 4 H+[side 2]
Other name(s): ubiquinone reductase (ambiguous); type 1 dehydrogenase; complex 1 dehydrogenase; coenzyme Q reductase (ambiguous); complex I (electron transport chain); complex I (mitochondrial electron transport); complex I (NADH:Q1 oxidoreductase); dihydronicotinamide adenine dinucleotide-coenzyme Q reductase (ambiguous); DPNH-coenzyme Q reductase (ambiguous); DPNH-ubiquinone reductase (ambiguous); mitochondrial electron transport complex 1; mitochondrial electron transport complex I; NADH coenzyme Q1 reductase; NADH-coenzyme Q oxidoreductase (ambiguous); NADH-coenzyme Q reductase (ambiguous); NADH-CoQ oxidoreductase (ambiguous); NADH-dehydrogenase (ubiquinone) (ambiguous); NADH-CoQ reductase (ambiguous); NADH-ubiquinone reductase (ambiguous); NADH-ubiquinone oxidoreductase (ambiguous); NADH-ubiquinone-1 reductase; reduced nicotinamide adenine dinucleotide-coenzyme Q reductase (ambiguous); NADH:ubiquinone oxidoreductase complex; NADH-Q6 oxidoreductase (ambiguous); electron transfer complex I; NADH2 dehydrogenase (ubiquinone)
Systematic name: NADH:ubiquinone oxidoreductase
Comments: The enzyme is a very large complex that participates in electron transfer chains of mitochondria and aerobic bacteria, transferring two electrons from NADH to a ubiquinone in the membrane's ubiquinone pool while pumping additional protons across the membrane, generating proton motive force. Different reports disagree whether the enzyme pumps 3 or 4 protons. Reversed electron transport through this enzyme can reduce NAD+ to NADH.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9028-04-0
References:
1.  Hatefi, Y., Ragan, C.I. and Galante, Y.M. The enzymes and the enzyme complexes of the mitochondrial oxidative phosphorylation system. In: Martonosi, A. (Ed.), The Enzymes of Biological Membranes, 2nd edn, vol. 4, Plenum Press, New York, 1985, pp. 1–70.
2.  Herter, S.M., Kortluke, C.M. and Drews, G. Complex I of Rhodobacter capsulatus and its role in reverted electron transport. Arch. Microbiol. 169 (1998) 98–105. [DOI] [PMID: 9446680]
3.  Hunte, C., Zickermann, V. and Brandt, U. Functional modules and structural basis of conformational coupling in mitochondrial complex I. Science 329 (2010) 448–451. [DOI] [PMID: 20595580]
4.  Efremov, R.G., Baradaran, R. and Sazanov, L.A. The architecture of respiratory complex I. Nature 465 (2010) 441–445. [DOI] [PMID: 20505720]
5.  Wikstrom, M. and Hummer, G. Stoichiometry of proton translocation by respiratory complex I and its mechanistic implications. Proc. Natl. Acad. Sci. USA 109 (2012) 4431–4436. [DOI] [PMID: 22392981]
[EC 7.1.1.2 created 1961 as EC 1.6.5.3, deleted 1965, reinstated 1983, modified 2011, modified 2013, transferred 2018 to EC 7.1.1.2, modified 2023]
 
 
EC 6.3.3.7     Relevance: 67.6%
Accepted name: Ni-sirohydrochlorin a,c-diamide reductive cyclase
Reaction: ATP + Ni-sirohydrochlorin a,c-diamide + 3 reduced electron acceptor + H2O = ADP + phosphate + 15,173-seco-F430-173-acid + 3 electron acceptor
Other name(s): cfbC (gene name); cfbD (gene name)
Systematic name: Ni-sirohydrochlorin a,c-diamide reductive cyclo-ligase (ADP-forming)
Comments: The enzyme, studied from the methanogenic archaeon Methanosarcina acetivorans, participates in the biosynthesis of the nickel-containing tetrapyrrole cofactor coenzyme F430, which is required by EC 2.8.4.1, coenzyme-B sulfoethylthiotransferase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Pfaltz, A., Kobelt, A., Huster, R. and Thauer, R.K. Biosynthesis of coenzyme F430 in methanogenic bacteria. Identification of 15,173-seco-F430-173-acid as an intermediate. Eur. J. Biochem. 170 (1987) 459–467. [PMID: 3691535]
2.  Zheng, K., Ngo, P.D., Owens, V.L., Yang, X.P. and Mansoorabadi, S.O. The biosynthetic pathway of coenzyme F430 in methanogenic and methanotrophic archaea. Science 354 (2016) 339–342. [DOI] [PMID: 27846569]
[EC 6.3.3.7 created 2017]
 
 
EC 2.1.1.377     Relevance: 67.6%
Accepted name: [methyl-Co(III) glycine betaine-specific corrinoid protein]—coenzyme M methyltransferase
Reaction: a [methyl-Co(III) glycine betaine-specific corrinoid protein] + CoM = methyl-CoM + a [Co(I) glycine betaine-specific corrinoid protein]
Other name(s): mtaA (gene name)
Systematic name: methylated glycine betaine-specific corrinoid protein:CoM methyltransferase
Comments: The enzyme, which is involved in methanogenesis from glycine betaine, catalyses the transfer of a methyl group bound to the cobalt cofactor of glycine betaine-specific corrinoid protein to coenzyme M, forming the substrate for EC 2.8.4.1, coenzyme-B sulfoethylthiotransferase, which catalyses the final step in methanogenesis. The enzyme from the methanogenic archaeon Methanolobus vulcani B1d can also catalyse the activity of EC 2.1.1.246, [methyl-Co(III) methanol-specific corrinoid protein]—coenzyme M methyltransferase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Creighbaum, A.J., Ticak, T., Shinde, S., Wang, X. and Ferguson, D.J., Jr. Examination of the glycine betaine-dependent methylotrophic methanogenesis pathway: insights into anaerobic quaternary amine methylotrophy. Front. Microbiol. 10:2572 (2019). [DOI] [PMID: 31787957]
[EC 2.1.1.377 created 2021]
 
 
EC 1.3.1.86     Relevance: 67.4%
Accepted name: crotonyl-CoA reductase
Reaction: butanoyl-CoA + NADP+ = (E)-but-2-enoyl-CoA + NADPH + H+
For diagram of lysine catabolism, click here
Glossary: (E)-but-2-enoyl-CoA = crotonyl-CoA
butanoyl-CoA = butyryl-CoA
Other name(s): butyryl-CoA dehydrogenase; butyryl dehydrogenase; unsaturated acyl-CoA reductase; ethylene reductase; enoyl-coenzyme A reductase; unsaturated acyl coenzyme A reductase; butyryl coenzyme A dehydrogenase; short-chain acyl CoA dehydrogenase; short-chain acyl-coenzyme A dehydrogenase; 3-hydroxyacyl CoA reductase; butanoyl-CoA:(acceptor) 2,3-oxidoreductase; CCR
Systematic name: butanoyl-CoA:NADP+ 2,3-oxidoreductase
Comments: Catalyses the reaction in the reverse direction. This enzyme from Streptomyces collinus is specific for (E)-but-2-enoyl-CoA, and is proposed to provide butanoyl-CoA as a starter unit for straight-chain fatty acid biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Wallace, K.K., Bao, Z.Y., Dai, H., Digate, R., Schuler, G., Speedie, M.K. and Reynolds, K.A. Purification of crotonyl-CoA reductase from Streptomyces collinus and cloning, sequencing and expression of the corresponding gene in Escherichia coli. Eur. J. Biochem. 233 (1995) 954–962. [DOI] [PMID: 8521864]
[EC 1.3.1.86 created 2011]
 
 


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