The Enzyme Database

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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 1.3.98.2      
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 1.8.7.3     
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]
 
 
EC 1.8.98.1     
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
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 1.8.98.4     
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 1.8.98.5     
Accepted name: H2:CoB-CoM heterodisulfide,ferredoxin reductase
Reaction: 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+ = 2 H2 + 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: CoB,CoM,ferredoxin:H2 oxidoreductase
Comments: This enzyme complex is found in H2-oxidizing CO2-reducing methanogenic archaea such as Methanothermobacter thermautotrophicus. It consists of a cytoplasmic complex of HdrABC reductase and MvhAGD hydrogenase. Electron pairs donated by the hydrogenase are transferred via its δ subunit to the HdrA subunit of the reductase, where they are bifurcated, reducing both ferredoxin and CoB-CoM heterodisulfide. The reductase can also form a similar complex with formate dehydrogenase, see EC 1.8.98.6, formate:CoB-CoM heterodisulfide,ferredoxin reductase. cf. EC 1.8.7.3, ferredoxin:CoB-CoM heterodisulfide reductase, EC 1.8.98.4, coenzyme F420: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.  Reeve, J.N., Beckler, G.S., Cram, D.S., Hamilton, P.T., Brown, J.W., Krzycki, J.A., Kolodziej, A.F., Alex, L., Orme-Johnson, W.H. and Walsh, C.T. A hydrogenase-linked gene in Methanobacterium thermoautotrophicum strain δ H encodes a polyferredoxin. Proc. Natl. Acad. Sci. USA 86 (1989) 3031–3035. [DOI] [PMID: 2654933]
2.  Hedderich, R., Koch, J., Linder, D. and Thauer, R.K. The heterodisulfide reductase from Methanobacterium thermoautotrophicum contains sequence motifs characteristic of pyridine-nucleotide-dependent thioredoxin reductases. Eur. J. Biochem. 225 (1994) 253–261. [DOI] [PMID: 7925445]
3.  Setzke, E., Hedderich, R., Heiden, S. and Thauer, R.K. H2: heterodisulfide oxidoreductase complex from Methanobacterium thermoautotrophicum. Composition and properties. Eur. J. Biochem. 220 (1994) 139–148. [DOI] [PMID: 8119281]
4.  Stojanowic, A., Mander, G.J., Duin, E.C. and Hedderich, R. Physiological role of the F420-non-reducing hydrogenase (Mvh) from Methanothermobacter marburgensis. Arch. Microbiol. 180 (2003) 194–203. [DOI] [PMID: 12856108]
5.  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]
6.  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 1.8.98.5 created 2017]
 
 
EC 1.8.98.6     
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 2.8.4.1     
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, EXPASY, KEGG, MetaCyc, PDB, UM-BBD
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]
 
 


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