The Enzyme Database

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EC 1.1.5.6      
Transferred entry: formate dehydrogenase-N. Now EC 1.17.5.3, formate dehydrogenase-N
[EC 1.1.5.6 created 2010, deleted 2017]
 
 
EC 1.1.99.33      
Transferred entry: formate dehydrogenase (acceptor). Now EC 1.17.99.7, formate dehydrogenase (acceptor)
[EC 1.1.99.33 created 2010, deleted 2017]
 
 
EC 1.2.2.4     
Accepted name: carbon-monoxide dehydrogenase (cytochrome b-561)
Reaction: CO + H2O + 2 ferricytochrome b-561 = CO2 + 2 H+ + 2 ferrocytochrome b-561
Other name(s): carbon monoxide oxidase; carbon monoxide oxygenase (cytochrome b-561); carbon monoxide:methylene blue oxidoreductase; CO dehydrogenase; carbon-monoxide dehydrogenase
Systematic name: carbon monoxide,water:cytochrome b-561 oxidoreductase
Comments: Contains molybdopterin cytosine dinucleotide, FAD and [2Fe-2S]-clusters. Oxygen, methylene blue and iodonitrotetrazolium chloride can act as nonphysiological electron acceptors.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, UM-BBD, CAS registry number: 395639-79-9
References:
1.  Meyer, O., Jacobitz, S. and Krüger, B. Biochemistry and physiology of aerobic carbon monoxide-utilizing bacteria. FEMS Microbiol. Rev. 39 (1986) 161–179.
2.  Jacobitz, S. and Meyer, O. Removal of CO dehydrogenase from Pseudomonas carboxydovorans cytoplasmic membranes, rebinding of CO dehydrogenase to depleted membranes and restoration of respiratory activities. J. Bacteriol. 171 (1989) 6294–6299. [DOI] [PMID: 2808305]
3.  Meyer, O. and Schlegel, H.-G. Carbon monoxide:methylene blue oxidoreductase from Pseudomonas carboxydovorans. J. Bacteriol. 141 (1980) 74–80. [PMID: 7354006]
4.  Dobbek, H., Gremer, L., Meyer, O. and Huber, R. Crystal structure and mechanism of CO dehydrogenase, a molybdo iron-sulfur flavoprotein containing S-selanylcysteine. Proc. Natl. Acad. Sci. USA 96 (1999) 8884–8889. [DOI] [PMID: 10430865]
5.  Hänzelmann, P., Dobbek, H., Gremer, L., Huber, R. and Meyer, O. The effect of intracellular molybdenum in Hydrogenophaga pseudoflava on the crystallographic structure of the seleno-molybdo-iron-sulfur flavoenzyme carbon monoxide dehydrogenase. J. Mol. Biol. 301 (2000) 1221–1235. [DOI] [PMID: 10966817]
[EC 1.2.2.4 created 1999 (EC 1.2.3.10 created 1990, incorporated 2003), modified 2003]
 
 
EC 1.2.5.3     
Accepted name: aerobic carbon monoxide dehydrogenase
Reaction: CO + a quinone + H2O = CO2 + a quinol
Other name(s): MoCu-CODH; coxSML (gene names); molybdoenzyme carbon monoxide dehydrogenase
Systematic name: carbon-monoxide:quinone oxidoreductase
Comments: This enzyme, found in carboxydotrophic bacteria, catalyses the oxidation of CO to CO2 under aerobic conditions. The enzyme contains a binuclear Mo-Cu cluster in which the copper is ligated to a molybdopterin center via a sulfur bridge. The enzyme also contains two [2Fe-2S] clusters and FAD, and belongs to the xanthine oxidoreductase family. The CO2 that is produced is assimilated by the Calvin-Benson-Basham cycle, while the electrons are transferred to a quinone via the FAD site, and continue through the electron transfer chain to a dioxygen terminal acceptor [5]. cf. EC 1.2.7.4, anaerobic carbon monoxide dehydrogenase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Gremer, L., Kellner, S., Dobbek, H., Huber, R. and Meyer, O. Binding of flavin adenine dinucleotide to molybdenum-containing carbon monoxide dehydrogenase from Oligotropha carboxidovorans. Structural and functional analysis of a carbon monoxide dehydrogenase species in which the native flavoprotein has been replaced by its recombinant counterpart produced in Escherichia coli. J. Biol. Chem. 275 (2000) 1864–1872. [DOI] [PMID: 10636886]
2.  Dobbek, H., Gremer, L., Kiefersauer, R., Huber, R. and Meyer, O. Catalysis at a dinuclear [CuSMo(==O)OH] cluster in a CO dehydrogenase resolved at 1.1-Å resolution. Proc. Natl. Acad. Sci. USA 99 (2002) 15971–15976. [DOI] [PMID: 12475995]
3.  Gnida, M., Ferner, R., Gremer, L., Meyer, O. and Meyer-Klaucke, W. A novel binuclear [CuSMo] cluster at the active site of carbon monoxide dehydrogenase: characterization by X-ray absorption spectroscopy. Biochemistry 42 (2003) 222–230. [DOI] [PMID: 12515558]
4.  Resch, M., Dobbek, H. and Meyer, O. Structural and functional reconstruction in situ of the [CuSMoO2] active site of carbon monoxide dehydrogenase from the carbon monoxide oxidizing eubacterium Oligotropha carboxidovorans. J. Biol. Inorg. Chem. 10 (2005) 518–528. [DOI] [PMID: 16091936]
5.  Wilcoxen, J., Zhang, B. and Hille, R. Reaction of the molybdenum- and copper-containing carbon monoxide dehydrogenase from Oligotropha carboxidovorans with quinones. Biochemistry 50 (2011) 1910–1916. [DOI] [PMID: 21275368]
6.  Pelzmann, A.M., Mickoleit, F. and Meyer, O. Insights into the posttranslational assembly of the Mo-, S- and Cu-containing cluster in the active site of CO dehydrogenase of Oligotropha carboxidovorans. J. Biol. Inorg. Chem. 19 (2014) 1399–1414. [DOI] [PMID: 25377894]
7.  Hille, R., Dingwall, S. and Wilcoxen, J. The aerobic CO dehydrogenase from Oligotropha carboxidovorans. J. Biol. Inorg. Chem. 20 (2015) 243–251. [DOI] [PMID: 25156151]
[EC 1.2.5.3 created 2016]
 
 
EC 1.2.7.5     
Accepted name: aldehyde ferredoxin oxidoreductase
Reaction: an aldehyde + H2O + 2 oxidized ferredoxin = a carboxylate + 2 H+ + 2 reduced ferredoxin
Other name(s): AOR
Systematic name: aldehyde:ferredoxin oxidoreductase
Comments: This is an oxygen-sensitive enzyme that contains tungsten-molybdopterin and iron-sulfur clusters. Catalyses the oxidation of aldehydes (including crotonaldehyde, acetaldehyde, formaldehyde and glyceraldehyde) to their corresponding acids. However, it does not oxidize glyceraldehyde 3-phosphate [see EC 1.2.7.6, glyceraldehyde-3-phosphate dehydrogenase (ferredoxin)]. Can use ferredoxin or methylviologen but not NAD(P)+ as electron acceptor.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 138066-90-7
References:
1.  Mukund, S. and Adams, M.W.W. The novel tungsten-iron-sulfur protein of the hyperthermophilic archaebacterium, Pyrococcus furiosus, is an aldehyde ferredoxin oxidoreductase - evidence for its participation in a unique glycolytic pathway. J. Biol. Chem. 266 (1991) 14208–14216. [PMID: 1907273]
2.  Johnson, J.L., Rajagopalan, K.V., Mukund, S. and Adams, M.W.W. Identification of molybdopterin as the organic-component of the tungsten cofactor in four enzymes from hyperthermophilic archaea. J. Biol. Chem. 268 (1993) 4848–4852. [PMID: 8444863]
3.  Chan, M.K., Mukund, S., Kletzin, A., Adams, M.W.W. and Rees, D.C. Structure of a hyperthermophilic tungstopterin enzyme, aldehyde ferredoxin oxidoreductase. Science 267 (1995) 1463–1469. [DOI] [PMID: 7878465]
4.  Roy, R., Menon, A.L. and Adams, M.W.W. Aldehyde oxidoreductases from Pyrococcus furiosus. Methods Enzymol. 331 (2001) 132–144. [DOI] [PMID: 11265456]
[EC 1.2.7.5 created 2003]
 
 
EC 1.2.7.6     
Accepted name: glyceraldehyde-3-phosphate dehydrogenase (ferredoxin)
Reaction: D-glyceraldehyde-3-phosphate + H2O + 2 oxidized ferredoxin = 3-phospho-D-glycerate + 2 H+ + 2 reduced ferredoxin
Other name(s): GAPOR; glyceraldehyde-3-phosphate Fd oxidoreductase; glyceraldehyde-3-phosphate ferredoxin reductase
Systematic name: D-glyceraldehyde-3-phosphate:ferredoxin oxidoreductase
Comments: Contains tungsten-molybdopterin and iron-sulfur clusters. This enzyme is thought to function in place of glyceralde-3-phosphate dehydrogenase and possibly phosphoglycerate kinase in the novel Embden-Meyerhof-type glycolytic pathway found in Pyrococcus furiosus [1]. It is specific for glyceraldehyde-3-phosphate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 162995-20-2
References:
1.  Mukund, S. and Adams, M.W.W. Glyceraldehyde-3-phosphate ferredoxin oxidoreductase, a novel tungsten-containing enzyme with a potential glycolytic role in the hyperthermophilic archaeon Pyrococcus furiosus. J. Biol. Chem. 270 (1995) 8389–8392. [DOI] [PMID: 7721730]
2.  Roy, R., Menon, A.L. and Adams, M.W.W. Aldehyde oxidoreductases from Pyrococcus furiosus. Methods Enzymol. 331 (2001) 132–144. [DOI] [PMID: 11265456]
[EC 1.2.7.6 created 2003]
 
 
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, EXPASY, KEGG, MetaCyc, UM-BBD, 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 1.2.99.7     
Accepted name: aldehyde dehydrogenase (FAD-independent)
Reaction: an aldehyde + H2O + acceptor = a carboxylate + reduced acceptor
Other name(s): aldehyde oxidase; aldehyde oxidoreductase; Mop; AORDd
Systematic name: aldehyde:acceptor oxidoreductase (FAD-independent)
Comments: Belongs to the xanthine oxidase family of enzymes. The enzyme from Desulfovibrio sp. contains a molybdenum-molybdopterin-cytosine dinucleotide (MCD) complex and two types of [2Fe-2S] cluster per monomer, but does not contain FAD.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Uchida, H., Kondo, D., Yamashita, A., Nagaosa, Y., Sakurai, T., Fujii, Y., Fujishiro, K., Aisaka, K. and Uwajima, T. Purification and characterization of an aldehyde oxidase from Pseudomonas sp. KY 4690. FEMS Microbiol. Lett. 229 (2003) 31–36. [DOI] [PMID: 14659539]
2.  Duarte, R.O., Archer, M., Dias, J.M., Bursakov, S., Huber, R., Moura, I., Romao, M.J. and Moura, J.J. Biochemical/spectroscopic characterization and preliminary X-ray analysis of a new aldehyde oxidoreductase isolated from Desulfovibrio desulfuricans ATCC 27774. Biochem. Biophys. Res. Commun. 268 (2000) 745–749. [DOI] [PMID: 10679276]
3.  Andrade, S.L., Brondino, C.D., Feio, M.J., Moura, I. and Moura, J.J. Aldehyde oxidoreductase activity in Desulfovibrio alaskensis NCIMB 13491. EPR assignment of the proximal [2Fe-2S] cluster to the Mo site. Eur. J. Biochem. 267 (2000) 2054–2061. [DOI] [PMID: 10727945]
4.  Romao, M.J., Archer, M., Moura, I., Moura, J.J., LeGall, J., Engh, R., Schneider, M., Hof, P. and Huber, R. Crystal structure of the xanthine oxidase-related aldehyde oxido-reductase from D. gigas. Science 270 (1995) 1170–1176. [DOI] [PMID: 7502041]
[EC 1.2.99.7 created 2004]
 
 
EC 1.2.99.8     
Accepted name: glyceraldehyde dehydrogenase (FAD-containing)
Reaction: D-glyceraldehyde + H2O + acceptor = D-glycerate + reduced acceptor
For diagram of the Entner-Doudoroff pathway, click here
Other name(s): glyceraldehyde oxidoreductase
Systematic name: D-glyceraldehyde:acceptor oxidoreductase (FAD-containing)
Comments: The enzyme from the archaeon Sulfolobus acidocaldarius catalyses the oxidation of D-glyceraldehyde in the nonphosphorylative Entner-Doudoroff pathway. With 2,6-dichlorophenolindophenol as artificial electron acceptor, the enzyme shows a broad substrate range, but is most active with D-glyceraldehyde. It is not known which acceptor is utilized in vivo. The iron-sulfur protein contains FAD and molybdopterin guanine dinucleotide.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kardinahl, S., Schmidt, C.L., Hansen, T., Anemuller, S., Petersen, A. and Schafer, G. The strict molybdate-dependence of glucose-degradation by the thermoacidophile Sulfolobus acidocaldarius reveals the first crenarchaeotic molybdenum containing enzyme—an aldehyde oxidoreductase. Eur. J. Biochem. 260 (1999) 540–548. [DOI] [PMID: 10095793]
[EC 1.2.99.8 created 2013]
 
 
EC 1.3.99.19     
Accepted name: quinoline-4-carboxylate 2-oxidoreductase
Reaction: quinoline-4-carboxylate + acceptor + H2O = 2-oxo-1,2-dihydroquinoline-4-carboxylate + reduced acceptor
For diagram of reaction, click here
Other name(s): quinaldic acid 4-oxidoreductase; quinoline-4-carboxylate:acceptor 2-oxidoreductase (hydroxylating)
Systematic name: quinoline-4-carboxylate:acceptor 2-oxidoreductase (hydroxylating)
Comments: A molybdenum—iron—sulfur flavoprotein with molybdopterin cytosine dinucleotide as the molybdenum cofactor. Quinoline, 4-methylquinoline and 4-chloroquinoline can also serve as substrates for the enzyme from Agrobacterium sp. 1B. Iodonitrotetrazolium chloride, thionine, menadione and 2,6-dichlorophenolindophenol can act as electron acceptors.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 175780-18-4
References:
1.  Bauer, G. and Lingens, F. Microbial metabolism of quinoline and related compounds. XV. Quinoline-4-carboxylic acid oxidoreductase from Agrobacterium spec.1B: a molybdenum-containing enzyme. Biol. Chem. Hoppe-Seyler 373 (1992) 699–705. [PMID: 1418685]
[EC 1.3.99.19 created 1999, modified 2006]
 
 
EC 1.5.99.14     
Accepted name: 6-hydroxypseudooxynicotine dehydrogenase
Reaction: 1-(6-hydroxypyridin-3-yl)-4-(methylamino)butan-1-one + acceptor + H2O = 1-(2,6-dihydroxypyridin-3-yl)-4-(methylamino)butan-1-one + reduced acceptor
For diagram of nicotine catabolism by arthrobacter, click here
Glossary: 1-(6-hydroxypyridin-3-yl)-4-(methylamino)butan-1-one = 6-hydroxypseudooxynicotine
1-(2,6-dihydroxypyridin-3-yl)-4-(methylamino)butan-1-one = 2,6-dihydroxypseudooxynicotine
Systematic name: 1-(6-hydroxypyridin-3-yl)-4-(methylamino)butan-1-one:acceptor 6-oxidoreductase (hydroxylating)
Comments: Contains a cytidylyl molybdenum cofactor [3]. The enzyme, which participates in the nicotine degradation pathway, has been characterized from the soil bacterium Arthrobacter nicotinovorans [1,2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, UM-BBD
References:
1.  Freudenberg, W., Konig, K. and Andreesen, J. R. Nicotine dehydrogenase from Arthrobacter oxidans: A molybdenum-containing hydroxylase. FEMS Microbiology Letters 52 (1988) 13–18.
2.  Grether-Beck, S., Igloi, G.L., Pust, S., Schilz, E., Decker, K. and Brandsch, R. Structural analysis and molybdenum-dependent expression of the pAO1-encoded nicotine dehydrogenase genes of Arthrobacter nicotinovorans. Mol. Microbiol. 13 (1994) 929–936. [DOI] [PMID: 7815950]
3.  Sachelaru, P., Schiltz, E. and Brandsch, R. A functional mobA gene for molybdopterin cytosine dinucleotide cofactor biosynthesis is required for activity and holoenzyme assembly of the heterotrimeric nicotine dehydrogenases of Arthrobacter nicotinovorans. Appl. Environ. Microbiol. 72 (2006) 5126–5131. [DOI] [PMID: 16820521]
[EC 1.5.99.14 created 2012]
 
 
EC 1.7.2.3     
Accepted name: trimethylamine-N-oxide reductase
Reaction: trimethylamine + 2 (ferricytochrome c)-subunit + H2O = trimethylamine N-oxide + 2 (ferrocytochrome c)-subunit + 2 H+
For diagram of dimethyl sulfide catabolism, click here
Other name(s): TMAO reductase; TOR; torA (gene name); torZ (gene name); bisZ (gene name); trimethylamine-N-oxide reductase (cytochrome c)
Systematic name: trimethylamine:cytochrome c oxidoreductase
Comments: Contains bis(molybdopterin guanine dinucleotide)molybdenum cofactor. The reductant is a membrane-bound multiheme cytochrome c. Also reduces dimethyl sulfoxide to dimethyl sulfide.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37256-34-1
References:
1.  Arata, H., Shimizu, M. and Takamiya, K. Purification and properties of trimethylamine N-oxide reductase from aerobic photosynthetic bacterium Roseobacter denitrificans. J. Biochem. (Tokyo) 112 (1992) 470–475. [PMID: 1337081]
2.  Knablein, J., Dobbek, H., Ehlert, S. and Schneider, F. Isolation, cloning, sequence analysis and X-ray structure of dimethyl sulfoxide trimethylamine N-oxide reductase from Rhodobacter capsulatus. Biol. Chem. 378 (1997) 293–302. [PMID: 9165084]
3.  Czjzek, M., Dos Santos, J.P., Pommier, J., Giordano, G., Méjean, V. and Haser, R. Crystal structure of oxidized trimethylamine N-oxide reductase from Shewanella massilia at 2.5 Å resolution. J. Mol. Biol. 284 (1998) 435–447. [DOI] [PMID: 9813128]
4.  Gon, S., Giudici-Orticoni, M.T., Mejean, V. and Iobbi-Nivol, C. Electron transfer and binding of the c-type cytochrome TorC to the trimethylamine N-oxide reductase in Escherichia coli. J. Biol. Chem. 276 (2001) 11545–11551. [DOI] [PMID: 11056172]
5.  Zhang, L., Nelson, K.J., Rajagopalan, K.V. and George, G.N. Structure of the molybdenum site of Escherichia coli trimethylamine N-oxide reductase. Inorg. Chem. 47 (2008) 1074–1078. [PMID: 18163615]
6.  Yin, Q.J., Zhang, W.J., Qi, X.Q., Zhang, S.D., Jiang, T., Li, X.G., Chen, Y., Santini, C.L., Zhou, H., Chou, I.M. and Wu, L.F. High hydrostatic pressure inducible trimethylamine N-oxide reductase improves the pressure tolerance of piezosensitive bacteria Vibrio fluvialis. Front. Microbiol. 8:2646 (2017). [PMID: 29375513]
[EC 1.7.2.3 created 2002, modified 2018]
 
 
EC 1.7.5.1     
Accepted name: nitrate reductase (quinone)
Reaction: nitrate + a quinol = nitrite + a quinone + H2O
Other name(s): nitrate reductase A; nitrate reductase Z; quinol/nitrate oxidoreductase; quinol-nitrate oxidoreductase; quinol:nitrate oxidoreductase; NarA; NarZ; NarGHI; dissimilatory nitrate reductase
Systematic name: nitrite:quinone oxidoreductase
Comments: A membrane-bound enzyme which supports anaerobic respiration on nitrate under anaerobic conditions and in the presence of nitrate. Contains the bicyclic form of the molybdo-bis(molybdopterin guanine dinucleotide) cofactor, iron-sulfur clusters and heme b. Escherichia coli expresses two forms NarA and NarZ, both being comprised of three subunits.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Enoch, H.G. and Lester, R.L. The role of a novel cytochrome b-containing nitrate reductase and quinone in the in vitro reconstruction of formate-nitrate reductase activity of E. coli. Biochem. Biophys. Res. Commun. 61 (1974) 1234–1241. [DOI] [PMID: 4616697]
2.  Bertero, M.G., Rothery, R.A., Palak, M., Hou, C., Lim, D., Blasco, F., Weiner, J.H. and Strynadka, N.C. Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A. Nat. Struct. Biol. 10 (2003) 681–687. [DOI] [PMID: 12910261]
3.  Lanciano, P., Magalon, A., Bertrand, P., Guigliarelli, B. and Grimaldi, S. High-stability semiquinone intermediate in nitrate reductase A (NarGHI) from Escherichia coli is located in a quinol oxidation site close to heme bD. Biochemistry 46 (2007) 5323–5329. [DOI] [PMID: 17439244]
4.  Bertero, M.G., Rothery, R.A., Boroumand, N., Palak, M., Blasco, F., Ginet, N., Weiner, J.H. and Strynadka, N.C. Structural and biochemical characterization of a quinol binding site of Escherichia coli nitrate reductase A. J. Biol. Chem. 280 (2005) 14836–14843. [DOI] [PMID: 15615728]
5.  Bonnefoy, V. and Demoss, J.A. Nitrate reductases in Escherichia coli. Antonie Van Leeuwenhoek 66 (1994) 47–56. [PMID: 7747940]
6.  Guigliarelli, B., Asso, M., More, C., Augier, V., Blasco, F., Pommier, J., Giordano, G. and Bertrand, P. EPR and redox characterization of iron-sulfur centers in nitrate reductases A and Z from Escherichia coli. Evidence for a high-potential and a low-potential class and their relevance in the electron-transfer mechanism. Eur. J. Biochem. 207 (1992) 61–68. [DOI] [PMID: 1321049]
7.  Iobbi-Nivol, C., Santini, C.L., Blasco, F. and Giordano, G. Purification and further characterization of the second nitrate reductase of Escherichia coli K12. Eur. J. Biochem. 188 (1990) 679–687. [DOI] [PMID: 2139607]
[EC 1.7.5.1 created 2010]
 
 
EC 1.8.2.4     
Accepted name: dimethyl sulfide:cytochrome c2 reductase
Reaction: dimethyl sulfide + 2 ferricytochrome c2 + H2O = dimethyl sulfoxide + 2 ferrocytochrome c2 + 2 H+
For diagram of dimethyl sulfide catabolism, click here
Other name(s): Ddh (gene name)
Systematic name: dimethyl sulfide:cytochrome-c2 oxidoreductase
Comments: The enzyme from the bacterium Rhodovulum sulfidophilum binds molybdopterin guanine dinucleotide, heme b and [4Fe-4S] clusters.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hanlon, S.P., Toh, T.H., Solomon, P.S., Holt, R.A. and McEwan, A.G. Dimethylsulfide:acceptor oxidoreductase from Rhodobacter sulfidophilus. The purified enzyme contains b-type haem and a pterin molybdenum cofactor. Eur. J. Biochem. 239 (1996) 391–396. [DOI] [PMID: 8706745]
2.  McDevitt, C.A., Hugenholtz, P., Hanson, G.R. and McEwan, A.G. Molecular analysis of dimethyl sulphide dehydrogenase from Rhodovulum sulfidophilum: its place in the dimethyl sulphoxide reductase family of microbial molybdopterin-containing enzymes. Mol. Microbiol. 44 (2002) 1575–1587. [DOI] [PMID: 12067345]
[EC 1.8.2.4 created 2011]
 
 
EC 1.8.5.3     
Accepted name: respiratory dimethylsulfoxide reductase
Reaction: dimethylsulfide + menaquinone + H2O = dimethylsulfoxide + menaquinol
For diagram of dimethyl sulfide catabolism, click here
Other name(s): dmsABC (gene names); DMSO reductase (ambiguous); dimethylsulfoxide reductase (ambiguous)
Systematic name: dimethyl sulfide:menaquinone oxidoreductase
Comments: The enzyme participates in bacterial electron transfer pathways in which dimethylsulfoxide (DMSO) is the terminal electron acceptor. It is composed of three subunits - DmsA contains a bis(guanylyl molybdopterin) cofactor and a [4Fe-4S] cluster, DmsB is an iron-sulfur protein, and DmsC is a transmembrane protein that anchors the enzyme and accepts electrons from the quinol pool. The electrons are passed through DmsB to DmsA and on to DMSO. The enzyme can also reduce pyridine-N-oxide and trimethylamine N-oxide to the corresponding amines with lower activity.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Daruwala, R. and Meganathan, R. Dimethyl sulfoxide reductase is not required for trimethylamine N-oxide reduction in Escherichia coli. FEMS Microbiol. Lett. 67 (1991) 255–259. [PMID: 1769531]
2.  Miguel, L. and Meganthan, R. Electron donors and the quinone involved in dimethyl sulfoxide reduction in Escherichia coli. Curr. Microbiol. 22 (1991) 109–115.
3.  Simala-Grant, J.L. and Weiner, J.H. Kinetic analysis and substrate specificity of Escherichia coli dimethyl sulfoxide reductase. Microbiology 142 (1996) 3231–3239. [DOI] [PMID: 8969520]
4.  Rothery, R.A., Trieber, C.A. and Weiner, J.H. Interactions between the molybdenum cofactor and iron-sulfur clusters of Escherichia coli dimethylsulfoxide reductase. J. Biol. Chem. 274 (1999) 13002–13009. [DOI] [PMID: 10224050]
[EC 1.8.5.3 created 2011, modified 2019]
 
 
EC 1.8.5.5     
Accepted name: thiosulfate reductase (quinone)
Reaction: sulfite + hydrogen sulfide + a quinone = thiosulfate + a quinol
Other name(s): phsABC (gene names)
Systematic name: sulfite,hydrogen sulfide:quinone oxidoreductase
Comments: The enzyme, characterized from the bacterium Salmonella enterica, is similar to EC 1.17.5.3, formate dehydrogenase-N. It contains a molybdopterin-guanine dinucleotide, five [4Fe-4S] clusters and two heme b groups. The reaction occurs in vivo in the direction of thiosulfate disproportionation, which is highly endergonic. It is driven by the proton motive force that occurs across the cytoplasmic membrane.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kwan, H.S. and Barrett, E.L. Map locations and functions of Salmonella typhimurium men genes. J. Bacteriol. 159 (1984) 1090–1092. [PMID: 6384182]
2.  Clark, M.A. and Barrett, E.L. The phs gene and hydrogen sulfide production by Salmonella typhimurium. J. Bacteriol. 169 (1987) 2391–2397. [DOI] [PMID: 3108233]
3.  Alami, N. and Hallenbeck, P.C. Cloning and characterization of a gene cluster, phsBCDEF, necessary for the production of hydrogen sulfide from thiosulfate by Salmonella typhimurium. Gene 156 (1995) 53–57. [DOI] [PMID: 7737516]
4.  Heinzinger, N.K., Fujimoto, S.Y., Clark, M.A., Moreno, M.S. and Barrett, E.L. Sequence analysis of the phs operon in Salmonella typhimurium and the contribution of thiosulfate reduction to anaerobic energy metabolism. J. Bacteriol. 177 (1995) 2813–2820. [DOI] [PMID: 7751291]
5.  Stoffels, L., Krehenbrink, M., Berks, B.C. and Unden, G. Thiosulfate reduction in Salmonella enterica is driven by the proton motive force. J. Bacteriol. 194 (2012) 475–485. [DOI] [PMID: 22081391]
[EC 1.8.5.5 created 2016, modified 2017]
 
 
EC 1.17.2.1     
Accepted name: nicotinate dehydrogenase (cytochrome)
Reaction: nicotinate + a ferricytochrome + H2O = 6-hydroxynicotinate + a ferrocytochrome + 2 H+
Other name(s): nicotinic acid hydroxylase; nicotinate hydroxylase
Systematic name: nicotinate:cytochrome 6-oxidoreductase (hydroxylating)
Comments: This two-component enzyme from Pseudomonas belongs to the family of xanthine dehydrogenases, but differs from most other members of this family. While most members contain an FAD cofactor, the large subunit of this enzyme contains three c-type cytochromes, enabling it to interact with the electron transfer chain, probably by delivering the electrons to a cytochrome oxidase. The small subunit contains a typical molybdopterin cytosine dinucleotide(MCD) cofactor and two [2Fe-2S] clusters [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Jimenez, J.I., Canales, A., Jimenez-Barbero, J., Ginalski, K., Rychlewski, L., Garcia, J.L. and Diaz, E. Deciphering the genetic determinants for aerobic nicotinic acid degradation: the nic cluster from Pseudomonas putida KT2440. Proc. Natl. Acad. Sci. USA 105 (2008) 11329–11334. [DOI] [PMID: 18678916]
2.  Yang, Y., Yuan, S., Chen, T., Ma, P., Shang, G. and Dai, Y. Cloning, heterologous expression, and functional characterization of the nicotinate dehydrogenase gene from Pseudomonas putida KT2440. Biodegradation 20 (2009) 541–549. [DOI] [PMID: 19118407]
[EC 1.17.2.1 created 2010]
 
 
EC 1.17.5.3     
Accepted name: formate dehydrogenase-N
Reaction: formate + a quinone = CO2 + a quinol
Other name(s): Fdh-N; FdnGHI; nitrate-inducible formate dehydrogenase; formate dehydrogenase N; FDH-N; nitrate inducible Fdn; nitrate inducible formate dehydrogenase
Systematic name: formate:quinone oxidoreductase
Comments: The enzyme contains molybdopterin-guanine dinucleotides, five [4Fe-4S] clusters and two heme b groups. Formate dehydrogenase-N oxidizes formate in the periplasm, transferring electrons via the menaquinone pool in the cytoplasmic membrane to a dissimilatory nitrate reductase (EC 1.7.5.1), which transfers electrons to nitrate in the cytoplasm. The system generates proton motive force under anaerobic conditions [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Enoch, H.G. and Lester, R.L. The purification and properties of formate dehydrogenase and nitrate reductase from Escherichia coli. J. Biol. Chem. 250 (1975) 6693–6705. [PMID: 1099093]
2.  Jormakka, M., Tornroth, S., Byrne, B. and Iwata, S. Molecular basis of proton motive force generation: structure of formate dehydrogenase-N. Science 295 (2002) 1863–1868. [DOI] [PMID: 11884747]
3.  Jormakka, M., Tornroth, S., Abramson, J., Byrne, B. and Iwata, S. Purification and crystallization of the respiratory complex formate dehydrogenase-N from Escherichia coli. Acta Crystallogr. D Biol. Crystallogr. 58 (2002) 160–162. [PMID: 11752799]
[EC 1.17.5.3 created 2010 as EC 1.1.5.6, transferred 2017 to EC 1.17.5.3]
 
 
EC 1.17.99.2     
Accepted name: ethylbenzene hydroxylase
Reaction: ethylbenzene + H2O + acceptor = (S)-1-phenylethanol + reduced acceptor
For diagram of reaction, click here
Other name(s): ethylbenzene dehydrogenase; ethylbenzene:(acceptor) oxidoreductase
Systematic name: ethylbenzene:acceptor oxidoreductase
Comments: Involved in the anaerobic catabolism of ethylbenzene by denitrifying bacteria. Ethylbenzene is the preferred substrate; the enzyme from some strains oxidizes propylbenzene, 1-ethyl-4-fluorobenzene, 3-methylpent-2-ene and ethylidenecyclohexane. Toluene is not oxidized. p-Benzoquinone or ferrocenium can act as electron acceptor. Contains molybdopterin, [4Fe-4S] clusters and heme b.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, UM-BBD, CAS registry number: 372947-56-3
References:
1.  Kniemeyer, O. and Heider, J. Ethylbenzene dehydrogenase, a novel hydrocarbon-oxidising molybdenum/iron-sulfur/heme enzyme. J. Biol. Chem. 276 (2001) 21381–21386. [DOI] [PMID: 11294876]
2.  Johnson, H.A., Pelletier, D.A. and Spormann, A.M. Isolation and characterisation of anaerobic ethylbenzene dehydrogenase, a novel Mo-Fe-S enzyme. J. Bacteriol. 183 (2001) 4536–4542. [DOI] [PMID: 11443088]
[EC 1.17.99.2 created 2001]
 
 
EC 1.17.99.7     
Accepted name: formate dehydrogenase (acceptor)
Reaction: formate + acceptor = CO2 + reduced acceptor
Other name(s): FDHH; FDH-H; FDH-O; formate dehydrogenase H; formate dehydrogenase O
Systematic name: formate:acceptor oxidoreductase
Comments: Formate dehydrogenase H is a cytoplasmic enzyme that oxidizes formate without oxygen transfer, transferring electrons to a hydrogenase. The two enzymes form the formate-hydrogen lyase complex [1]. The enzyme contains an [4Fe-4S] cluster, a selenocysteine residue and a molybdopterin cofactor [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Axley, M.J., Grahame, D.A. and Stadtman, T.C. Escherichia coli formate-hydrogen lyase. Purification and properties of the selenium-dependent formate dehydrogenase component. J. Biol. Chem. 265 (1990) 18213–18218. [PMID: 2211698]
2.  Gladyshev, V.N., Boyington, J.C., Khangulov, S.V., Grahame, D.A., Stadtman, T.C. and Sun, P.D. Characterization of crystalline formate dehydrogenase H from Escherichia coli. Stabilization, EPR spectroscopy, and preliminary crystallographic analysis. J. Biol. Chem. 271 (1996) 8095–8100. [DOI] [PMID: 8626495]
3.  Khangulov, S.V., Gladyshev, V.N., Dismukes, G.C. and Stadtman, T.C. Selenium-containing formate dehydrogenase H from Escherichia coli: a molybdopterin enzyme that catalyzes formate oxidation without oxygen transfer. Biochemistry 37 (1998) 3518–3528. [DOI] [PMID: 9521673]
[EC 1.17.99.7 created 2010 as EC 1.1.99.33, transferred 2017 to EC 1.17.99.7]
 
 
EC 1.20.9.1     
Accepted name: arsenate reductase (azurin)
Reaction: arsenite + H2O + 2 oxidized azurin = arsenate + 2 reduced azurin + 2 H+
For diagram of arsenate catabolism, click here
Glossary: Azurin is a blue copper protein found in many bacteria, which undergoes oxidation-reduction between Cu(I) and Cu(II), and transfers single electrons between enzymes.
Other name(s): arsenite oxidase (ambiguous)
Systematic name: arsenite:azurin oxidoreductase
Comments: Contains a molybdopterin centre comprising two molybdopterin guanosine dinucleotide cofactors bound to molybdenum, a [3Fe-4S] cluster and a Rieske-type [2Fe-2S] cluster. Isolated from β-proteobacteria. Also uses a c-type cytochrome or O2 as acceptors.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, UM-BBD, CAS registry number: 146907-46-2
References:
1.  Anderson, G.L., Williams, J. and Hille, R. The purification and characterization of arsenite oxidase from Alcaligenes faecalis, a molybdenum-containing hydroxylase. J. Biol. Chem. 267 (1992) 23674–23682. [PMID: 1331097]
2.  Ellis, P.J., Conrads, T., Hille, R. and Kuhn, P. Crystal structure of the 100 kDa arsenite oxidase from Alcaligenes faecalis in two crystal forms at 1.64 Å and 2.03 Å. Structure 9 (2001) 125–132. [DOI] [PMID: 11250197]
[EC 1.20.9.1 created 2001 as EC 1.20.98.1, transferred 2011 to EC 1.20.9.1]
 
 
EC 1.20.98.1      
Transferred entry: arsenate reductase (azurin). Now EC 1.20.9.1, arsenate reductase (azurin)
[EC 1.20.98.1 created 2001, deleted 2011]
 
 
EC 2.7.1.164     
Accepted name: O-phosphoseryl-tRNASec kinase
Reaction: ATP + L-seryl-tRNASec = ADP + O-phospho-L-seryl-tRNASec
Other name(s): PSTK; phosphoseryl-tRNA[Ser]Sec kinase; phosphoseryl-tRNASec kinase
Systematic name: ATP:L-seryl-tRNASec O-phosphotransferase
Comments: In archaea and eukarya selenocysteine formation is achieved by a two-step process: O-phosphoseryl-tRNASec kinase (PSTK) phosphorylates the endogenous L-seryl-tRNASec to O-phospho-L-seryl-tRNASec, and then this misacylated amino acid-tRNA species is converted to L-selenocysteinyl-tRNASec by EC 2.9.1.2 (Sep-tRNA:Sec-tRNA synthase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 91273-83-5
References:
1.  Carlson, B.A., Xu, X.M., Kryukov, G.V., Rao, M., Berry, M.J., Gladyshev, V.N. and Hatfield, D.L. Identification and characterization of phosphoseryl-tRNA[Ser]Sec kinase. Proc. Natl. Acad. Sci. USA 101 (2004) 12848–12853. [DOI] [PMID: 15317934]
2.  Sherrer, R.L., O'Donoghue, P. and Soll, D. Characterization and evolutionary history of an archaeal kinase involved in selenocysteinyl-tRNA formation. Nucleic Acids Res. 36 (2008) 1247–1259. [DOI] [PMID: 18174226]
3.  Khangulov, S.V., Gladyshev, V.N., Dismukes, G.C. and Stadtman, T.C. Selenium-containing formate dehydrogenase H from Escherichia coli: a molybdopterin enzyme that catalyzes formate oxidation without oxygen transfer. Biochemistry 37 (1998) 3518–3528. [DOI] [PMID: 9521673]
[EC 2.7.1.164 created 2009]
 
 
EC 2.7.7.75     
Accepted name: molybdopterin adenylyltransferase
Reaction: ATP + molybdopterin = diphosphate + adenylyl-molybdopterin
For diagram of MoCo biosynthesis, click here
Glossary: molybdopterin = H2Dtpp-mP = ((5aR,8R,9aR)-2-amino-6,7-dimercapto-4-oxo-4,5,5a,8,9a,10-hexahydro-1H-pyrano[3,2-g]pteridin-8-yl)methyl dihydrogen phosphate = [(5aR,8R,9aR)-2-amino-4-oxo-6,7-disulfanyl-1,5,5a,8,9a,10-hexahydro-4H-pyrano[3,2-g]pteridin-8-yl]methyl dihydrogen phosphate
Other name(s): MogA; Cnx1 (ambiguous)
Systematic name: ATP:molybdopterin adenylyltransferase
Comments: Catalyses the activation of molybdopterin for molybdenum insertion. In eukaryotes, this reaction is catalysed by the C-terminal domain of a fusion protein that also includes molybdopterin molybdotransferase (EC 2.10.1.1). The reaction requires a divalent cation such as Mg2+ or Mn2+.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Nichols, J.D. and Rajagopalan, K.V. In vitro molybdenum ligation to molybdopterin using purified components. J. Biol. Chem. 280 (2005) 7817–7822. [DOI] [PMID: 15632135]
2.  Kuper, J., Palmer, T., Mendel, R.R. and Schwarz, G. Mutations in the molybdenum cofactor biosynthetic protein Cnx1G from Arabidopsis thaliana define functions for molybdopterin binding, molybdenum insertion, and molybdenum cofactor stabilization. Proc. Natl. Acad. Sci. USA 97 (2000) 6475–6480. [DOI] [PMID: 10823911]
3.  Llamas, A., Mendel, R.R. and Schwarz, G. Synthesis of adenylated molybdopterin: an essential step for molybdenum insertion. J. Biol. Chem. 279 (2004) 55241–55246. [DOI] [PMID: 15504727]
[EC 2.7.7.75 created 2011]
 
 
EC 2.7.7.76     
Accepted name: molybdenum cofactor cytidylyltransferase
Reaction: CTP + molybdenum cofactor = diphosphate + cytidylyl molybdenum cofactor
For diagram of MoCo biosynthesis, click here
Glossary: molybdenum cofactor = MoCo = MoO2(OH)Dtpp-mP = {[(5aR,8R,9aR)-2-amino-4-oxo-6,7-di(sulfanyl-κS)-1,5,5a,8,9a,10-hexahydro-4H-pyrano[3,2-g]pteridin-8-yl]methyl dihydrogenato(2-) phosphate}(dioxo)molybdate
Other name(s): MocA; CTP:molybdopterin cytidylyltransferase; MoCo cytidylyltransferase; Mo-MPT cytidyltransferase
Systematic name: CTP:molybdenum cofactor cytidylyltransferase
Comments: Catalyses the cytidylation of the molybdenum cofactor. This modification occurs only in prokaryotes. Divalent cations such as Mg2+ or Mn2+ are required for activity. ATP or GTP cannot replace CTP.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Neumann, M., Mittelstadt, G., Seduk, F., Iobbi-Nivol, C. and Leimkuhler, S. MocA is a specific cytidylyltransferase involved in molybdopterin cytosine dinucleotide biosynthesis in Escherichia coli. J. Biol. Chem. 284 (2009) 21891–21898. [DOI] [PMID: 19542235]
2.  Neumann, M., Seduk, F., Iobbi-Nivol, C. and Leimkuhler, S. Molybdopterin dinucleotide biosynthesis in Escherichia coli: Identification of amino acid residues of molybdopterin dinucleotide transferases that determine specificity for binding of guanine or cytosine nucleotides. J. Biol. Chem. 286 (2011) 1400–1408. [DOI] [PMID: 21081498]
[EC 2.7.7.76 created 2011]
 
 
EC 2.7.7.77     
Accepted name: molybdenum cofactor guanylyltransferase
Reaction: GTP + molybdenum cofactor = diphosphate + guanylyl molybdenum cofactor
For diagram of MoCo biosynthesis, click here
Glossary: molybdenum cofactor = MoCo = MoO2(OH)Dtpp-mP = {[(5aR,8R,9aR)-2-amino-4-oxo-6,7-di(sulfanyl-κS)-1,5,5a,8,9a,10-hexahydro-4H-pyrano[3,2-g]pteridin-8-yl]methyl dihydrogenato(2-) phosphate}(dioxo)molybdate
Other name(s): MobA; MoCo guanylyltransferase
Systematic name: GTP:molybdenum cofactor guanylyltransferase
Comments: Catalyses the guanylation of the molybdenum cofactor. This modification occurs only in prokaryotes.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Lake, M.W., Temple, C.A., Rajagopalan, K.V. and Schindelin, H. The crystal structure of the Escherichia coli MobA protein provides insight into molybdopterin guanine dinucleotide biosynthesis. J. Biol. Chem. 275 (2000) 40211–40217. [DOI] [PMID: 10978347]
2.  Temple, C.A. and Rajagopalan, K.V. Mechanism of assembly of the bis(molybdopterin guanine dinucleotide)molybdenum cofactor in Rhodobacter sphaeroides dimethyl sulfoxide reductase. J. Biol. Chem. 275 (2000) 40202–40210. [DOI] [PMID: 10978348]
3.  Guse, A., Stevenson, C.E., Kuper, J., Buchanan, G., Schwarz, G., Giordano, G., Magalon, A., Mendel, R.R., Lawson, D.M. and Palmer, T. Biochemical and structural analysis of the molybdenum cofactor biosynthesis protein MobA. J. Biol. Chem. 278 (2003) 25302–25307. [DOI] [PMID: 12719427]
[EC 2.7.7.77 created 2011]
 
 
EC 2.7.7.80     
Accepted name: molybdopterin-synthase adenylyltransferase
Reaction: ATP + [molybdopterin-synthase sulfur-carrier protein]-Gly-Gly = diphosphate + [molybdopterin-synthase sulfur-carrier protein]-Gly-Gly-AMP
For diagram of MoCo biosynthesis, click here
Glossary: small subunit of the molybdopterin synthase = molybdopterin-synthase sulfur-carrier protein = MoaD
Other name(s): MoeB; adenylyltransferase and sulfurtransferase MOCS3
Systematic name: ATP:molybdopterin-synthase adenylyltransferase
Comments: Adenylates the C-terminus of the small subunit of the molybdopterin synthase. This activation is required to form the thiocarboxylated C-terminus of the active molybdopterin synthase small subunit. The reaction occurs in prokaryotes and eukaryotes. In the human, the reaction is catalysed by the N-terminal domain of the protein MOCS3, which also includes a molybdopterin-synthase sulfurtransferase (EC 2.8.1.11) C-terminal domain.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Leimkuhler, S., Wuebbens, M.M. and Rajagopalan, K.V. Characterization of Escherichia coli MoeB and its involvement in the activation of molybdopterin synthase for the biosynthesis of the molybdenum cofactor. J. Biol. Chem. 276 (2001) 34695–34701. [DOI] [PMID: 11463785]
2.  Matthies, A., Nimtz, M. and Leimkuhler, S. Molybdenum cofactor biosynthesis in humans: identification of a persulfide group in the rhodanese-like domain of MOCS3 by mass spectrometry. Biochemistry 44 (2005) 7912–7920. [DOI] [PMID: 15910006]
[EC 2.7.7.80 created 2011]
 
 
EC 2.7.7.100     
Accepted name: SAMP-activating enzyme
Reaction: ATP + [SAMP]-Gly-Gly = diphosphate + [SAMP]-Gly-Gly-AMP
Glossary: SAMP = small archaeal modifier protein = ubiquitin-like small archaeal modifier protein
Other name(s): UbaA (ambiguous); SAMP-activating enzyme E1 (ambiguous)
Systematic name: ATP:[SAMP]-Gly-Gly adenylyltransferase
Comments: Contains Zn2+. The enzyme catalyses the activation of SAMPs (Small Archaeal Modifier Proteins), which are ubiquitin-like proteins found only in the Archaea, by catalysing the ATP-dependent formation of a SAMP adenylate in which the C-terminal glycine of SAMP is bound to AMP via an acyl-phosphate linkage. The product of this activity can accept a sulfur atom to form a thiocarboxylate moiety that acts as a sulfur carrier involved in thiolation of tRNA and other metabolites such as molybdopterin. Alternatively, the enzyme can also catalyse the transfer of SAMP from its activated form to an internal cysteine residue, leading to a process termed SAMPylation (see EC 6.2.1.55, E1 SAMP-activating enzyme).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Miranda, H.V., Nembhard, N., Su, D., Hepowit, N., Krause, D.J., Pritz, J.R., Phillips, C., Soll, D. and Maupin-Furlow, J.A. E1- and ubiquitin-like proteins provide a direct link between protein conjugation and sulfur transfer in archaea. Proc. Natl. Acad. Sci. USA 108 (2011) 4417–4422. [DOI] [PMID: 21368171]
2.  Maupin-Furlow, J.A. Ubiquitin-like proteins and their roles in archaea. Trends Microbiol. 21 (2013) 31–38. [DOI] [PMID: 23140889]
3.  Hepowit, N.L., de Vera, I.M., Cao, S., Fu, X., Wu, Y., Uthandi, S., Chavarria, N.E., Englert, M., Su, D., Söll, D., Kojetin, D.J. and Maupin-Furlow, J.A. Mechanistic insight into protein modification and sulfur mobilization activities of noncanonical E1 and associated ubiquitin-like proteins of Archaea. FEBS J. 283 (2016) 3567–3586. [DOI] [PMID: 27459543]
[EC 2.7.7.100 created 2018]
 
 
EC 2.8.1.7     
Accepted name: cysteine desulfurase
Reaction: L-cysteine + acceptor = L-alanine + S-sulfanyl-acceptor (overall reaction)
(1a) L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine
(1b) [enzyme]-S-sulfanylcysteine + acceptor = [enzyme]-cysteine + S-sulfanyl-acceptor
For diagram of moco biosynthesis, click here
Other name(s): IscS; NIFS; NifS; SufS; cysteine desulfurylase
Systematic name: L-cysteine:acceptor sulfurtransferase
Comments: A pyridoxal-phosphate protein. The sulfur from free L-cysteine is first transferred to a cysteine residue in the active site, and then passed on to various other acceptors. The enzyme is involved in the biosynthesis of iron-sulfur clusters, thio-nucleosides in tRNA, thiamine, biotin, lipoate and pyranopterin (molybdopterin) [2]. In Azotobacter vinelandii, this sulfur provides the inorganic sulfide required for nitrogenous metallocluster formation [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 149371-08-4
References:
1.  Zheng, L.M., White, R.H., Cash, V.L., Jack, R.F. and Dean, D.R. Cysteine desulfurase activity indicates a role for NIFS in metallocluster biosynthesis. Proc. Natl. Acad. Sci. USA 90 (1993) 2754–2758. [DOI] [PMID: 8464885]
2.  Mihara, H. and Esaki, N. Bacterial cysteine desulfurases: Their function and mechanisms. Appl. Microbiol. Biotechnol. 60 (2002) 12–23. [DOI] [PMID: 12382038]
3.  Frazzon, J. and Dean, D.R. Formation of iron-sulfur clusters in bacteria: An emerging field in bioinorganic chemistry. Curr. Opin. Chem. Biol. 7 (2003) 166–173. [DOI] [PMID: 12714048]
[EC 2.8.1.7 created 2003, modified 2011]
 
 
EC 2.8.1.11     
Accepted name: molybdopterin synthase sulfurtransferase
Reaction: [molybdopterin-synthase sulfur-carrier protein]-Gly-Gly-AMP + [cysteine desulfurase]-S-sulfanyl-L-cysteine + reduced acceptor = AMP + [molybdopterin-synthase sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + [cysteine desulfurase]-L-cysteine + oxidized acceptor
For diagram of MoCo biosynthesis, click here
Other name(s): adenylyltransferase and sulfurtransferase MOCS3; Cnx5 (gene name); molybdopterin synthase sulfurylase
Systematic name: [cysteine desulfurase]-S-sulfanyl-L-cysteine:[molybdopterin-synthase sulfur-carrier protein]-Gly-Gly sulfurtransferase
Comments: The enzyme transfers sulfur to form a thiocarboxylate moiety on the C-terminal glycine of the small subunit of EC 2.8.1.12, molybdopterin synthase. In the human, the reaction is catalysed by the rhodanese-like C-terminal domain (cf. EC 2.8.1.1) of the MOCS3 protein, a bifunctional protein that also contains EC 2.7.7.80, molybdopterin-synthase adenylyltransferase, at the N-terminal domain.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Matthies, A., Nimtz, M. and Leimkuhler, S. Molybdenum cofactor biosynthesis in humans: identification of a persulfide group in the rhodanese-like domain of MOCS3 by mass spectrometry. Biochemistry 44 (2005) 7912–7920. [DOI] [PMID: 15910006]
2.  Leimkuhler, S. and Rajagopalan, K.V. A sulfurtransferase is required in the transfer of cysteine sulfur in the in vitro synthesis of molybdopterin from precursor Z in Escherichia coli. J. Biol. Chem. 276 (2001) 22024–22031. [DOI] [PMID: 11290749]
3.  Hanzelmann, P., Dahl, J.U., Kuper, J., Urban, A., Muller-Theissen, U., Leimkuhler, S. and Schindelin, H. Crystal structure of YnjE from Escherichia coli, a sulfurtransferase with three rhodanese domains. Protein Sci. 18 (2009) 2480–2491. [DOI] [PMID: 19798741]
4.  Dahl, J.U., Urban, A., Bolte, A., Sriyabhaya, P., Donahue, J.L., Nimtz, M., Larson, T.J. and Leimkuhler, S. The identification of a novel protein involved in molybdenum cofactor biosynthesis in Escherichia coli. J. Biol. Chem. 286 (2011) 35801–35812. [DOI] [PMID: 21856748]
[EC 2.8.1.11 created 2011, modified 2016]
 
 
EC 2.8.1.12     
Accepted name: molybdopterin synthase
Reaction: cyclic pyranopterin phosphate + 2 [molybdopterin-synthase sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + H2O = molybdopterin + 2 molybdopterin-synthase sulfur-carrier protein
For diagram of MoCo biosynthesis, click here
Glossary: molybdopterin = H2Dtpp-mP = {[(5aR,8R,9aR)-2-amino-4-oxo-6,7-di(sulfanyl-κS)-1,5,5a,8,9a,10-hexahydro-4H-pyrano[3,2-g]pteridin-8-yl]methyl dihydrogenato(2-) phosphate}(dioxo)molybdate(2-)
cyclic pyranopterin phosphate = cPMP = precursor Z = 8-amino-2,12,12-trihydroxy-4a,5a,6,9,11,11a,12,12a-octahydro[1,3,2]dioxaphosphinino[4′,5′:5,6]pyrano[3,2-g]pteridin-10(4H)-one 2-oxide = 8-amino-2,12,12-trihydroxy-4,4a,5a,6,9,10,11,11a,12,12a-decahydro-[1,3,2]dioxaphosphinino[4′,5′:5,6]pyrano[3,2-g]pteridine 2-oxide
Other name(s): MPT synthase
Systematic name: thiocarboxylated molybdopterin synthase:cyclic pyranopterin phosphate sulfurtransferase
Comments: Catalyses the synthesis of molybdopterin from cyclic pyranopterin monophosphate. Two sulfur atoms are transferred to cyclic pyranopterin monophosphate in order to form the characteristic ene-dithiol group found in the molybdenum cofactor. Molybdopterin synthase consists of two large subunits forming a central dimer and two small subunits (molybdopterin-synthase sulfur-carrier proteins) that are thiocarboxylated at the C-terminus by EC 2.8.1.11, molybdopterin synthase sulfurtransferase. The reaction occurs in prokaryotes and eukaryotes.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Daniels, J.N., Wuebbens, M.M., Rajagopalan, K.V. and Schindelin, H. Crystal structure of a molybdopterin synthase-precursor Z complex: insight into its sulfur transfer mechanism and its role in molybdenum cofactor deficiency. Biochemistry 47 (2008) 615–626. [DOI] [PMID: 18092812]
2.  Wuebbens, M.M. and Rajagopalan, K.V. Mechanistic and mutational studies of Escherichia coli molybdopterin synthase clarify the final step of molybdopterin biosynthesis. J. Biol. Chem. 278 (2003) 14523–14532. [DOI] [PMID: 12571226]
[EC 2.8.1.12 created 2011]
 
 
EC 2.10.1.1     
Accepted name: molybdopterin molybdotransferase
Reaction: adenylyl-molybdopterin + molybdate = molybdenum cofactor + AMP + H2O
For diagram of MoCo biosynthesis, click here
Glossary: molybdopterin = H2Dtpp-mP = ((5aR,8R,9aR)-2-amino-6,7-dimercapto-4-oxo-4,5,5a,8,9a,10-hexahydro-1H-pyrano[3,2-g]pteridin-8-yl)methyl dihydrogen phosphate = [(5aR,8R,9aR)-2-amino-4-oxo-6,7-disulfanyl-1,5,5a,8,9a,10-hexahydro-4H-pyrano[3,2-g]pteridin-8-yl]methyl dihydrogen phosphate
molybdate = tetraoxidomolybdate(2-) = MoO42-
molybdenum cofactor = MoCo = MoO2(OH)Dtpp-mP = {[(5aR,8R,9aR)-2-amino-4-oxo-6,7-di(sulfanyl-κS)-1,5,5a,8,9a,10-hexahydro-4H-pyrano[3,2-g]pteridin-8-yl]methyl dihydrogenato(2-) phosphate}(dioxo)molybdate
Other name(s): MoeA; Cnx1 (ambiguous)
Systematic name: adenylyl-molybdopterin:molybdate molybdate transferase (AMP-forming)
Comments: Catalyses the insertion of molybdenum into the ene-dithiol group of molybdopterin. In eukaryotes this reaction is catalysed by the N-terminal domain of a fusion protein whose C-terminal domain catalyses EC 2.7.7.75, molybdopterin adenylyltransferase. Requires divalent cations such as Mg2+ or Zn2+ for activity.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Nichols, J.D. and Rajagopalan, K.V. In vitro molybdenum ligation to molybdopterin using purified components. J. Biol. Chem. 280 (2005) 7817–7822. [DOI] [PMID: 15632135]
2.  Nichols, J.D., Xiang, S., Schindelin, H. and Rajagopalan, K.V. Mutational analysis of Escherichia coli MoeA: two functional activities map to the active site cleft. Biochemistry 46 (2007) 78–86. [DOI] [PMID: 17198377]
3.  Llamas, A., Otte, T., Multhaup, G., Mendel, R.R. and Schwarz, G. The Mechanism of nucleotide-assisted molybdenum insertion into molybdopterin. A novel route toward metal cofactor assembly. J. Biol. Chem. 281 (2006) 18343–18350. [DOI] [PMID: 16636046]
[EC 2.10.1.1 created 2011]
 
 
EC 4.1.99.18      
Transferred entry: cyclic pyranopterin phosphate synthase. Now known to be catalysed by the combined effort of EC 4.1.99.22, GTP 3,8-cyclase, and EC 4.6.1.17, cyclic pyranopterin monophosphate synthase
[EC 4.1.99.18 created 2011, deleted 2016]
 
 
EC 4.2.1.112     
Accepted name: acetylene hydratase
Reaction: acetaldehyde = acetylene + H2O
Other name(s): AH; acetaldehyde hydro-lyase
Systematic name: acetaldehyde hydro-lyase (acetylene-forming)
Comments: This is a non-redox-active enzyme that contains two molybdopterin guanine dinucleotide (MGD) cofactors, a tungsten centre and a cubane type [4Fe-4S] cluster [2].The tungsten centre binds a water molecule that is activated by an adjacent aspartate residue, enabling it to attack acetylene bound in a distinct hydrophobic pocket [2]. Ethylene cannot act as a substrate [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, UM-BBD, CAS registry number: 75788-81-7
References:
1.  Rosner, B.M. and Schink, B. Purification and characterization of acetylene hydratase of Pelobacter acetylenicus, a tungsten iron-sulfur protein. J. Bacteriol. 177 (1995) 5767–5772. [DOI] [PMID: 7592321]
2.  Seiffert, G.B., Ullmann, G.M., Messerschmidt, A., Schink, B., Kroneck, P.M. and Einsle, O. Structure of the non-redox-active tungsten/[4Fe:4S] enzyme acetylene hydratase. Proc. Natl. Acad. Sci. USA 104 (2007) 3073–3077. [DOI] [PMID: 17360611]
[EC 4.2.1.112 created 2007]
 
 
EC 4.6.1.17     
Accepted name: cyclic pyranopterin monophosphate synthase
Reaction: (8S)-3′,8-cyclo-7,8-dihydroguanosine 5′-triphosphate = cyclic pyranopterin phosphate + diphosphate
Other name(s): MOCS1B (gene name); moaC (gene name); cnx3 (gene name)
Systematic name: (8S)-3′,8-cyclo-7,8-dihydroguanosine 5′-triphosphate lyase (cyclic pyranopterin phosphate-forming)
Comments: The enzyme catalyses an early step in the biosynthesis of the molybdenum cofactor (MoCo). In bacteria and plants the reaction is catalysed by MoaC and Cnx3, respectively. In mammals the reaction is catalysed by the MOCS1B domain of the bifuctional MOCS1 protein, which also catalyses EC 4.1.99.22, GTP 3′,8-cyclase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Rieder, C., Eisenreich, W., O'Brien, J., Richter, G., Götze, E., Boyle, P., Blanchard, S., Bacher, A. and Simon, H. Rearrangement reactions in the biosynthesis of molybdopterin - an NMR study with multiply 13C/15N labelled precursors. Eur. J. Biochem. 255 (1998) 24–36. [DOI] [PMID: 9692897]
2.  Wuebbens, M.M. and Rajagopalan, K.V. Investigation of the early steps of molybdopterin biosynthesis in Escherichia coli through the use of in vivo labeling studies. J. Biol. Chem. 270 (1995) 1082–1087. [DOI] [PMID: 7836363]
3.  Hover, B.M., Tonthat, N.K., Schumacher, M.A. and Yokoyama, K. Mechanism of pyranopterin ring formation in molybdenum cofactor biosynthesis. Proc. Natl. Acad. Sci. USA 112 (2015) 6347–6352. [DOI] [PMID: 25941396]
[EC 4.6.1.17 created 2011 as EC 4.1.99.18, part transferred 2016 to EC 4.6.1.17]
 
 
EC 6.2.1.55     
Accepted name: E1 SAMP-activating enzyme
Reaction: ATP + [SAMP]-Gly-Gly + [E1 SAMP-activating enzyme]-L-cysteine = S-[[SAMP]-Gly-Gly]-[[E1 SAMP-activating enzyme]-L-cysteine] + AMP + diphosphate (overall reaction)
(1a) ATP + [SAMP]-Gly-Gly = diphosphate + [SAMP]-Gly-Gly-AMP
(1b) [SAMP]-Gly-Gly-AMP + [E1 SAMP-activating enzyme]-L-cysteine = S-[[SAMP]-Gly-Gly]-[[E1 SAMP-activating enzyme]-L-cysteine] + AMP
Glossary: SAMP = small archaeal modifier protein = ubiquitin-like small archaeal modifier protein
Other name(s): UbaA; SAMP-activating enzyme E1
Systematic name: [SAMP]:[E1 SAMP-activating enzyme] ligase (AMP-forming)
Comments: Contains Zn2+. The enzyme catalyses the activation of SAMPs (Small Archaeal Modifier Proteins), which are ubiquitin-like proteins found only in the Archaea. SAMPs are involved in protein degradation, and also act as sulfur carriers involved in thiolation of tRNA and other metabolites such as molybdopterin. The enzyme catalyses the ATP-dependent formation of a SAMP adenylate intermediate in which the C-terminal glycine of SAMP is bound to AMP via an acyl-phosphate linkage (reaction 1). This intermediate can accept a sulfur atom to form a thiocarboxylate moiety in a mechanism that is not yet understood. Alternatively, the E1 enzyme can transfer SAMP from its activated form to an internal cysteine residue, releasing AMP (reaction 2). In this case SAMP is subsequently transferred to a lysine residue in a target protein in a process termed SAMPylation. Auto-SAMPylation (attachment of SAMP to lysine residues within the E1 enzyme) has been observed. cf. EC 2.7.7.100, SAMP-activating enzyme.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Miranda, H.V., Nembhard, N., Su, D., Hepowit, N., Krause, D.J., Pritz, J.R., Phillips, C., Soll, D. and Maupin-Furlow, J.A. E1- and ubiquitin-like proteins provide a direct link between protein conjugation and sulfur transfer in archaea. Proc. Natl. Acad. Sci. USA 108 (2011) 4417–4422. [DOI] [PMID: 21368171]
2.  Maupin-Furlow, J.A. Ubiquitin-like proteins and their roles in archaea. Trends Microbiol. 21 (2013) 31–38. [DOI] [PMID: 23140889]
3.  Miranda, H.V., Antelmann, H., Hepowit, N., Chavarria, N.E., Krause, D.J., Pritz, J.R., Basell, K., Becher, D., Humbard, M.A., Brocchieri, L. and Maupin-Furlow, J.A. Archaeal ubiquitin-like SAMP3 is isopeptide-linked to proteins via a UbaA-dependent mechanism. Mol. Cell. Proteomics 13 (2014) 220–239. [DOI] [PMID: 24097257]
4.  Hepowit, N.L., de Vera, I.M., Cao, S., Fu, X., Wu, Y., Uthandi, S., Chavarria, N.E., Englert, M., Su, D., Söll, D., Kojetin, D.J. and Maupin-Furlow, J.A. Mechanistic insight into protein modification and sulfur mobilization activities of noncanonical E1 and associated ubiquitin-like proteins of Archaea. FEBS J. 283 (2016) 3567–3586. [DOI] [PMID: 27459543]
[EC 6.2.1.55 created 2018]
 
 


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