The Enzyme Database

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EC 1.7.1.14     
Accepted name: nitric oxide reductase [NAD(P)+, nitrous oxide-forming]
Reaction: N2O + NAD(P)+ + H2O = 2 NO + NAD(P)H + H+
Other name(s): fungal nitric oxide reductase; cytochrome P450nor; NOR (ambiguous)
Systematic name: nitrous oxide:NAD(P) oxidoreductase
Comments: A heme-thiolate protein (P-450). The enzyme from Fusarium oxysporum utilizes only NADH, but the isozyme from Trichosporon cutaneum utilizes both NADH and NADPH. The electron transfer from NAD(P)H to heme occurs directly, not requiring flavin or other redox cofactors.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Shoun, H. and Tanimoto, T. Denitrification by the fungus Fusarium oxysporum and involvement of cytochrome P-450 in the respiratory nitrite reduction. J. Biol. Chem. 266 (1991) 11078–11082. [PMID: 2040619]
2.  Shiro, Y., Fujii, M., Iizuka, T., Adachi, S., Tsukamoto, K., Nakahara, K. and Shoun, H. Spectroscopic and kinetic studies on reaction of cytochrome P450nor with nitric oxide. Implication for its nitric oxide reduction mechanism. J. Biol. Chem. 270 (1995) 1617–1623. [DOI] [PMID: 7829493]
3.  Zhang, L., Kudo, T., Takaya, N. and Shoun, H. The B′ helix determines cytochrome P450nor specificity for the electron donors NADH and NADPH. J. Biol. Chem. 277 (2002) 33842–33847. [DOI] [PMID: 12105197]
4.  Oshima, R., Fushinobu, S., Su, F., Zhang, L., Takaya, N. and Shoun, H. Structural evidence for direct hydride transfer from NADH to cytochrome P450nor. J. Mol. Biol. 342 (2004) 207–217. [DOI] [PMID: 15313618]
[EC 1.7.1.14 created 2011]
 
 
EC 1.7.2.1     
Accepted name: nitrite reductase (NO-forming)
Reaction: nitric oxide + H2O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H+
Glossary: nitric oxide = NO = nitrogen(II) oxide
Other name(s): cd-cytochrome nitrite reductase; [nitrite reductase (cytochrome)] [misleading, see comments.]; cytochrome c-551:O2, NO2+ oxidoreductase; cytochrome cd; cytochrome cd1; hydroxylamine (acceptor) reductase; methyl viologen-nitrite reductase; nitrite reductase (cytochrome; NO-forming)
Systematic name: nitric-oxide:ferricytochrome-c oxidoreductase
Comments: The reaction is catalysed by two types of enzymes, found in the perimplasm of denitrifying bacteria. One type comprises proteins containing multiple copper centres, the other a heme protein, cytochrome cd1. Acceptors include c-type cytochromes such as cytochrome c-550 or cytochrome c-551 from Paracoccus denitrificans or Pseudomonas aeruginosa, and small blue copper proteins such as azurin and pseudoazurin. Cytochrome cd1 also has oxidase and hydroxylamine reductase activities. May also catalyse the reaction of hydroxylamine reductase (EC 1.7.99.1) since this is a well-known activity of cytochrome cd1.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, UM-BBD, CAS registry number: 9080-03-9
References:
1.  Miyata, M. and Mori, T. Studies on denitrification. X. The "denitrifying enzyme" as a nitrite reductase and the electron donating system for denitrification. J. Biochem. (Tokyo) 66 (1969) 463–471. [PMID: 5354021]
2.  Chung, C.W. and Najjar, V.A. Cofactor requirements for enzymatic denitrification. I. Nitrite reductase. J. Biol. Chem. 218 (1956) 617–625. [PMID: 13295215]
3.  Walker, G.C. and Nicholas, D.J.D. Nitrite reductase from Pseudomonas aeruginosa. Biochim. Biophys. Acta 49 (1961) 350–360. [DOI] [PMID: 13782716]
4.  Singh, J. Cytochrome oxidase from Pseudomonas aeruginosa. III. Reduction of hydroxylamine. Biochim. Biophys. Acta 333 (1974) 28–36. [PMID: 19396990]
5.  Michalski, W.P. and Nicholas, D.J.D. Molecular characterization of a copper-containing nitrite reductase from Rhodopseudomonas sphaeriodes forma sp. Denitrificans. Biochim. Biophys. Acta 828 (1985) 130–137.
6.  Godden, J.W., Turley, S., Teller, D.C., Adman, E.T., Liu, M.Y., Payne, W.J. and Legall, J. The 2.3 angstrom X-ray structure of nitrite reductase from Achromobacter cycloclastes. Science 253 (1991) 438–442. [DOI] [PMID: 1862344]
7.  Williams, P.A., Fulop, V., Leung, Y.C., Chan, C., Moir, J.W.B., Howlett, G., Ferguson, S.J., Radford, S.E. and Hajdu, J. Pseudospecific docking surfaces on electron transfer proteins as illustrated by pseudoazurin, cytochrome c-550 and cytochrome cd1 nitrite reductase. Nat. Struct. Biol. 2 (1995) 975–982. [PMID: 7583671]
8.  Hole, U.H., Vollack, K.U., Zumft, W.G., Eisenmann, E., Siddiqui, R.A., Friedrich, B. and Kroneck, P.M.H. Characterization of the membranous denitrification enzymes nitrite reductase (cytochrome cd1) and copper-containing nitrous oxide reductase from Thiobacillus denitrificans. Arch. Microbiol. 165 (1996) 55–61. [PMID: 8639023]
9.  Zumft, W.G. Cell biology and molecular basis of denitrification. Microbiol. Mol. Biol. Rev. 61 (1997) 533–616. [PMID: 9409151]
10.  Ferguson, S.J. Nitrogen cycle enzymology. Curr. Opin. Chem. Biol. 2 (1998) 182–193. [DOI] [PMID: 9667932]
11.  Vijgenboom, E., Busch, J.E. and Canters, G.W. In vitro studies disprove the obligatory role of azurin in denitrification in Pseudomonas aeruginosa and show that azu expression is under the control of RpoS and ANR. Microbiology 143 (1997) 2853–2863. [DOI] [PMID: 9308169]
[EC 1.7.2.1 created 1961, modified 1976, modified 2001, modified 2002 (EC 1.7.99.3 created 1961 as EC 1.6.6.5, transferred 1964 to EC 1.7.99.3, modified 1976, incorporated 2002, EC 1.9.3.2 created 1965, incorporated 2002)]
 
 
EC 1.7.2.2     
Accepted name: nitrite reductase (cytochrome; ammonia-forming)
Reaction: NH3 + 2 H2O + 6 ferricytochrome c = nitrite + 6 ferrocytochrome c + 7 H+
Other name(s): cytochrome c nitrite reductase; multiheme nitrite reductase
Systematic name: ammonia:ferricytochrome-c oxidoreductase
Comments: Found as a multiheme cytochrome in many bacteria. The enzyme from Escherichia coli contains five hemes c and requires Ca2+. It also reduces nitric oxide and hydroxylamine to ammonia, and sulfite to sulfide.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, UM-BBD
References:
1.  Einsle, O., Messerschmidt, A., Stach, P. Bourenkov, G.P., Bartunik, H.D., Huber, R. and Kroneck, P.M.H. Structure of cytochrome c nitrite reductase. Nature 400 (1999) 476–480. [DOI] [PMID: 10440380]
[EC 1.7.2.2 created 2001]
 
 
EC 1.7.2.5     
Accepted name: nitric oxide reductase (cytochrome c)
Reaction: nitrous oxide + 2 ferricytochrome c + H2O = 2 nitric oxide + 2 ferrocytochrome c + 2 H+
Systematic name: nitrous oxide:ferricytochrome-c oxidoreductase
Comments: The enzyme from Pseudomonas aeruginosa contains a dinuclear centre comprising a non-heme iron centre and heme b3, plus heme c, heme b and calcium; the acceptor is cytochrome c551
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, UM-BBD
References:
1.  Hendriks, J., Warne, A., Gohlke, U., Haltia, T., Ludovici, C., Lubben, M. and Saraste, M. The active site of the bacterial nitric oxide reductase is a dinuclear iron center. Biochemistry 37 (1998) 13102–13109. [DOI] [PMID: 9748316]
2.  Hendriks, J., Gohlke, U. and Saraste, M. From NO to OO: nitric oxide and dioxygen in bacterial respiration. J. Bioenerg. Biomembr. 30 (1998) 15–24. [PMID: 9623801]
3.  Heiss, B., Frunzke, K. and Zumpft, W.G. Formation of the N-N bond from nitric oxide by a membrane-bound cytochrome bc complex of nitrate-respiring (denitrifying) Pseudomonas stutzeri. J. Bacteriol. 171 (1989) 3288–3297. [DOI] [PMID: 2542222]
4.  Cheesman, M.R., Zumft, W.G. and Thomson, A.J. The MCD and EPR of the heme centers of nitric oxide reductase from Pseudomonas stutzeri: evidence that the enzyme is structurally related to the heme-copper oxidases. Biochemistry 37 (1998) 3994–4000. [DOI] [PMID: 9521721]
5.  Kumita, H., Matsuura, K., Hino, T., Takahashi, S., Hori, H., Fukumori, Y., Morishima, I. and Shiro, Y. NO reduction by nitric-oxide reductase from denitrifying bacterium Pseudomonas aeruginosa: characterization of reaction intermediates that appear in the single turnover cycle. J. Biol. Chem. 279 (2004) 55247–55254. [DOI] [PMID: 15504726]
6.  Hino, T., Matsumoto, Y., Nagano, S., Sugimoto, H., Fukumori, Y., Murata, T., Iwata, S. and Shiro, Y. Structural basis of biological N2O generation by bacterial nitric oxide reductase. Science 330 (2010) 1666–1670. [DOI] [PMID: 21109633]
[EC 1.7.2.5 created 1992 as EC 1.7.99.7, transferred 2011 to EC 1.7.2.5]
 
 
EC 1.7.2.6     
Accepted name: hydroxylamine dehydrogenase
Reaction: (1) hydroxylamine + H2O + 4 ferricytochrome c = nitrite + 4 ferrocytochrome c + 5 H+
(2) hydroxylamine + 3 ferricytochrome c = nitric oxide + 3 ferrocytochrome c + 3 H+
Other name(s): HAO (ambiguous); hydroxylamine oxidoreductase (ambiguous); hydroxylamine oxidase (misleading)
Systematic name: hydroxylamine:ferricytochrome-c oxidoreductase
Comments: The enzymes from the nitrifying bacterium Nitrosomonas europaea [1,4] and the methylotrophic bacterium Methylococcus capsulatus [5] are hemoproteins with seven c-type hemes and one specialized P-460-type heme per subunit. The enzyme converts hydroxylamine to nitrite via an enzyme-bound nitroxyl intermediate [3]. While nitrite is the main product, the enzyme from Nitrosomonas europaea can produce nitric oxide as well [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9075-43-8
References:
1.  Rees, M. Studies of the hydroxylamine metabolism of Nitrosomonas europaea. I. Purification of hydroxylamine oxidase. Biochemistry 7 (1968) 353–366. [PMID: 5758552]
2.  Hooper, A.B. and Terry, K.R. Hydroxylamine oxidoreductase of Nitrosomonas. Production of nitric oxide from hydroxylamine. Biochim. Biophys. Acta 571 (1979) 12–20. [DOI] [PMID: 497235]
3.  Hooper, A.B. and Balny, C. Reaction of oxygen with hydroxylamine oxidoreductase of Nitrosomonas: fast kinetics. FEBS Lett. 144 (1982) 299–303. [DOI] [PMID: 7117545]
4.  Lipscomb, J.D. and Hooper, A.B. Resolution of multiple heme centers of hydroxylamine oxidoreductase from Nitrosomonas. 1. Electron paramagnetic resonance spectroscopy. Biochemistry 21 (1982) 3965–3972. [PMID: 6289867]
5.  Poret-Peterson, A.T., Graham, J.E., Gulledge, J. and Klotz, M.G. Transcription of nitrification genes by the methane-oxidizing bacterium, Methylococcus capsulatus strain Bath. ISME J. 2 (2008) 1213–1220. [DOI] [PMID: 18650926]
[EC 1.7.2.6 created 1972 as EC 1.7.3.4, part transferred 2012 to EC 1.7.2.6]
 
 
EC 1.7.2.7     
Accepted name: hydrazine synthase
Reaction: hydrazine + H2O + 3 ferricytochrome c = nitric oxide + ammonium + 3 ferrocytochrome c
Glossary: nitric oxide = nitrogen monoxide = NO
Other name(s): HZS
Systematic name: hydrazine:ferricytochrome-c oxidoreductase
Comments: The enzyme, characterized from anaerobic ammonia oxidizers (anammox bacteria), is one of only two enzymes that are known to form an N-N bond (the other being EC 1.7.1.14, nitric oxide reductase [NAD(P)+, nitrous oxide-forming]). The enzyme from the bacterium Candidatus Kuenenia stuttgartiensis is heterotrimeric and contains multiple c-type cytochromes.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kartal, B., Maalcke, W.J., de Almeida, N.M., Cirpus, I., Gloerich, J., Geerts, W., Op den Camp, H.J., Harhangi, H.R., Janssen-Megens, E.M., Francoijs, K.J., Stunnenberg, H.G., Keltjens, J.T., Jetten, M.S. and Strous, M. Molecular mechanism of anaerobic ammonium oxidation. Nature 479 (2011) 127–130. [DOI] [PMID: 21964329]
[EC 1.7.2.7 created 2016]
 
 
EC 1.7.5.2     
Accepted name: nitric oxide reductase (menaquinol)
Reaction: 2 nitric oxide + menaquinol = nitrous oxide + menaquinone + H2O
Comments: Contains copper.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Cramm, R., Pohlmann, A. and Friedrich, B. Purification and characterization of the single-component nitric oxide reductase from Ralstonia eutropha H16. FEBS Lett. 460 (1999) 6–10. [DOI] [PMID: 10571051]
2.  Suharti, Strampraad, M.J., Schroder, I. and de Vries, S. A novel copper A containing menaquinol NO reductase from Bacillus azotoformans. Biochemistry 40 (2001) 2632–2639. [DOI] [PMID: 11327887]
3.  Suharti, Heering, H.A. and de Vries, S. NO reductase from Bacillus azotoformans is a bifunctional enzyme accepting electrons from menaquinol and a specific endogenous membrane-bound cytochrome c551. Biochemistry 43 (2004) 13487–13495. [DOI] [PMID: 15491156]
[EC 1.7.5.2 created 2011]
 
 
EC 1.7.6.1     
Accepted name: nitrite dismutase
Reaction: 3 nitrite + 2 H+ = 2 nitric oxide + nitrate + H2O
Other name(s): Prolixin S; Nitrophorin 7
Systematic name: nitrite:nitrite oxidoreductase
Comments: Contains ferriheme b. The enzyme is one of the nitrophorins from the salivary gland of the blood-feeding insect Rhodnius prolixus. Nitric oxide produced induces vasodilation after injection. Nitrophorins 2 and 4 can also catalyse this reaction.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  He, C. and Knipp, M. Formation of nitric oxide from nitrite by the ferriheme b protein nitrophorin 7. J. Am. Chem. Soc. 131 (2009) 12042–12043. [DOI] [PMID: 19655755]
2.  He, C., Ogata, H. and Knipp, M. Formation of the complex of nitrite with the ferriheme b β-barrel proteins nitrophorin 4 and nitrophorin 7. Biochemistry 49 (2010) 5841–5851. [DOI] [PMID: 20524697]
[EC 1.7.6.1 created 2011]
 
 
EC 1.7.99.7      
Transferred entry: nitric-oxide reductase. Now EC 1.7.2.5 nitric oxide reductase (cytochrome c)
[EC 1.7.99.7 created 1992, modified 1999, deleted 2011]
 
 
EC 1.14.12.17     
Accepted name: nitric oxide dioxygenase
Reaction: 2 nitric oxide + 2 O2 + NAD(P)H = 2 nitrate + NAD(P)+ + H+
Glossary: nitric oxide = NO = nitrogen(II) oxide
Systematic name: nitric oxide,NAD(P)H:oxygen oxidoreductase
Comments: A flavohemoglobin (FAD). It has been proposed that FAD functions as the electron carrier from NADPH to the ferric heme prosthetic group.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 214466-78-1
References:
1.  Gardner, P.R., Costantino, G. and Salzman, A.L. Constitutive and adaptive detoxification of nitric oxide in Escherichia coli. Role of nitric-oxide dioxygenase in the protection of aconitase. J. Biol. Chem. 273 (1998) 26528–26533. [DOI] [PMID: 9756889]
2.  Gardner, P.R., Gardner, A.M., Martin, L.A. and Salzman, A.L. Nitric oxide dioxygenase: an enzymic function for flavohemoglobin. Proc. Natl. Acad. Sci. USA 95 (1998) 10378–10383. [DOI] [PMID: 9724711]
[EC 1.14.12.17 created 2000]
 
 
EC 1.14.13.39     
Accepted name: nitric-oxide synthase (NADPH)
Reaction: 2 L-arginine + 3 NADPH + 3 H+ + 4 O2 = 2 L-citrulline + 2 nitric oxide + 3 NADP+ + 4 H2O (overall reaction)
(1a) 2 L-arginine + 2 NADPH + 2 H+ + 2 O2 = 2 Nω-hydroxy-L-arginine + 2 NADP+ + 2 H2O
(1b) 2 Nω-hydroxy-L-arginine + NADPH + H+ + 2 O2 = 2 L-citrulline + 2 nitric oxide + NADP+ + 2 H2O
Glossary: nitric oxide = NO = nitrogen(II) oxide
Other name(s): NOS (gene name); nitric oxide synthetase (ambiguous); endothelium-derived relaxation factor-forming enzyme; endothelium-derived relaxing factor synthase; NO synthase (ambiguous); NADPH-diaphorase (ambiguous)
Systematic name: L-arginine,NADPH:oxygen oxidoreductase (nitric-oxide-forming)
Comments: The enzyme consists of linked oxygenase and reductase domains. The eukaryotic enzyme binds FAD, FMN, heme (iron protoporphyrin IX) and tetrahydrobiopterin, and its two domains are linked via a regulatory calmodulin-binding domain. Upon calcium-induced calmodulin binding, the reductase and oxygenase domains form a complex, allowing electrons to flow from NADPH via FAD and FMN to the active center. The reductase domain of the enzyme from the bacterium Sorangium cellulosum utilizes a [2Fe-2S] cluster to transfer the electrons from NADPH to the active center. cf. EC 1.14.14.47, nitric-oxide synthase (flavodoxin).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 125978-95-2
References:
1.  Bredt, D.S. and Snyder, S.H. Isolation of nitric oxide synthetase, a calmodulin-requiring enzyme. Proc. Natl. Acad. Sci. USA 87 (1990) 682–685. [DOI] [PMID: 1689048]
2.  Stuehr, D.J., Kwon, N.S., Nathan, C.F., Griffith, O.W., Feldman, P.L. and Wiseman, J. Nω-hydroxy-L-arginine is an intermediate in the biosynthesis of nitric oxide from L-arginine. J. Biol. Chem. 266 (1991) 6259–6263. [PMID: 1706713]
3.  Stuehr, D., Pou, S. and Rosen, G.M. Oxygen reduction by nitric-oxide synthases. J. Biol. Chem. 276 (2001) 14533–14536. [DOI] [PMID: 11279231]
4.  Agapie, T., Suseno, S., Woodward, J.J., Stoll, S., Britt, R.D. and Marletta, M.A. NO formation by a catalytically self-sufficient bacterial nitric oxide synthase from Sorangium cellulosum. Proc. Natl. Acad. Sci. USA 106 (2009) 16221–16226. [DOI] [PMID: 19805284]
5.  Foresi, N., Correa-Aragunde, N., Parisi, G., Calo, G., Salerno, G. and Lamattina, L. Characterization of a nitric oxide synthase from the plant kingdom: NO generation from the green alga Ostreococcus tauri is light irradiance and growth phase dependent. Plant Cell 22 (2010) 3816–3830. [DOI] [PMID: 21119059]
[EC 1.14.13.39 created 1992, modified 2012, modified 2017]
 
 
EC 1.14.13.165      
Transferred entry: nitric-oxide synthase [NAD(P)H]. Now classified as EC 1.14.14.47, nitric-oxide synthase (flavodoxin)
[EC 1.14.13.165 created 2012, deleted 2017]
 
 
EC 1.14.14.47     
Accepted name: nitric-oxide synthase (flavodoxin)
Reaction: 2 L-arginine + 3 reduced flavodoxin + 4 O2 = 2 L-citrulline + 2 nitric oxide + 3 oxidized flavodoxin + 4 H2O (overall reaction)
(1a) 2 L-arginine + 2 reduced flavodoxin + 2 O2 = 2 Nω-hydroxy-L-arginine + 2 oxidized flavodoxin + 2 H2O
(1b) 2 Nω-hydroxy-L-arginine + reduced flavodoxin + 2 O2 = 2 L-citrulline + 2 nitric oxide + oxidized flavodoxin + 2 H2O
Glossary: nitric oxide = NO = nitrogen(II) oxide
Other name(s): nitric oxide synthetase (ambiguous); NO synthase (ambiguous)
Systematic name: L-arginine,reduced-flavodoxin:oxygen oxidoreductase (nitric-oxide-forming)
Comments: Binds heme (iron protoporphyrin IX) and tetrahydrobiopterin. The enzyme, found in bacteria and archaea, consist of only an oxygenase domain and functions together with bacterial ferredoxins or flavodoxins. The orthologous enzymes from plants and animals also contain a reductase domain and use only NADPH as the electron donor (cf. EC 1.14.13.39).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Pant, K., Bilwes, A.M., Adak, S., Stuehr, D.J. and Crane, B.R. Structure of a nitric oxide synthase heme protein from Bacillus subtilis. Biochemistry 41 (2002) 11071–11079. [DOI] [PMID: 12220171]
2.  Adak, S., Aulak, K.S. and Stuehr, D.J. Direct evidence for nitric oxide production by a nitric-oxide synthase-like protein from Bacillus subtilis. J. Biol. Chem. 277 (2002) 16167–16171. [DOI] [PMID: 11856757]
3.  Wang, Z.Q., Lawson, R.J., Buddha, M.R., Wei, C.C., Crane, B.R., Munro, A.W. and Stuehr, D.J. Bacterial flavodoxins support nitric oxide production by Bacillus subtilis nitric-oxide synthase. J. Biol. Chem. 282 (2007) 2196–2202. [DOI] [PMID: 17127770]
4.  Agapie, T., Suseno, S., Woodward, J.J., Stoll, S., Britt, R.D. and Marletta, M.A. NO formation by a catalytically self-sufficient bacterial nitric oxide synthase from Sorangium cellulosum. Proc. Natl. Acad. Sci. USA 106 (2009) 16221–16226. [DOI] [PMID: 19805284]
5.  Holden, J.K., Lim, N. and Poulos, T.L. Identification of redox partners and development of a novel chimeric bacterial nitric oxide synthase for structure activity analyses. J. Biol. Chem. 289 (2014) 29437–29445. [DOI] [PMID: 25194416]
[EC 1.14.14.47 created 2012 as EC 1.14.13.165, transferred 2017 to EC 1.14.14.47]
 
 


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