EzCatDB: D00055

DB codeD00055
CATH domainDomain 11.10.760.10Catalytic domain
Domain 22.140.10.20Catalytic domain
E.C.1.7.2.1,1.7.99.1,1.9.3.1
CSA1nir

CATH domainRelated DB codes (homologues)
1.10.760.10D00498,M00179
2.140.10.20D00498

Enzyme Name
Swiss-protKEGG

P24474
Protein nameNitrite reductasenitrite reductase (NO-forming)
   (EC 1.7.2.1)
cd-cytochrome nitrite reductase
   (EC 1.7.2.1)
[nitrite reductase (cytochrome)] [misleading, see comments.]
   (EC 1.7.2.1)
cytochrome c-551:O2, NO2+ oxidoreductase
   (EC 1.7.2.1)
cytochrome cd
   (EC 1.7.2.1)
cytochrome cd1
   (EC 1.7.2.1)
hydroxylamine (acceptor) reductase
   (EC 1.7.2.1)
methyl viologen-nitrite reductase
   (EC 1.7.2.1)
nitrite reductase (cytochrome
   (EC 1.7.2.1)
NO-forming)
   (EC 1.7.2.1)
hydroxylamine reductase
   (EC 1.7.99.1)
hydroxylamine (acceptor) reductase
   (EC 1.7.99.1)
ammonia:(acceptor) oxidoreductase
   (EC 1.7.99.1)
cytochrome-c oxidase
   (EC 1.9.3.1)
cytochrome oxidase
   (EC 1.9.3.1)
cytochrome a3
   (EC 1.9.3.1)
cytochrome aa3
   (EC 1.9.3.1)
Warburg's respiratory enzyme
   (EC 1.9.3.1)
indophenol oxidase
   (EC 1.9.3.1)
indophenolase
   (EC 1.9.3.1)
complex IV (mitochondrial electron transport)
   (EC 1.9.3.1)
ferrocytochrome c oxidase
   (EC 1.9.3.1)
NADH cytochrome c oxidase
   (EC 1.9.3.1)
SynonymsEC 1.7.2.1
Cytochrome cd1
Cytochrome oxidase
Hydroxylamine reductase
EC 1.7.99.1

KEGG pathways
MAP codePathwaysE.C.
MAP00190Oxidative phosphorylation1.9.3.1
MAP00910Nitrogen metabolism1.7.2.1,1.7.99.1

Swiss-prot:Accession NumberP24474
Entry nameNIRS_PSEAE
ActivityNitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+).,NH(3) + H(2)O + acceptor = hydroxylamine + reduced acceptor.
SubunitHomodimer.
Subcellular locationPeriplasm.
CofactorBinds 2 heme groups per subunit.


CofactorsSubstratesProducts
KEGG-idC00032C00032C00088C00126C00080C00014C00028C00007C00533C00001C00125C00192C00030
E.C.1.7.2.1,1.7.99.1,1.9.3.11.7.2.1,1.7.99.1,1.9.3.11.7.2.11.7.2.1,1.9.3.11.7.2.1,1.9.3.11.7.99.11.7.99.11.9.3.11.7.2.11.7.2.1,1.7.99.1,1.9.3.11.7.2.1,1.9.3.11.7.99.11.7.99.1
Compoundc hemed1 hemeNitriteFerrocytochrome cH+AmmoniaAcceptorO2Nitric oxideH2OFerricytochrome cHydroxylamineReduced acceptor
Typearomatic ring (with nitrogen atoms),carboxyl group,heavy metalaromatic ring (with nitrogen atoms),carboxyl group,heavy metalothersamide group,amine group,aromatic ring (with nitrogen atoms),carboxyl group,heavy metal,sulfide groupothersamine group,organic ionothersothersothersH2Oamide group,amine group,aromatic ring (with nitrogen atoms),carboxyl group,heavy metal,sulfide groupamine groupothers
1bl9A01Bound:HECUnboundUnboundUnbound
UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1bl9B01Bound:HECUnboundUnboundUnbound
UnboundUnboundUnboundUnboundBound:_OHUnboundUnboundUnbound
1gjqA01Bound:HECUnboundUnboundUnbound
UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1gjqB01Bound:HECUnboundUnboundUnbound
UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1hzuA01Bound:HECUnboundUnboundUnbound
UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1hzvA01Bound:HECUnboundUnboundUnbound
UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1n15A01Bound:HECUnboundUnboundUnbound
UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1n15B01Bound:HECUnboundUnboundUnbound
UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1n50A01Bound:HECUnboundUnboundUnbound
UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1n50B01Bound:HECUnboundUnboundUnbound
UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1n90A01Bound:HECUnboundUnboundUnbound
UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1n90B01Bound:HECUnboundUnboundUnbound
UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1nirA01Bound:HECUnboundUnboundUnbound
UnboundUnboundUnboundUnboundBound:_OHUnboundUnboundUnbound
1nirB01Bound:HECUnboundUnboundUnbound
UnboundUnboundUnboundUnboundBound:_OHUnboundUnboundUnbound
1nnoA01Bound:HECUnboundUnboundUnbound
UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1nnoB01Bound:HECUnboundUnboundUnbound
UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1bl9A02UnboundBound:DHEUnboundUnbound
UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1bl9B02UnboundAnalogue:DHE-_OHUnboundUnbound
UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1gjqA02UnboundBound:DHEUnboundUnbound
UnboundUnboundUnboundAnalogue:CYN
UnboundUnboundUnbound
1gjqB02UnboundBound:DHEUnboundUnbound
UnboundUnboundUnboundAnalogue:CYN
UnboundUnboundUnbound
1hzuA02UnboundBound:DHEUnboundUnbound
UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1hzvA02UnboundBound:DHEUnboundUnbound
UnboundUnboundUnboundBound:_NO
UnboundUnboundUnbound
1n15A02UnboundBound:DHEUnboundUnbound
UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1n15B02UnboundBound:DHEUnboundUnbound
UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1n50A02UnboundBound:DHEUnboundUnbound
UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1n50B02UnboundBound:DHEUnboundUnbound
UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1n90A02UnboundBound:DHEUnboundUnbound
UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1n90B02UnboundBound:DHEUnboundUnbound
UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1nirA02UnboundAnalogue:DHE-_OHUnboundUnbound
UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1nirB02UnboundAnalogue:DHE-_OHUnboundUnbound
UnboundUnboundUnboundUnbound
UnboundUnboundUnbound
1nnoA02UnboundBound:DHEUnboundUnbound
UnboundUnboundUnboundBound:_NO
UnboundUnboundUnbound
1nnoB02UnboundBound:DHEUnboundUnbound
UnboundUnboundUnboundBound:_NO
UnboundUnboundUnbound

Active-site residues
resource
literature [12]
pdbCatalytic residuesCofactor-binding residuescomment
1bl9A01
HIS  51;MET  88(Heme c axial binding);CYS  47;CYS  50(Heme c covalent binding)

1bl9B01
HIS  51;MET  88(Heme c axial binding);CYS  47;CYS  50(Heme c covalent binding)

1gjqA01
HIS  51;MET  88(Heme c axial binding);CYS  47;CYS  50(Heme c covalent binding)

1gjqB01
HIS  51;MET  88(Heme c axial binding);CYS  47;CYS  50(Heme c covalent binding)

1hzuA01
HIS  51;MET  88(Heme c axial binding);CYS  47;CYS  50(Heme c covalent binding)

1hzvA01
HIS  51;MET  88(Heme c axial binding);CYS  47;CYS  50(Heme c covalent binding)

1n15A01
HIS  51;MET  88(Heme c axial binding);CYS  47;CYS  50(Heme c covalent binding)

1n15B01
HIS  51;MET  88(Heme c axial binding);CYS  47;CYS  50(Heme c covalent binding)

1n50A01
HIS  51;MET  88(Heme c axial binding);CYS  47;CYS  50(Heme c covalent binding)

1n50B01
HIS  51;MET  88(Heme c axial binding);CYS  47;CYS  50(Heme c covalent binding)

1n90A01
HIS  51;MET  88(Heme c axial binding);CYS  47;CYS  50(Heme c covalent binding)

1n90B01
HIS  51;MET  88(Heme c axial binding);CYS  47;CYS  50(Heme c covalent binding)

1nirA01
HIS  51;MET  88(Heme c axial binding);CYS  47;CYS  50(Heme c covalent binding)

1nirB01
HIS  51;MET  88(Heme c axial binding);CYS  47;CYS  50(Heme c covalent binding)

1nnoA01
HIS  51;MET  88(Heme c axial binding);CYS  47;CYS  50(Heme c covalent binding)

1nnoB01
HIS  51;MET  88(Heme c axial binding);CYS  47;CYS  50(Heme c covalent binding)

1bl9A02HIS 327;HIS 369
HIS 182(Heme d1 proximal binding)

1bl9B02HIS 327;HIS 369
HIS 182(Heme d1 proximal binding)

1gjqA02HIS 327;HIS 369
HIS 182(Heme d1 proximal binding)

1gjqB02HIS 327;HIS 369
HIS 182(Heme d1 proximal binding)

1hzuA02       ;HIS 369
HIS 182(Heme d1 proximal binding)
mutant H327A
1hzvA02HIS 327;       
HIS 182(Heme d1 proximal binding)
mutant H369A
1n15A02HIS 327;HIS 369
HIS 182(Heme d1 proximal binding)

1n15B02HIS 327;HIS 369
HIS 182(Heme d1 proximal binding)

1n50A02HIS 327;HIS 369
HIS 182(Heme d1 proximal binding)

1n50B02HIS 327;HIS 369
HIS 182(Heme d1 proximal binding)

1n90A02HIS 327;HIS 369
HIS 182(Heme d1 proximal binding)

1n90B02HIS 327;HIS 369
HIS 182(Heme d1 proximal binding)

1nirA02HIS 327;HIS 369
HIS 182(Heme d1 proximal binding)

1nirB02HIS 327;HIS 369
HIS 182(Heme d1 proximal binding)

1nnoA02HIS 327;HIS 369
HIS 182(Heme d1 proximal binding)

1nnoB02HIS 327;HIS 369
HIS 182(Heme d1 proximal binding)


References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[6]p.1165-1168
[7]p.13991-13993
[8]Fig.3, p.236-239
[9]Scheme 1
[10]Fig.3, 57-61
[12]Fig.3, p.2236-2237

references
[1]
PubMed ID3722163
JournalJ Biol Chem
Year1986
Volume261
Pages8593-6
AuthorsChang CK, Wu W
TitleThe porphinedione structure of heme d1. Synthesis and spectral properties of model compounds of the prosthetic group of dissimilatory nitrite reductase.
[2]
PubMed ID2166031
JournalJ Biol Chem
Year1990
Volume265
Pages13498-500
AuthorsYap-Bondoc F, Bondoc LL, Timkovich R, Baker DC, Hebbler A
TitleC-methylation occurs during the biosynthesis of heme d1.
[3]
PubMed ID8396650
JournalJ Mol Biol
Year1993
Volume232
Pages1211-2
AuthorsFulop V, Moir JW, Ferguson SJ, Hajdu J
TitleCrystallization and preliminary crystallographic study of cytochrome cd1 nitrite reductase from Thiosphaera pantotropha.
[4]
PubMed ID7893816
JournalBiochimie
Year1994
Volume76
Pages641-54
AuthorsSilvestrini MC, Falcinelli S, Ciabatti I, Cutruzzola F, Brunori M
TitlePseudomonas aeruginosa nitrite reductase (or cytochrome oxidase): an overview.
[5]
PubMed ID7932760
JournalJ Mol Biol
Year1994
Volume243
Pages347-50
AuthorsTegoni M, Silvestrini MC, Lamzin VS, Brunori M, Cambillau C
TitleCrystallization and preliminary X-ray analysis of a new crystal form of nitrite reductase from Pseudomonas aeruginosa.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS)
Medline ID97473000
PubMed ID9331415
JournalStructure
Year1997
Volume5
Pages1157-71
AuthorsNurizzo D, Silvestrini MC, Mathieu M, Cutruzzola F, Bourgeois D, Fulop V, Hajdu J, Brunori M, Tegoni M, Cambillau C
TitleN-terminal arm exchange is observed in the 2.15 A crystal structure of oxidized nitrite reductase from Pseudomonas aeruginosa.
Related PDB1nir
Related Swiss-protP24474
[7]
CommentsX-RAY CRYSTALLOGRAPHY (2.65 ANGSTROMS)
Medline ID98434370
PubMed ID9760233
JournalBiochemistry
Year1998
Volume37
Pages13987-96
AuthorsNurizzo D, Cutruzzola F, Arese M, Bourgeois D, Brunori M, Cambillau C, Tegoni M
TitleConformational changes occurring upon reduction and NO binding in nitrite reductase from Pseudomonas aeruginosa.
Related PDB1nno
Related Swiss-protP24474
[8]
PubMed ID10320660
JournalBiochim Biophys Acta
Year1999
Volume1411
Pages231-49
AuthorsCutruzzola F
TitleBacterial nitric oxide synthesis.
[9]
CommentsX-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS)
Medline ID99262655
PubMed ID10329702
JournalJ Biol Chem
Year1999
Volume274
Pages14997-5004
AuthorsNurizzo D, Cutruzzola F, Arese M, Bourgeois D, Brunori M, Cambillau C, Tegoni M
TitleDoes the reduction of c heme trigger the conformational change of crystalline nitrite reductase?
Related PDB1n15,1n50,1n90,1bl9
Related Swiss-protP24474
[10]
PubMed ID11191223
JournalJ Biol Inorg Chem
Year2001
Volume6
Pages55-62
AuthorsLopes H, Besson S, Moura I, Moura JJ
TitleKinetics of inter- and intramolecular electron transfer of Pseudomonas nautica cytochrome cd1 nitrite reductase: regulation of the NO-bound end product.
[11]
CommentsX-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF H394A AND H352A MUTANTS
Medline ID21448825
PubMed ID11563915
JournalJ Mol Biol
Year2001
Volume312
Pages541-54
AuthorsBrown K, Roig-Zamboni V, Cutruzzola' F, Arese M, Sun W, Brunori M, Cambillau C, Tegoni M
TitleDomain swing upon His to Ala mutation in nitrite reductase of Pseudomonas aeruginosa.
Related PDB1hzu,1hzv
Related Swiss-protP24474
[12]
CommentsX-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF H394A AND H352A MUTANTS
Medline ID21126867
PubMed ID11226222
JournalProc Natl Acad Sci U S A
Year2001
Volume98
Pages2232-7
AuthorsCutruzzola F, Brown K, Wilson EK, Bellelli A, Arese M, Tegoni M, Cambillau C, Brunori M
TitleThe nitrite reductase from Pseudomonas aeruginosa: essential role of two active-site histidines in the catalytic and structural properties.
Related Swiss-protP24474
[13]
PubMed ID11829453
JournalBiochem Biophys Res Commun
Year2002
Volume291
Pages1-7
AuthorsSun W, Arese M, Brunori M, Nurizzo D, Brown K, Cambillau C, Tegoni M, Cutruzzola F
TitleCyanide binding to cd(1) nitrite reductase from Pseudomonas aeruginosa: role of the active-site His369 in ligand stabilization.
Related PDB1gjq
[14]
PubMed ID11897350
JournalJ Inorg Biochem
Year2002
Volume88
Pages353-61
AuthorsCutruzzola F, Arese M, Ranghino G, van Pouderoyen G, Canters G, Brunori M
TitlePseudomonas aeruginosa cytochrome C(551): probing the role of the hydrophobic patch in electron transfer.

comments
According to the literature [6], cytochrome c551 seems to be an electron acceptor/donor protein.
Although this enzyme is homologous to the counterpart from Paracoccus pantophus (Swiss-prot; P72181, D00498 in EzCatDB), the active site residues and positions are slightly different from that.
Although only two E.C. numbers (1.7.2.1 and 1.7.99.1) have been annotated in Swiss-prot data (Swiss-prot; P24474), this enzyme also seems to catalyze the reaction, corresponding to E.C. 1.9.3.1, according to the literature.
Thus, this enzyme catalyzes the following reactions:
(a) NO2 + 2 H+ + e- = NO) + H2O
(b) NH3 + H2O + acceptor = hydroxylamine + reduced acceptor.
(c) O2 + 4 H+ + 4 e- = 2 H2O
#####
There are some other kind of "nitrite reductases":
E.C. 1.7.1.4 nitrite reductase [NAD(P)H]
E.C. 1.7.2.2 nitrite reductase (cytochrome; ammonia-forming)
E.C. 1.7.7.1 ferredoxin-nitrite reductase
Another nitrite reductase enzyme (E.C. 1.7.2.1) which contains multiple copper centres, is described in D00449 in EzCatDB.

createdupdated
2005-07-052009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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