DB code: D00055

CATH domain 1.10.760.10 : Cytochrome Bc1 Complex; Chain D, domain 2 Catalytic domain
2.140.10.20 : Methanol Dehydrogenase; Chain A Catalytic domain
E.C. 1.7.2.1 1.7.99.1 1.9.3.1
CSA 1nir
M-CSA 1nir
MACiE

CATH domain Related DB codes (homologues)
1.10.760.10 : Cytochrome Bc1 Complex; Chain D, domain 2 D00498 M00179
2.140.10.20 : Methanol Dehydrogenase; Chain A D00498

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq
P24474 Nitrite reductase
EC 1.7.2.1
Cytochrome cd1
Cytochrome oxidase
Hydroxylamine reductase
EC 1.7.99.1
NP_249210.1 (Protein)
NC_002516.2 (DNA/RNA sequence)

KEGG enzyme name
nitrite 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 )

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P24474 NIRS_PSEAE Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+). NH(3) + H(2)O + acceptor = hydroxylamine + reduced acceptor. Homodimer. Periplasm. Binds 2 heme groups per subunit.

KEGG Pathways
Map code Pathways E.C.
MAP00190 Oxidative phosphorylation 1.9.3.1
MAP00910 Nitrogen metabolism 1.7.2.1 1.7.99.1

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00032 C00032 C00088 C00126 C00080 C00014 C00028 C00007 C00533 C00001 C00125 C00192 C00030
E.C. 1.7.2.1
1.7.99.1
1.9.3.1
1.7.2.1
1.7.99.1
1.9.3.1
1.7.2.1
1.7.2.1
1.9.3.1
1.7.2.1
1.9.3.1
1.7.99.1
1.7.99.1
1.9.3.1
1.7.2.1
1.7.2.1
1.7.99.1
1.9.3.1
1.7.2.1
1.9.3.1
1.7.99.1
1.7.99.1
Compound c heme d1 heme Nitrite Ferrocytochrome c H+ Ammonia Acceptor O2 Nitric oxide H2O Ferricytochrome c Hydroxylamine Reduced acceptor
Type aromatic ring (with nitrogen atoms),carboxyl group,heavy metal aromatic ring (with nitrogen atoms),carboxyl group,heavy metal others amide group,amine group,aromatic ring (with nitrogen atoms),carboxyl group,heavy metal,sulfide group others amine group,organic ion others others others H2O amide group,amine group,aromatic ring (with nitrogen atoms),carboxyl group,heavy metal,sulfide group amine group others
ChEBI 17627
 26355
 17627
 26355
 		17627
 26355
 17627
 26355
 		25567
 25567
 		15378
 15378
 		16134
 16134
 		15379
 26689
 27140
 15379
 26689
 27140
 		16480
 16480
 		15377
 15377
 		15429
 15429
PubChem 24529
 24529
 		1038
 1038
 		222
 222
 		977
 977
 		145068
 145068
 		22247451
 962
 22247451
 962
 		787
 787
1bl9A01 Bound:HEC Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1bl9B01 Bound:HEC Unbound Unbound Unbound Unbound Unbound Unbound Unbound Bound:_OH Unbound Unbound Unbound
1gjqA01 Bound:HEC Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1gjqB01 Bound:HEC Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1hzuA01 Bound:HEC Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1hzvA01 Bound:HEC Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1n15A01 Bound:HEC Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1n15B01 Bound:HEC Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1n50A01 Bound:HEC Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1n50B01 Bound:HEC Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1n90A01 Bound:HEC Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1n90B01 Bound:HEC Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1nirA01 Bound:HEC Unbound Unbound Unbound Unbound Unbound Unbound Unbound Bound:_OH Unbound Unbound Unbound
1nirB01 Bound:HEC Unbound Unbound Unbound Unbound Unbound Unbound Unbound Bound:_OH Unbound Unbound Unbound
1nnoA01 Bound:HEC Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1nnoB01 Bound:HEC Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1bl9A02 Unbound Bound:DHE Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1bl9B02 Unbound Analogue:DHE-_OH Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1gjqA02 Unbound Bound:DHE Unbound Unbound Unbound Unbound Unbound Analogue:CYN Unbound Unbound Unbound
1gjqB02 Unbound Bound:DHE Unbound Unbound Unbound Unbound Unbound Analogue:CYN Unbound Unbound Unbound
1hzuA02 Unbound Bound:DHE Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1hzvA02 Unbound Bound:DHE Unbound Unbound Unbound Unbound Unbound Bound:_NO Unbound Unbound Unbound
1n15A02 Unbound Bound:DHE Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1n15B02 Unbound Bound:DHE Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1n50A02 Unbound Bound:DHE Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1n50B02 Unbound Bound:DHE Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1n90A02 Unbound Bound:DHE Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1n90B02 Unbound Bound:DHE Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1nirA02 Unbound Analogue:DHE-_OH Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1nirB02 Unbound Analogue:DHE-_OH Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1nnoA02 Unbound Bound:DHE Unbound Unbound Unbound Unbound Unbound Bound:_NO Unbound Unbound Unbound
1nnoB02 Unbound Bound:DHE Unbound Unbound Unbound Unbound Unbound Bound:_NO Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [12]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
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)
1bl9A02 HIS 327;HIS 369 HIS 182(Heme d1 proximal binding)
1bl9B02 HIS 327;HIS 369 HIS 182(Heme d1 proximal binding)
1gjqA02 HIS 327;HIS 369 HIS 182(Heme d1 proximal binding)
1gjqB02 HIS 327;HIS 369 HIS 182(Heme d1 proximal binding)
1hzuA02 ;HIS 369 HIS 182(Heme d1 proximal binding) mutant H327A
1hzvA02 HIS 327; HIS 182(Heme d1 proximal binding) mutant H369A
1n15A02 HIS 327;HIS 369 HIS 182(Heme d1 proximal binding)
1n15B02 HIS 327;HIS 369 HIS 182(Heme d1 proximal binding)
1n50A02 HIS 327;HIS 369 HIS 182(Heme d1 proximal binding)
1n50B02 HIS 327;HIS 369 HIS 182(Heme d1 proximal binding)
1n90A02 HIS 327;HIS 369 HIS 182(Heme d1 proximal binding)
1n90B02 HIS 327;HIS 369 HIS 182(Heme d1 proximal binding)
1nirA02 HIS 327;HIS 369 HIS 182(Heme d1 proximal binding)
1nirB02 HIS 327;HIS 369 HIS 182(Heme d1 proximal binding)
1nnoA02 HIS 327;HIS 369 HIS 182(Heme d1 proximal binding)
1nnoB02 HIS 327;HIS 369 HIS 182(Heme d1 proximal binding)

References for Catalytic Mechanism
References Sections No. 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]
Resource
Comments
Medline ID
PubMed ID 3722163
Journal J Biol Chem
Year 1986
Volume 261
Pages 8593-6
Authors Chang CK, Wu W
Title The porphinedione structure of heme d1. Synthesis and spectral properties of model compounds of the prosthetic group of dissimilatory nitrite reductase.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 2166031
Journal J Biol Chem
Year 1990
Volume 265
Pages 13498-500
Authors Yap-Bondoc F, Bondoc LL, Timkovich R, Baker DC, Hebbler A
Title C-methylation occurs during the biosynthesis of heme d1.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 8396650
Journal J Mol Biol
Year 1993
Volume 232
Pages 1211-2
Authors Fulop V, Moir JW, Ferguson SJ, Hajdu J
Title Crystallization and preliminary crystallographic study of cytochrome cd1 nitrite reductase from Thiosphaera pantotropha.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 7893816
Journal Biochimie
Year 1994
Volume 76
Pages 641-54
Authors Silvestrini MC, Falcinelli S, Ciabatti I, Cutruzzola F, Brunori M
Title Pseudomonas aeruginosa nitrite reductase (or cytochrome oxidase): an overview.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 7932760
Journal J Mol Biol
Year 1994
Volume 243
Pages 347-50
Authors Tegoni M, Silvestrini MC, Lamzin VS, Brunori M, Cambillau C
Title Crystallization and preliminary X-ray analysis of a new crystal form of nitrite reductase from Pseudomonas aeruginosa.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS)
Medline ID 97473000
PubMed ID 9331415
Journal Structure
Year 1997
Volume 5
Pages 1157-71
Authors Nurizzo D, Silvestrini MC, Mathieu M, Cutruzzola F, Bourgeois D, Fulop V, Hajdu J, Brunori M, Tegoni M, Cambillau C
Title N-terminal arm exchange is observed in the 2.15 A crystal structure of oxidized nitrite reductase from Pseudomonas aeruginosa.
Related PDB 1nir
Related UniProtKB P24474
[7]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.65 ANGSTROMS)
Medline ID 98434370
PubMed ID 9760233
Journal Biochemistry
Year 1998
Volume 37
Pages 13987-96
Authors Nurizzo D, Cutruzzola F, Arese M, Bourgeois D, Brunori M, Cambillau C, Tegoni M
Title Conformational changes occurring upon reduction and NO binding in nitrite reductase from Pseudomonas aeruginosa.
Related PDB 1nno
Related UniProtKB P24474
[8]
Resource
Comments
Medline ID
PubMed ID 10320660
Journal Biochim Biophys Acta
Year 1999
Volume 1411
Pages 231-49
Authors Cutruzzola F
Title Bacterial nitric oxide synthesis.
Related PDB
Related UniProtKB
[9]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS)
Medline ID 99262655
PubMed ID 10329702
Journal J Biol Chem
Year 1999
Volume 274
Pages 14997-5004
Authors Nurizzo D, Cutruzzola F, Arese M, Bourgeois D, Brunori M, Cambillau C, Tegoni M
Title Does the reduction of c heme trigger the conformational change of crystalline nitrite reductase?
Related PDB 1n15 1n50 1n90 1bl9
Related UniProtKB P24474
[10]
Resource
Comments
Medline ID
PubMed ID 11191223
Journal J Biol Inorg Chem
Year 2001
Volume 6
Pages 55-62
Authors Lopes H, Besson S, Moura I, Moura JJ
Title Kinetics of inter- and intramolecular electron transfer of Pseudomonas nautica cytochrome cd1 nitrite reductase: regulation of the NO-bound end product.
Related PDB
Related UniProtKB
[11]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF H394A AND H352A MUTANTS
Medline ID 21448825
PubMed ID 11563915
Journal J Mol Biol
Year 2001
Volume 312
Pages 541-54
Authors Brown K, Roig-Zamboni V, Cutruzzola' F, Arese M, Sun W, Brunori M, Cambillau C, Tegoni M
Title Domain swing upon His to Ala mutation in nitrite reductase of Pseudomonas aeruginosa.
Related PDB 1hzu 1hzv
Related UniProtKB P24474
[12]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF H394A AND H352A MUTANTS
Medline ID 21126867
PubMed ID 11226222
Journal Proc Natl Acad Sci U S A
Year 2001
Volume 98
Pages 2232-7
Authors Cutruzzola F, Brown K, Wilson EK, Bellelli A, Arese M, Tegoni M, Cambillau C, Brunori M
Title The nitrite reductase from Pseudomonas aeruginosa: essential role of two active-site histidines in the catalytic and structural properties.
Related PDB
Related UniProtKB P24474
[13]
Resource
Comments
Medline ID
PubMed ID 11829453
Journal Biochem Biophys Res Commun
Year 2002
Volume 291
Pages 1-7
Authors Sun W, Arese M, Brunori M, Nurizzo D, Brown K, Cambillau C, Tegoni M, Cutruzzola F
Title Cyanide binding to cd(1) nitrite reductase from Pseudomonas aeruginosa: role of the active-site His369 in ligand stabilization.
Related PDB 1gjq
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 11897350
Journal J Inorg Biochem
Year 2002
Volume 88
Pages 353-61
Authors Cutruzzola F, Arese M, Ranghino G, van Pouderoyen G, Canters G, Brunori M
Title Pseudomonas aeruginosa cytochrome C(551): probing the role of the hydrophobic patch in electron transfer.
Related PDB
Related UniProtKB

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.

Created Updated
2005-07-05 2009-02-26