1NIR

OXYDIZED NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1nira1	All alpha proteins	Cytochrome c	Cytochrome c	N-terminal (heme c) domain of cytochrome cd1-nitrite reductase	N-terminal (heme c) domain of cytochrome cd1-nitrite reductase	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
A	d1nira2	All beta proteins	8-bladed beta-propeller	C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase	C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase	C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
B	d1nirb1	All alpha proteins	Cytochrome c	Cytochrome c	N-terminal (heme c) domain of cytochrome cd1-nitrite reductase	N-terminal (heme c) domain of cytochrome cd1-nitrite reductase	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
B	d1nirb2	All beta proteins	8-bladed beta-propeller	C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase	C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase	C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	N-terminal (heme c) domain of cytochrome cd1-nitrite reductase	8024119	4000654	SCOP2 (2022-06-29)
A	SCOP2 Family	C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase	8030492	4002629	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cytochrome c	8036498	3000815	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase	8042871	3001509	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Cytochrome c	8036498	3000815	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase	8042871	3001509	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Cytochrom_D1	e1nirA3	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 8-bladed	F: Cytochrom_D1	ECOD (1.6)
A	Cytochrome_CBB3	e1nirA4	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrome_CBB3	ECOD (1.6)
B	Cytochrom_D1	e1nirB3	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 8-bladed	F: Cytochrom_D1	ECOD (1.6)
B	Cytochrome_CBB3	e1nirB4	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrome_CBB3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
A	2.140.10.20	Mainly Beta	8 Propeller	Methanol Dehydrogenase	Chain A	CATH (4.3.0)
B	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
B	2.140.10.20	Mainly Beta	8 Propeller	Methanol Dehydrogenase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02239	Cytochrome D1 heme domain (Cytochrom_D1)	Cytochrome D1 heme domain	-	Repeat
A, B	PF13442	Cytochrome C oxidase, cbb3-type, subunit III (Cytochrome_CBB3)	Cytochrome C oxidase, cbb3-type, subunit III	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	NITRITE REDUCTASE	hydroxylamine reductase activity oxidoreductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors catalytic activity binding organic cyclic compound binding tetrapyrrole binding heme binding oxidoreductase activity, acting on other nitrogenous compounds as donors, cytochrome as acceptor nitrite reductase (NO-forming) activity nitrite reductase activity electron transfer activity cation binding ion binding hydroxylamine reductase activity oxidoreductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors catalytic activity binding organic cyclic compound binding tetrapyrrole binding heme binding oxidoreductase activity, acting on other nitrogenous compounds as donors, cytochrome as acceptor nitrite reductase (NO-forming) activity nitrite reductase activity electron transfer activity cation binding ion binding metal ion binding small molecule binding	-	periplasmic space cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
A, B	IPR011048	Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily	Homologous Superfamily
A, B	IPR009056	Cytochrome c-like domain	Domain
A, B	IPR003143	Cytochrome cd1-nitrite reductase, C-terminal domain superfamily	Homologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	nitrite reductase (cytochrome cd1 type) M-CSA #903	Cytochrome cd1 (cyt cd1) nitrite reductase is a dimeric enzyme of the bacterial periplasm that plays a key role in denitrification, the respiratory reduction of nitrite to nitric oxide in the nitrogen cycle. Each subunit of the cyt cd1 dimer contains one cytochrome c and one d1 haem group [PMID:12556530]. The active site contains a specialised d1 haem, where the nitrite substrate is bound and reduced. This d1 haem is bound in an 8-bladed beta-propeller, which is also found in some members of the WD40 repeat-containing proteins (IPR001680).	Defined by 6 residues: CYS:A-47CYS:A-50HIS:A-51MET:A-88HIS:A-327HIS:A-369 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.9.3.2 (PDB Primary Data) Search M-CSA Motif + EC 1.9.3.2 EC: 1.7.99.1 (UniProt) Search M-CSA Motif + EC 1.7.99.1 EC: 1.7.2.1 (UniProt) Search M-CSA Motif + EC 1.7.2.1

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.