2AKJ

Structure of spinach nitrite reductase

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	d2akja1	Alpha and beta proteins (a+b)	Ferredoxin-like	Nitrite/Sulfite reductase N-terminal domain-like	Duplicated SiR/NiR-like domains 1 and 3	Ferredoxin-nitrite reductase, NIR, C-terminal domain	spinach (Spinacia oleracea ) [TaxId: 3562 ],	SCOPe (2.08)
A	d2akja2	Alpha and beta proteins (a+b)	Ferredoxin-like	Nitrite/Sulfite reductase N-terminal domain-like	Duplicated SiR/NiR-like domains 1 and 3	Ferredoxin-nitrite reductase, NIR, N-terminal domain	spinach (Spinacia oleracea ) [TaxId: 3562 ],	SCOPe (2.08)
A	d2akja3	Alpha and beta proteins (a+b)	Nitrite and sulphite reductase 4Fe-4S domain-like	Nitrite and sulphite reductase 4Fe-4S domain-like	Nitrite and sulphite reductase 4Fe-4S domain-like	Ferredoxin--nitrite reductase, NIR	spinach (Spinacia oleracea ) [TaxId: 3562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Duplicated SiR/NiR-like domains 1 and 3	8021095	4001354	SCOP2 (2022-06-29)
A	SCOP2 Family	Duplicated SiR/NiR-like domains 1 and 3	8021096	4001354	SCOP2 (2022-06-29)
A	SCOP2 Family	Nitrite and sulphite reductase 4Fe-4S domain-like	8021100	4001988	SCOP2 (2022-06-29)
A	SCOP2 Family	Nitrite and sulphite reductase 4Fe-4S domain-like	8021101	4001988	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nitrite/Sulfite reductase N-terminal domain-like	8033475	3001366	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nitrite/Sulfite reductase N-terminal domain-like	8033476	3001366	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nitrite and sulphite reductase 4Fe-4S domain-like	8033480	3000646	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nitrite and sulphite reductase 4Fe-4S domain-like	8033481	3000646	SCOP2 (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	PF03460	e2akjA1	A: a+b two layers	X: Alpha-beta plaits	H: Sulfite reductase, domains 1 and 3 (From Topology)	T: Sulfite reductase, domains 1 and 3	F: PF03460	ECOD (1.6)
A	PF01077	e2akjA3	A: a+b three layers	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 (From Topology)	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 (From Topology)	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: PF01077	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.480.20	Alpha Beta	Alpha-Beta Complex	Sulfite Reductase Hemoprotein	domain 2	CATH (4.3.0)
A	3.30.413.10	Alpha Beta	2-Layer Sandwich	Sulfite Reductase Hemoprotein	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03460	Nitrite/Sulfite reductase ferredoxin-like half domain (NIR_SIR_ferr)	Nitrite/Sulfite reductase ferredoxin-like half domain	-	Repeat
A	PF01077	Nitrite and sulphite reductase 4Fe-4S domain (NIR_SIR)	Nitrite and sulphite reductase 4Fe-4S domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ferredoxin--nitrite reductase, chloroplast	iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding oxidoreductase activity, acting on other nitrogenous compounds as donors, iron-sulfur protein as acceptor oxidoreductase activity ferredoxin-nitrite reductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors nitrite reductase activity catalytic activity organic cyclic compound binding tetrapyrrole binding heme binding iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding oxidoreductase activity, acting on other nitrogenous compounds as donors, iron-sulfur protein as acceptor oxidoreductase activity ferredoxin-nitrite reductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors nitrite reductase activity catalytic activity organic cyclic compound binding tetrapyrrole binding heme binding cation binding ion binding metal ion binding	nitrate assimilation oxoacid metabolic process cellular metabolic process organic acid metabolic process reactive nitrogen species metabolic process nitrogen cycle metabolic process organic substance metabolic process metabolic process small molecule metabolic process cellular process nitrate metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle chloroplast

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006067	Nitrite/sulphite reductase 4Fe-4S domain	Domain
A	IPR005117	Nitrite/Sulfite reductase ferredoxin-like domain	Domain
A	IPR006066	Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site	Binding Site
A	IPR045854	Nitrite and sulphite reductase 4Fe-4S domain-like superfamily	Homologous Superfamily
A	IPR036136	Nitrite/Sulfite reductase ferredoxin-like domain superfamily	Homologous Superfamily

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

Chains	Enzyme Name	Description	Catalytic Residues
A	nitrate reductase M-CSA #323	This chloroplastic, ferredoxin dependent nitrate reductase contains a siroheme with a distal cysteine ligand that also serves as a ligand of the iron sulfur ([4Fe-4S]) cluster. The physiological ferredoxin electron donor is reduced by the NADPH pool, produced via the reductive pentose phosphate cycle. The binding of ferredoxin is thought to induce large conformational changes within the enzyme, controlling the access of solvent to the active site and therefore the pKa associated with proximate, ionisable residues [PMID:7487061, PMID:14717606]. It is involved in the pathway nitrate reduction (assimilation), which is part of nitrogen metabolism.	Defined by 6 residues: ARG:A-155 [auth A-109]ARG:A-269 [auth A-223]LYS:A-270 [auth A-224]GLY:A-527 [auth A-481]CYS:A-532 [auth A-486]GLY:A-533 [auth A-487] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.7.7.1 (PDB Primary Data) Search M-CSA Motif + EC 1.7.7.1

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.