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 2AKJ | pdb_00002akj

Structure of spinach nitrite reductase

External Resource: Annotation


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

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Ad2akja1 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)
Ad2akja2 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)
Ad2akja3 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

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2 FamilyDuplicated SiR/NiR-like domains 1 and 3 8021095 4001354 SCOP2 (2022-06-29)
ASCOP2 FamilyDuplicated SiR/NiR-like domains 1 and 3 8021096 4001354 SCOP2 (2022-06-29)
ASCOP2 FamilyNitrite and sulphite reductase 4Fe-4S domain-like 8021100 4001988 SCOP2 (2022-06-29)
ASCOP2 FamilyNitrite and sulphite reductase 4Fe-4S domain-like 8021101 4001988 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyNitrite/Sulfite reductase N-terminal domain-like 8033475 3001366 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyNitrite/Sulfite reductase N-terminal domain-like 8033476 3001366 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyNitrite and sulphite reductase 4Fe-4S domain-like 8033480 3000646 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyNitrite and sulphite reductase 4Fe-4S domain-like 8033481 3000646 SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
ANIR_SIR_ferre2akjA1 A: a+b two layersX: Alpha-beta plaitsH: Sulfite reductase, domains 1 and 3T: Sulfite reductase, domains 1 and 3F: NIR_SIR_ferrECOD (v295.2)
ANIR_SIRe2akjA3 A: a+b three layersX: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4F: NIR_SIRECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A3.90.480.20 Alpha Beta Alpha-Beta Complex Sulfite Reductase Hemoprotein domain 2CATH (4.3.0)
A3.30.413.10 Alpha Beta 2-Layer Sandwich Sulfite Reductase Hemoprotein domain 1CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF03460Nitrite/Sulfite reductase ferredoxin-like half domain (NIR_SIR_ferr)Nitrite/Sulfite reductase ferredoxin-like half domain- Repeat
PF01077Nitrite 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

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Ferredoxin--nitrite reductase, chloroplast

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR006067Nitrite/sulphite reductase 4Fe-4S domainDomain
IPR005117Nitrite/Sulfite reductase ferredoxin-like domainDomain
IPR051329Nitrite and Sulfite Reductase 4Fe-4S Domain-Containing ProteinFamily
IPR006066Nitrite/sulphite reductase iron-sulphur/sirohaem-binding siteBinding Site
IPR045854Nitrite and sulphite reductase 4Fe-4S domain-like superfamilyHomologous Superfamily
IPR036136Nitrite/Sulfite reductase ferredoxin-like domain superfamilyHomologous Superfamily

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

ChainsEnzyme NameDescriptionCatalytic Residues
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]
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Explore in 3D: M-CSA Motif Definition
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EC: 1.7.7.1 (PDB Primary Data)