2AKJ
Structure of spinach nitrite reductase
External Resource: 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 | NIR_SIR_ferr | 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: NIR_SIR_ferr | ECOD (1.6) |
A | NIR_SIR | 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: NIR_SIR | 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 |
---|---|---|---|---|---|
PF03460 | Nitrite/Sulfite reductase ferredoxin-like half domain (NIR_SIR_ferr) | Nitrite/Sulfite reductase ferredoxin-like half domain | - | Repeat | |
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
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR006067 | Nitrite/sulphite reductase 4Fe-4S domain | Domain | |
IPR005117 | Nitrite/Sulfite reductase ferredoxin-like domain | Domain | |
IPR051329 | Nitrite and Sulfite Reductase 4Fe-4S Domain-Containing Protein | Family | |
IPR006066 | Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site | Binding Site | |
IPR045854 | Nitrite and sulphite reductase 4Fe-4S domain-like superfamily | Homologous Superfamily | |
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 |
---|---|---|---|
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] | EC: 1.7.7.1 (PDB Primary Data) |