1NIA | pdb_00001nia

THE STRUCTURE OF CU-NITRITE REDUCTASE FROM ACHROMOBACTER CYCLOCLASTES AT FIVE PH VALUES, WITH NITRITE BOUND AND WITH TYPE II CU DEPLETED

External Resource: Annotation


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

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Ad1niaa2 All beta proteins Cupredoxin-like Cupredoxins Multidomain cupredoxins Nitrite reductase, NIR, C-terminal domain (Achromobacter cycloclastes ) [TaxId: 223 ], SCOPe (2.08)
Ad1niaa1 All beta proteins Cupredoxin-like Cupredoxins Multidomain cupredoxins Nitrite reductase, NIR, N-terminal domain (Achromobacter cycloclastes ) [TaxId: 223 ], SCOPe (2.08)
Cd1niac2 All beta proteins Cupredoxin-like Cupredoxins Multidomain cupredoxins Nitrite reductase, NIR, C-terminal domain (Achromobacter cycloclastes ) [TaxId: 223 ], SCOPe (2.08)
Cd1niac1 All beta proteins Cupredoxin-like Cupredoxins Multidomain cupredoxins Nitrite reductase, NIR, N-terminal domain (Achromobacter cycloclastes ) [TaxId: 223 ], SCOPe (2.08)
Bd1niab2 All beta proteins Cupredoxin-like Cupredoxins Multidomain cupredoxins Nitrite reductase, NIR, C-terminal domain (Achromobacter cycloclastes ) [TaxId: 223 ], SCOPe (2.08)
Bd1niab1 All beta proteins Cupredoxin-like Cupredoxins Multidomain cupredoxins Nitrite reductase, NIR, N-terminal domain (Achromobacter cycloclastes ) [TaxId: 223 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyCupredoxins 8038727 3000886 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyCupredoxins 8038726 3000886 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyCupredoxins 8038727 3000886 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyCupredoxins 8038726 3000886 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyCupredoxins 8038726 3000886 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyCupredoxins 8038727 3000886 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
Ae1niaA1 A: Cloacin translocation domainX: Cloacin translocation domainH: Cloacin translocation domainT: Ldl_recept_bF:ECOD (20:10:01)
Ce1niaC1 A: Cloacin translocation domainX: Cloacin translocation domainH: Cloacin translocation domainT: Ldl_recept_bF:ECOD (20:10:01)
Be1niaB1 A: Cloacin translocation domainX: Cloacin translocation domainH: Cloacin translocation domainT: Ldl_recept_bF:ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A2.60.40.420 Mainly Beta Sandwich Immunoglobulin-like Cupredoxins - blue copper proteinsCATH (4.3.0)
C2.60.40.420 Mainly Beta Sandwich Immunoglobulin-like Cupredoxins - blue copper proteinsCATH (4.3.0)
B2.60.40.420 Mainly Beta Sandwich Immunoglobulin-like Cupredoxins - blue copper proteinsCATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B, C
NITRITE REDUCTASE

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, B, C
IPR006311Twin-arginine translocation pathway, signal sequenceConserved Site
A, B, C
IPR008972CupredoxinHomologous Superfamily
A, B, C
IPR001117Multicopper oxidase, second cupredoxin domainDomain
A, B, C
IPR045087Multicopper oxidaseFamily
A, B, C
IPR001287Nitrite reductase, copper-typeFamily
A, B, C
IPR011707Multicopper oxidase-like, N-terminalDomain

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

ChainsEnzyme NameDescriptionCatalytic Residues
A, B
nitrite reductase (copper type)  M-CSA #4

This family of enzymes is found in both denitrifying bacteria and fungi which reside in soil and aquatic ecosystems.

Denitrification, the reduction of dissolved nitrate and nitrite to gaseous NO, N20 and N2 is an important process in the recycling of nitrogen in the biosphere, and is a key step in the nitrogen cycle resulting in the loss of terrestrial nitrogen to the atmosphere.

It is chiefly carried out by denitrifying bacteria, which contain nitrate and nitrite reductases. The copper-containing family of enzymes is found in both denitrifying bacteria and fungi which reside in soil and aquatic ecosystems and uses copper ions as cofactors rather than the more common haem cd1

The enzymes in question catalyse the reduction of nitrite (NO2-) to NO + H2O. They contain two copper centres, a Type I centre which receives electrons from pseudoazurin (a copper containing protein), and a type II centre which is the site of nitrite reduction.

Defined by 11 residues: HIS:A-95ASP:A-98HIS:A-100HIS:A-135CYS:A-136HIS:A-145MET:A-150HIS:B-255GLU:B-279THR:B-280HIS:B-306
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Explore in 3D: M-CSA Motif Definition
Up to 10 residues are supported for Structure Motif searching, this motif has 11 residues.
EC: 1.7.99.3 (PDB Primary Data)
EC: 1.7.2.1 (UniProt)