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Protein

Copper-containing nitrite reductase

Gene

nirK

Organism
Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Catalytic activityi

Nitric oxide + H2O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H+.

Cofactori

Protein has several cofactor binding sites:
  • Cu2+By similarityNote: Binds 1 Cu(2+) ion. The Cu(2+) ion is held by residues from each of 2 monomers of the trimer. Nitrite is bound to the Cu2+ ion site. Pseudoazurin is the physiological electron donor for the Cu-NIR in vitro.By similarity
  • Cu(+)By similarityNote: Binds 1 Cu(+) ion. The Cu(+) ion is bound within a single monomer.By similarity
  • FADBy similarity

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi131 – 1311Copper 1; type 1By similarity
Metal bindingi136 – 1361Copper 2; type 2By similarity
Metal bindingi171 – 1711Copper 2; type 2By similarity
Metal bindingi172 – 1721Copper 1; type 1By similarity
Metal bindingi181 – 1811Copper 1; type 1By similarity
Metal bindingi186 – 1861Copper 1; type 1By similarity
Metal bindingi342 – 3421Copper 2; type 2By similarity

GO - Molecular functioni

  1. copper ion binding Source: InterPro
  2. nitrite reductase (NO-forming) activity Source: UniProtKB-EC

GO - Biological processi

  1. denitrification pathway Source: UniProtKB-UniPathway
  2. nitrate assimilation Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Nitrate assimilation

Keywords - Ligandi

Copper, FAD, Flavoprotein, Metal-binding

Enzyme and pathway databases

BioCyciSMEL266834:GJF6-5689-MONOMER.
UniPathwayiUPA00652; UER00707.

Names & Taxonomyi

Protein namesi
Recommended name:
Copper-containing nitrite reductase (EC:1.7.2.1)
Alternative name(s):
Cu-NIR
Gene namesi
Name:nirK
Ordered Locus Names:RA0681
ORF Names:SMa1250
Encoded oniPlasmid pSymA (megaplasmid 1)0 Publication
OrganismiRhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)
Taxonomic identifieri266834 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeSinorhizobium/Ensifer groupSinorhizobium
ProteomesiUP000001976 Componenti: Plasmid pSymA

Subcellular locationi

Periplasm By similarity

GO - Cellular componenti

  1. periplasmic space Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3333Tat-type signalPROSITE-ProRule annotationAdd
BLAST
Chaini34 – 376343Copper-containing nitrite reductasePRO_0000002991Add
BLAST

Post-translational modificationi

Predicted to be exported by the Tat system. The position of the signal peptide cleavage has not been experimentally proven.

Interactioni

Subunit structurei

Homotrimer.By similarity

Protein-protein interaction databases

STRINGi266834.SMa1250.

Structurei

3D structure databases

SMRiQ92Z29. Positions 45-376.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini98 – 19396Plastocyanin-like 1Add
BLAST
Domaini258 – 359102Plastocyanin-like 2Add
BLAST

Domaini

The type I copper site in NIR plays a crucial role for electron transfer from pseudoazurin to the type II copper site of NIR, which comprises the catalytic center of NIR for the reduction of nitrite.

Sequence similaritiesi

Belongs to the multicopper oxidase family.Curated
Contains 2 plastocyanin-like domains.Curated

Keywords - Domaini

Repeat, Signal

Phylogenomic databases

eggNOGiCOG2132.
HOGENOMiHOG000217143.
KOiK00368.
OMAiTNTMPHN.
OrthoDBiEOG66B40C.

Family and domain databases

Gene3Di2.60.40.420. 2 hits.
InterProiIPR001117. Cu-oxidase.
IPR011707. Cu-oxidase_3.
IPR008972. Cupredoxin.
IPR001287. NO2-reductase_Cu.
IPR006311. TAT_signal.
[Graphical view]
PfamiPF00394. Cu-oxidase. 1 hit.
PF07732. Cu-oxidase_3. 1 hit.
[Graphical view]
PRINTSiPR00695. CUNO2RDTASE.
SUPFAMiSSF49503. SSF49503. 2 hits.
TIGRFAMsiTIGR02376. Cu_nitrite_red. 1 hit.
PROSITEiPS51318. TAT. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q92Z29-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSEQFQMTRR SMLAGAAIAG AVTPLIGAVS AHAEEAVAKT AHINVASLPR
60 70 80 90 100
VKVDLVKPPF VHAHTQKAEG GPKVVEFTLT IEEKKIVIDE QGTELHAMTF
110 120 130 140 150
NGSVPGPLMV VHQDDYVELT LINPDTNTLQ HNIDFHSATG ALGGGALTVV
160 170 180 190 200
NPGDTTVLRF KASKAGVFVY HCAPPGMVPW HVTSGMNGAI MVLPREGLTD
210 220 230 240 250
GKGNSITYDK VYYVGEQDFY VPRDANGKFK KYESVGEAYA DTLEVMRTLT
260 270 280 290 300
PSHIVFNGAV GALTGDSALK AAVGEKVLIV HSQANRDTRP HLIGGHGDYV
310 320 330 340 350
WATGKFRNAP DVDQETWFIP GGTAGAAFYT FEQPGIYAYV NHNLIEAFEL
360 370
GAAAHFAVTG DWNDDLMTSV RAPSGT
Length:376
Mass (Da):40,259
Last modified:November 30, 2001 - v1
Checksum:i9B7999273001DC63
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE006469 Genomic DNA. Translation: AAK65339.1.
PIRiA95347.
RefSeqiNP_435927.1. NC_003037.1.

Genome annotation databases

EnsemblBacteriaiAAK65339; AAK65339; SMa1250.
GeneIDi1235717.
KEGGisme:SMa1250.
PATRICi23627844. VBISinMel96828_0701.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE006469 Genomic DNA. Translation: AAK65339.1.
PIRiA95347.
RefSeqiNP_435927.1. NC_003037.1.

3D structure databases

SMRiQ92Z29. Positions 45-376.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi266834.SMa1250.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAK65339; AAK65339; SMa1250.
GeneIDi1235717.
KEGGisme:SMa1250.
PATRICi23627844. VBISinMel96828_0701.

Phylogenomic databases

eggNOGiCOG2132.
HOGENOMiHOG000217143.
KOiK00368.
OMAiTNTMPHN.
OrthoDBiEOG66B40C.

Enzyme and pathway databases

UniPathwayiUPA00652; UER00707.
BioCyciSMEL266834:GJF6-5689-MONOMER.

Family and domain databases

Gene3Di2.60.40.420. 2 hits.
InterProiIPR001117. Cu-oxidase.
IPR011707. Cu-oxidase_3.
IPR008972. Cupredoxin.
IPR001287. NO2-reductase_Cu.
IPR006311. TAT_signal.
[Graphical view]
PfamiPF00394. Cu-oxidase. 1 hit.
PF07732. Cu-oxidase_3. 1 hit.
[Graphical view]
PRINTSiPR00695. CUNO2RDTASE.
SUPFAMiSSF49503. SSF49503. 2 hits.
TIGRFAMsiTIGR02376. Cu_nitrite_red. 1 hit.
PROSITEiPS51318. TAT. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 1021.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 1021.

Entry informationi

Entry nameiNIRK_RHIME
AccessioniPrimary (citable) accession number: Q92Z29
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2003
Last sequence update: November 30, 2001
Last modified: March 31, 2015
This is version 91 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Plasmid, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.