Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Copper-containing nitrite reductase

Gene

nirK

Organism
Rhodobacter sphaeroides (strain ATCC 17025 / ATH 2.4.3)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

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 Cu2+ ion. The Cu2+ 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: nitrate reduction (denitrification)

This protein is involved in step 2 of the subpathway that synthesizes dinitrogen from nitrate.
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. no protein annotated in this organism
  2. Copper-containing nitrite reductase (nirK)
  3. no protein annotated in this organism
  4. no protein annotated in this organism
This subpathway is part of the pathway nitrate reduction (denitrification), which is itself part of Nitrogen metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes dinitrogen from nitrate, the pathway nitrate reduction (denitrification) and in Nitrogen metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi126Copper 1; type 1By similarity1
Metal bindingi131Copper 2; type 2By similarity1
Metal bindingi166Copper 2; type 2By similarity1
Metal bindingi167Copper 1; type 1By similarity1
Metal bindingi177Copper 1; type 1By similarity1
Metal bindingi182Copper 1; type 1By similarity1
Metal bindingi338Copper 2; type 2By similarity1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Nitrate assimilation

Keywords - Ligandi

Copper, FAD, Flavoprotein, Metal-binding

Enzyme and pathway databases

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:Rsph17025_1595
OrganismiRhodobacter sphaeroides (strain ATCC 17025 / ATH 2.4.3)
Taxonomic identifieri349102 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaeRhodobacter
Proteomesi
  • UP000000234 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 31Tat-type signalPROSITE-ProRule annotationAdd BLAST31
ChainiPRO_000000299232 – 374Copper-containing nitrite reductaseAdd BLAST343

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

STRINGi349102.Rsph17025_1595.

Structurei

Secondary structure

1374
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi46 – 48Combined sources3
Beta strandi65 – 67Combined sources3
Beta strandi70 – 85Combined sources16
Beta strandi88 – 95Combined sources8
Beta strandi98 – 100Combined sources3
Beta strandi103 – 107Combined sources5
Beta strandi111 – 118Combined sources8
Helixi136 – 142Combined sources7
Beta strandi149 – 156Combined sources8
Beta strandi161 – 166Combined sources6
Helixi173 – 179Combined sources7
Beta strandi183 – 189Combined sources7
Beta strandi205 – 215Combined sources11
Beta strandi223 – 225Combined sources3
Helixi231 – 242Combined sources12
Turni243 – 245Combined sources3
Beta strandi248 – 252Combined sources5
Turni256 – 259Combined sources4
Helixi261 – 263Combined sources3
Beta strandi265 – 268Combined sources4
Beta strandi272 – 282Combined sources11
Beta strandi286 – 289Combined sources4
Beta strandi293 – 297Combined sources5
Beta strandi307 – 312Combined sources6
Beta strandi319 – 326Combined sources8
Beta strandi331 – 339Combined sources9
Helixi340 – 344Combined sources5
Beta strandi349 – 356Combined sources8
Turni360 – 362Combined sources3
Beta strandi363 – 371Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1MZYX-ray1.46A39-371[»]
1MZZX-ray2.00A/B/C39-371[»]
1N70X-ray1.60A41-374[»]
1ZV2X-ray1.74A44-371[»]
2A3TX-ray1.85A44-371[»]
2DWSX-ray1.85A44-371[»]
2DWTX-ray1.90A44-372[»]
2DY2X-ray2.26A44-372[»]
ProteinModelPortaliQ53239.
SMRiQ53239.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ53239.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini93 – 189Plastocyanin-like 1Add BLAST97
Domaini254 – 355Plastocyanin-like 2Add BLAST102

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

eggNOGiENOG4105CEI. Bacteria.
COG2132. LUCA.
HOGENOMiHOG000217143.
KOiK00368.
OMAiPLMVVHE.
OrthoDBiPOG091H0B7S.

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.

Q53239-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFTRRAALVG AAALASAPLV IRTAGAEEAP AQLASAAPVD LSNLPRVKHT
60 70 80 90 100
LVPPPFAHAH EQVAASGPVI NEFEMRIIEK EVQLDEDAYL QAMTFDGSIP
110 120 130 140 150
GPLMIVHEGD YVELTLINPP ENTMPHNIDF HAATGALGGG GLTLINPGEK
160 170 180 190 200
VVLRFKATRA GAFVYHCAPG GPMIPWHVVS GMAGCIMVLP RDGLKDHEGK
210 220 230 240 250
PVRYDTVYYI GESDHYIPKD EDGTYMRFSD PSEGYEDMVA VMDTLIPSHI
260 270 280 290 300
VFNGAVGALT GEGALKAKVG DNVLFVHSQP NRDSRPHLIG GHGDLVWETG
310 320 330 340 350
KFHNAPERDL ETWFIRGGSA GAALYKFLQP GVYAYVNHNL IEAVHKGATA
360 370
HVLVEGEWDN DLMEQVVAPV GLTG
Length:374
Mass (Da):40,232
Last modified:October 23, 2007 - v2
Checksum:iBD0FACA94A991F3B
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti27E → Q in AAB05767 (PubMed:9023188).Curated1
Sequence conflicti230D → T in AAB05767 (PubMed:9023188).Curated1
Sequence conflicti281N → K in AAB05767 (PubMed:9023188).Curated1
Sequence conflicti319S → T in AAB05767 (PubMed:9023188).Curated1
Sequence conflicti351H → S in AAB05767 (PubMed:9023188).Curated1
Sequence conflicti367 – 368VA → WP in AAB05767 (PubMed:9023188).Curated2

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U62291 Genomic DNA. Translation: AAB05767.1.
CP000661 Genomic DNA. Translation: ABP70488.1.
RefSeqiWP_011908617.1. NC_009428.1.

Genome annotation databases

EnsemblBacteriaiABP70488; ABP70488; Rsph17025_1595.
KEGGirsq:Rsph17025_1595.
PATRICi23161440. VBIRhoSph94549_1644.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U62291 Genomic DNA. Translation: AAB05767.1.
CP000661 Genomic DNA. Translation: ABP70488.1.
RefSeqiWP_011908617.1. NC_009428.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1MZYX-ray1.46A39-371[»]
1MZZX-ray2.00A/B/C39-371[»]
1N70X-ray1.60A41-374[»]
1ZV2X-ray1.74A44-371[»]
2A3TX-ray1.85A44-371[»]
2DWSX-ray1.85A44-371[»]
2DWTX-ray1.90A44-372[»]
2DY2X-ray2.26A44-372[»]
ProteinModelPortaliQ53239.
SMRiQ53239.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi349102.Rsph17025_1595.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABP70488; ABP70488; Rsph17025_1595.
KEGGirsq:Rsph17025_1595.
PATRICi23161440. VBIRhoSph94549_1644.

Phylogenomic databases

eggNOGiENOG4105CEI. Bacteria.
COG2132. LUCA.
HOGENOMiHOG000217143.
KOiK00368.
OMAiPLMVVHE.
OrthoDBiPOG091H0B7S.

Enzyme and pathway databases

UniPathwayiUPA00652; UER00707.

Miscellaneous databases

EvolutionaryTraceiQ53239.

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...

Entry informationi

Entry nameiNIR_RHOS5
AccessioniPrimary (citable) accession number: Q53239
Secondary accession number(s): A4WSX4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: October 23, 2007
Last modified: November 2, 2016
This is version 113 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

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 one 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.