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Q53239 (NIR_RHOS5) Reviewed, UniProtKB/Swiss-Prot

Last modified November 13, 2013. Version 95. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Copper-containing nitrite reductase

EC=1.7.2.1
Alternative name(s):
Cu-NIR
Gene names
Name:nirK
Ordered Locus Names:Rsph17025_1595
OrganismRhodobacter sphaeroides (strain ATCC 17025 / ATH 2.4.3) [Complete proteome] [HAMAP]
Taxonomic identifier349102 [NCBI]
Taxonomic lineageBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaeRhodobacter

Protein attributes

Sequence length374 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Catalytic activity

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

Cofactor

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.

Binds 1 Cu+ ion. The Cu+ ion is bound within a single monomer By similarity.

FAD By similarity.

Pathway

Nitrogen metabolism; nitrate reduction (denitrification); dinitrogen from nitrate: step 2/4.

Subunit structure

Homotrimer By similarity.

Subcellular location

Periplasm By similarity.

Domain

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.

Post-translational modification

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

Sequence similarities

Belongs to the multicopper oxidase family.

Contains 2 plastocyanin-like domains.

Ontologies

Keywords
   Biological processNitrate assimilation
   Cellular componentPeriplasm
   DomainRepeat
Signal
   LigandCopper
FAD
Flavoprotein
Metal-binding
   Molecular functionOxidoreductase
   Technical term3D-structure
Complete proteome
Gene Ontology (GO)
   Biological_processdenitrification pathway

Inferred from electronic annotation. Source: UniProtKB-UniPathway

nitrate assimilation

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentperiplasmic space

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functioncopper ion binding

Inferred from electronic annotation. Source: InterPro

nitrite reductase (NO-forming) activity

Inferred from electronic annotation. Source: UniProtKB-EC

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 3131Tat-type signal Potential
Chain32 – 374343Copper-containing nitrite reductase
PRO_0000002992

Regions

Domain93 – 18997Plastocyanin-like 1
Domain254 – 355102Plastocyanin-like 2

Sites

Metal binding1261Copper 1; type 1 By similarity
Metal binding1311Copper 2; type 2 By similarity
Metal binding1661Copper 2; type 2 By similarity
Metal binding1671Copper 1; type 1 By similarity
Metal binding1771Copper 1; type 1 By similarity
Metal binding1821Copper 1; type 1 By similarity
Metal binding3381Copper 2; type 2 By similarity

Experimental info

Sequence conflict271E → Q in AAB05767. Ref.1
Sequence conflict2301D → T in AAB05767. Ref.1
Sequence conflict2811N → K in AAB05767. Ref.1
Sequence conflict3191S → T in AAB05767. Ref.1
Sequence conflict3511H → S in AAB05767. Ref.1
Sequence conflict367 – 3682VA → WP in AAB05767. Ref.1

Secondary structure

.......................................................... 374
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q53239 [UniParc].

Last modified October 23, 2007. Version 2.
Checksum: BD0FACA94A991F3B

FASTA37440,232
        10         20         30         40         50         60 
MFTRRAALVG AAALASAPLV IRTAGAEEAP AQLASAAPVD LSNLPRVKHT LVPPPFAHAH 

        70         80         90        100        110        120 
EQVAASGPVI NEFEMRIIEK EVQLDEDAYL QAMTFDGSIP GPLMIVHEGD YVELTLINPP 

       130        140        150        160        170        180 
ENTMPHNIDF HAATGALGGG GLTLINPGEK VVLRFKATRA GAFVYHCAPG GPMIPWHVVS 

       190        200        210        220        230        240 
GMAGCIMVLP RDGLKDHEGK PVRYDTVYYI GESDHYIPKD EDGTYMRFSD PSEGYEDMVA 

       250        260        270        280        290        300 
VMDTLIPSHI VFNGAVGALT GEGALKAKVG DNVLFVHSQP NRDSRPHLIG GHGDLVWETG 

       310        320        330        340        350        360 
KFHNAPERDL ETWFIRGGSA GAALYKFLQP GVYAYVNHNL IEAVHKGATA HVLVEGEWDN 

       370 
DLMEQVVAPV GLTG 

« Hide

References

« Hide 'large scale' references
[1]"Characterization and regulation of the gene encoding nitrite reductase in Rhodobacter sphaeroides 2.4.3."
Tosques I.E., Kwiatkowski A.V., Shi J., Shapleigh J.P.
J. Bacteriol. 179:1090-1095(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Complete sequence of chromosome of Rhodobacter sphaeroides ATCC 17025."
US DOE Joint Genome Institute
Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Chertkov O., Brettin T., Bruce D., Han C., Schmutz J., Larimer F., Land M. expand/collapse author list , Hauser L., Kyrpides N., Kim E., Richardson P., Mackenzie C., Choudhary M., Donohue T.J., Kaplan S.
Submitted (APR-2007) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 17025 / ATH 2.4.3.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U62291 Genomic DNA. Translation: AAB05767.1.
CP000661 Genomic DNA. Translation: ABP70488.1.
RefSeqYP_001167793.1. NC_009428.1.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalQ53239.
SMRQ53239. Positions 44-372.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING349102.Rsph17025_1595.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaABP70488; ABP70488; Rsph17025_1595.
GeneID5082406.
KEGGrsq:Rsph17025_1595.
PATRIC23161440. VBIRhoSph94549_1644.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG2132.
HOGENOMHOG000217143.
KOK00368.
OMANIDFHSA.
OrthoDBEOG66B40C.
ProtClustDBCLSK891937.

Enzyme and pathway databases

BioCycRSPH349102:GHE1-2922-MONOMER.
UniPathwayUPA00652; UER00707.

Family and domain databases

Gene3D2.60.40.420. 2 hits.
InterProIPR001117. Cu-oxidase.
IPR011707. Cu-oxidase_3.
IPR008972. Cupredoxin.
IPR001287. NO2-reductase_Cu.
IPR006311. TAT_signal.
[Graphical view]
PfamPF00394. Cu-oxidase. 1 hit.
PF07732. Cu-oxidase_3. 1 hit.
[Graphical view]
PRINTSPR00695. CUNO2RDTASE.
SUPFAMSSF49503. SSF49503. 2 hits.
TIGRFAMsTIGR02376. Cu_nitrite_red. 1 hit.
PROSITEPS51318. TAT. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ53239.

Entry information

Entry nameNIR_RHOS5
AccessionPrimary (citable) accession number: Q53239
Secondary accession number(s): A4WSX4
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: October 23, 2007
Last modified: November 13, 2013
This is version 95 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways