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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 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

Pathway: 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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi126 – 1261Copper 1; type 1By similarity
Metal bindingi131 – 1311Copper 2; type 2By similarity
Metal bindingi166 – 1661Copper 2; type 2By similarity
Metal bindingi167 – 1671Copper 1; type 1By similarity
Metal bindingi177 – 1771Copper 1; type 1By similarity
Metal bindingi182 – 1821Copper 1; type 1By similarity
Metal bindingi338 – 3381Copper 2; type 2By similarity

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

BioCyciRSPH349102:GHE1-2922-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:Rsph17025_1595
OrganismiRhodobacter sphaeroides (strain ATCC 17025 / ATH 2.4.3)
Taxonomic identifieri349102 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaeRhodobacter
ProteomesiUP000000234 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3131Tat-type signalPROSITE-ProRule annotationAdd
BLAST
Chaini32 – 374343Copper-containing nitrite reductasePRO_0000002992Add
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

STRINGi349102.Rsph17025_1595.

Structurei

Secondary structure

1
374
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi46 – 483Combined sources
Beta strandi65 – 673Combined sources
Beta strandi70 – 8516Combined sources
Beta strandi88 – 958Combined sources
Beta strandi98 – 1003Combined sources
Beta strandi103 – 1075Combined sources
Beta strandi111 – 1188Combined sources
Helixi136 – 1427Combined sources
Beta strandi149 – 1568Combined sources
Beta strandi161 – 1666Combined sources
Helixi173 – 1797Combined sources
Beta strandi183 – 1897Combined sources
Beta strandi205 – 21511Combined sources
Beta strandi223 – 2253Combined sources
Helixi231 – 24212Combined sources
Turni243 – 2453Combined sources
Beta strandi248 – 2525Combined sources
Turni256 – 2594Combined sources
Helixi261 – 2633Combined sources
Beta strandi265 – 2684Combined sources
Beta strandi272 – 28211Combined sources
Beta strandi286 – 2894Combined sources
Beta strandi293 – 2975Combined sources
Beta strandi307 – 3126Combined sources
Beta strandi319 – 3268Combined sources
Beta strandi331 – 3399Combined sources
Helixi340 – 3445Combined sources
Beta strandi349 – 3568Combined sources
Turni360 – 3623Combined sources
Beta strandi363 – 3719Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 44-372.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ53239.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini93 – 18997Plastocyanin-like 1Add
BLAST
Domaini254 – 355102Plastocyanin-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.

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti27 – 271E → Q in AAB05767 (PubMed:9023188).Curated
Sequence conflicti230 – 2301D → T in AAB05767 (PubMed:9023188).Curated
Sequence conflicti281 – 2811N → K in AAB05767 (PubMed:9023188).Curated
Sequence conflicti319 – 3191S → T in AAB05767 (PubMed:9023188).Curated
Sequence conflicti351 – 3511H → S in AAB05767 (PubMed:9023188).Curated
Sequence conflicti367 – 3682VA → WP in AAB05767 (PubMed:9023188).Curated

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.
YP_001167793.1. 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.
YP_001167793.1. NC_009428.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 44-372.
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

eggNOGiCOG2132.
HOGENOMiHOG000217143.
KOiK00368.
OMAiTNTMPHN.
OrthoDBiEOG66B40C.

Enzyme and pathway databases

UniPathwayiUPA00652; UER00707.
BioCyciRSPH349102:GHE1-2922-MONOMER.

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...

Publicationsi

« Hide 'large scale' publications
  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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 17025 / ATH 2.4.3.

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: May 27, 2015
This is version 105 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

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.