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Protein

Copper-containing nitrite reductase

Gene

nirK

Organism
Rhizobium sullae (Rhizobium hedysari)
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

Pathway:initrate 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 bindingi132 – 1321Copper 1; type 1By similarity
Metal bindingi137 – 1371Copper 2; type 2By similarity
Metal bindingi172 – 1721Copper 2; type 2By similarity
Metal bindingi173 – 1731Copper 1; type 1By similarity
Metal bindingi182 – 1821Copper 1; type 1By similarity
Metal bindingi187 – 1871Copper 1; type 1By similarity
Metal bindingi343 – 3431Copper 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

BioCyciRETL1328306-WGS:GSTH-4432-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
OrganismiRhizobium sullae (Rhizobium hedysari)
Taxonomic identifieri50338 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeRhizobium/Agrobacterium groupRhizobium

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3535Tat-type signalPROSITE-ProRule annotationAdd
BLAST
Chaini36 – 377342Copper-containing nitrite reductasePRO_0000002990Add
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

Structurei

3D structure databases

ProteinModelPortaliQ60214.
SMRiQ60214. Positions 42-377.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini99 – 19496Plastocyanin-like 1Add
BLAST
Domaini259 – 360102Plastocyanin-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

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.

Q60214-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTNTLQMTRR TMLTGAAVAG ALTPILTSGG GNASPTPVRK LSATEIAALP
60 70 80 90 100
RRKLDLVKPP FVHVHTQKAE GGPKVVEVTL TIEEKKLVID GKGTEVNAMT
110 120 130 140 150
FDGSVPGPLI VVHQDDYVEV TLVNPETNTL QHNIDFHSAT GALGGGALTV
160 170 180 190 200
VNPGESAVLR FKATKAGVFV YHCAPPGMVP WHVTSGMNGA IMVLPREGLT
210 220 230 240 250
DGHGKELVYD KVYYLGEQDF YIPRDEKGEF KKYDSPGEAY EDTVAVMRTL
260 270 280 290 300
TPTHIVFNGA VGALTGENAL TAAVGERVLI VHSQANRDTR PHLIGGHGEY
310 320 330 340 350
VWRTGKFVNV PDRDQETWFI PGPTRGAAYY TFEQPGIYAY VNHNLIEAFE
360 370
LGAAAHFKVT GDWNDDLMTT VRSPSGS
Length:377
Mass (Da):40,719
Last modified:November 1, 1996 - v1
Checksum:iC7AFEE9AE639E2F8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U65658 Genomic DNA. Translation: AAB05880.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U65658 Genomic DNA. Translation: AAB05880.1.

3D structure databases

ProteinModelPortaliQ60214.
SMRiQ60214. Positions 42-377.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayiUPA00652; UER00707.
BioCyciRETL1328306-WGS:GSTH-4432-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. "Characterization of the gene encoding nitrite reductase and the physiological consequences of its expression in the nondenitrifying Rhizobium 'hedysari' strain HCNT1."
    Toffanin A., Wu Q., Maskus M., Caselia S., Abruna H.D., Shapleigh J.P.
    Appl. Environ. Microbiol. 62:4019-4025(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: HCNT1.

Entry informationi

Entry nameiNIR_RHISU
AccessioniPrimary (citable) accession number: Q60214
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: January 7, 2015
This is version 79 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.