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Protein

Copper-containing nitrite reductase

Gene

nirK

Organism
Alcaligenes xylosoxydans xylosoxydans (Achromobacter xylosoxidans)
Status
Reviewed-Annotation score: Annotation score: 4 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+Note: 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.
  • Cu(+)Note: Binds 1 Cu(+) ion. The Cu(+) ion is bound within a single monomer.
  • FAD

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi85 – 851Copper 1; type 1
Metal bindingi90 – 901Copper 2; type 2
Metal bindingi125 – 1251Copper 2; type 2
Metal bindingi126 – 1261Copper 1; type 1
Metal bindingi135 – 1351Copper 1; type 1
Metal bindingi140 – 1401Copper 1; type 1
Metal bindingi296 – 2961Copper 2; type 2

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

SABIO-RKP81445.
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
OrganismiAlcaligenes xylosoxydans xylosoxydans (Achromobacter xylosoxidans)
Taxonomic identifieri85698 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesAlcaligenaceaeAchromobacter

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
Chaini1 – 330330Copper-containing nitrite reductasePRO_0000085586Add
BLAST

Interactioni

Subunit structurei

Homotrimer.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1NDRX-ray3.00A/B/C1-329[»]
1NDSX-ray2.80A/B/C1-329[»]
ProteinModelPortaliP81445.
SMRiP81445. Positions 2-329.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP81445.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 165165Plastocyanin-like 1Add
BLAST
Domaini166 – 330165Plastocyanin-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

Family and domain databases

Gene3Di2.60.40.420. 2 hits.
InterProiIPR001117. Cu-oxidase.
IPR011707. Cu-oxidase_3.
IPR008972. Cupredoxin.
IPR001287. NO2-reductase_Cu.
[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.

Sequencei

Sequence statusi: Complete.

P81445-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
GLPRVAVDLV APPLVHPHSQ VAAGAPKVVQ FRMSIEEKKM VADDDGTTAQ
60 70 80 90 100
AMTFNGSVPG PTLVVHEGDY IELTLVNPAT NSMPHNVDFH AATGALGGAG
110 120 130 140 150
LTQVVPGQEA VLRFKADRSG TFVYHCAPAG MVPWHVVSGM NGALMVLPRD
160 170 180 190 200
GLRDAAGAAL AYDRVYTIGE SDLYVPKAAD GNYSDYPALA SAYADTVAVM
210 220 230 240 250
RTLTPSHAVF NGAVGALTGA NALTAAVGES VLIIHSQANR DSRPHLIGGH
260 270 280 290 300
GDWVWTTGKF ANPPQLNMET WFIPGGSAAA ALYTFKQPGT YAYLSHNLIE
310 320 330
AMELGAAAQA SVEGQWDDDL MTSVAAPGPA
Length:330
Mass (Da):34,413
Last modified:November 1, 1998 - v1
Checksum:iE2C38C3A2CEBFCE8
GO

Cross-referencesi

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1NDRX-ray3.00A/B/C1-329[»]
1NDSX-ray2.80A/B/C1-329[»]
ProteinModelPortaliP81445.
SMRiP81445. Positions 2-329.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayiUPA00652; UER00707.
SABIO-RKP81445.

Miscellaneous databases

EvolutionaryTraceiP81445.

Family and domain databases

Gene3Di2.60.40.420. 2 hits.
InterProiIPR001117. Cu-oxidase.
IPR011707. Cu-oxidase_3.
IPR008972. Cupredoxin.
IPR001287. NO2-reductase_Cu.
[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.
ProtoNetiSearch...

Publicationsi

  1. "Structures of a blue-copper nitrite reductase and its substrate-bound complex."
    Dodd F.E., Hasnain S.S., Abraham Z.H.L., Eady R.R., Smith B.E.
    Acta Crystallogr. D 53:406-418(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
    Strain: LMG 1865 / NCIMB 11015 / Iwasaki.
  2. "Purification and characterization of the dissimilatory nitrite reductase from Alcaligenes xylosoxidans subsp. xylosoxidans (N.C.I.M.B. 11015): evidence for the presence of both type 1 and type 2 copper centres."
    Abraham Z.H.L., Lowe D.J., Smith B.E.
    Biochem. J. 295:587-593(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
    Strain: LMG 1865 / NCIMB 11015 / Iwasaki.

Entry informationi

Entry nameiNIR_ALCXX
AccessioniPrimary (citable) accession number: P81445
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 11, 2002
Last sequence update: November 1, 1998
Last modified: January 7, 2015
This is version 74 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

3D-structure

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.