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P25006 (NIR_ACHCY) Reviewed, UniProtKB/Swiss-Prot

Last modified October 16, 2013. Version 98. 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
OrganismAchromobacter cycloclastes
Taxonomic identifier223 [NCBI]
Taxonomic lineageBacteriaProteobacteriaBetaproteobacteriaBurkholderialesAlcaligenaceaeAchromobacter

Protein attributes

Sequence length378 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 Cu+ ion.

Binds 1 Cu2+ ion.

FAD.

Pathway

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

Subunit structure

Homotrimer.

Subcellular location

Periplasm.

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 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
Direct protein sequencing
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 – 3838Tat-type signal Ref.2
Chain39 – 378340Copper-containing nitrite reductase
PRO_0000002986

Regions

Domain39 – 213175Plastocyanin-like 1
Domain214 – 378165Plastocyanin-like 2

Sites

Metal binding1331Copper 1; type 1
Metal binding1381Copper 2; type 2
Metal binding1731Copper 2; type 2
Metal binding1741Copper 1; type 1
Metal binding1831Copper 1; type 1
Metal binding1881Copper 1; type 1
Metal binding3441Copper 2; type 2

Secondary structure

.............................................................. 378
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P25006 [UniParc].

Last modified November 1, 1997. Version 2.
Checksum: A70B52B814090EA5

FASTA37840,771
        10         20         30         40         50         60 
MTEQLQMTRR TMLAGAALAG AVAPLLHTAQ AHAAGAAAAA GAAPVDISTL PRVKVDLVKP 

        70         80         90        100        110        120 
PFVHAHDQVA KTGPRVVEFT MTIEEKKLVI DREGTEIHAM TFNGSVPGPL MVVHENDYVE 

       130        140        150        160        170        180 
LRLINPDTNT LLHNIDFHAA TGALGGGALT QVNPGEETTL RFKATKPGVF VYHCAPEGMV 

       190        200        210        220        230        240 
PWHVTSGMNG AIMVLPRDGL KDEKGQPLTY DKIYYVGEQD FYVPKDEAGN YKKYETPGEA 

       250        260        270        280        290        300 
YEDAVKAMRT LTPTHIVFNG AVGALTGDHA LTAAVGERVL VVHSQANRDT RPHLIGGHGD 

       310        320        330        340        350        360 
YVWATGKFRN PPDLDQETWL IPGGTAGAAF YTFRQPGVYA YVNHNLIEAF ELGAAGHFKV 

       370 
TGEWNDDLMT SVVKPASM 

« Hide

References

[1]"Cloning, characterization, and expression of the nitric oxide-generating nitrite reductase and of the blue copper protein genes of Achromobacter cycloclastes."
Chen J.-Y., Chang W.-C., Chang T., Chang W.-C., Liu M.-Y., Payne W.J., le Gall J.
Biochem. Biophys. Res. Commun. 219:423-428(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 21921 / IAM 1013.
[2]"Amino acid sequence of nitrite reductase: a copper protein from Achromobacter cycloclastes."
Fenderson F.F., Kumar S., Adman E.T., Liu M.-Y., Payne W.J., le Gall J.
Biochemistry 30:7180-7185(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 39-378.
Strain: ATCC 21921 / IAM 1013.
[3]"The 2.3-A X-ray structure of nitrite reductase from Achromobacter cycloclastes."
Godden J.W., Turley S., Teller D.C., Adman E.T., Liu M.-Y., Payne W.J., le Gall J.
Science 253:438-442(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
[4]"The structure of copper-nitrite reductase from Achromobacter cycloclastes at five pH values, with NO2-bound and with type II copper depleted."
Adman E.T., Godden J.W., Turley S.
J. Biol. Chem. 270:27458-27474(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
Z48635 Genomic DNA. Translation: CAA88564.1.
PIRJC4648.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1KCBX-ray1.65A39-378[»]
1NIAX-ray2.50A/B/C39-378[»]
1NIBX-ray2.70A/B/C39-378[»]
1NICX-ray1.90A39-378[»]
1NIDX-ray2.20A39-378[»]
1NIEX-ray1.90A39-378[»]
1NIFX-ray1.70A39-378[»]
1RZPX-ray1.90A/B/C39-373[»]
1RZQX-ray2.20A/B/C39-373[»]
2AVFX-ray2.60A/B/C/D/E/F39-367[»]
2BW4X-ray0.90A39-378[»]
2BW5X-ray1.12A39-378[»]
2BWDX-ray1.15A39-378[»]
2BWIX-ray1.10A39-378[»]
2NRDX-ray2.10A39-378[»]
2Y1AX-ray1.95A39-378[»]
ProteinModelPortalP25006.
SMRP25006. Positions 45-378.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Enzyme and pathway databases

SABIO-RKP25006.
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

EvolutionaryTraceP25006.

Entry information

Entry nameNIR_ACHCY
AccessionPrimary (citable) accession number: P25006
Entry history
Integrated into UniProtKB/Swiss-Prot: March 1, 1992
Last sequence update: November 1, 1997
Last modified: October 16, 2013
This is version 98 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