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P38501 (NIR_ALCFA) 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
Synonyms:nir
OrganismAlcaligenes faecalis
Taxonomic identifier511 [NCBI]
Taxonomic lineageBacteriaProteobacteriaBetaproteobacteriaBurkholderialesAlcaligenaceaeAlcaligenes

Protein attributes

Sequence length376 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.

Subcellular location

Periplasm.

Induction

Under anaerobic growth conditions and by nitrite.

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
   PTMPyrrolidone carboxylic acid
   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 – 3333Tat-type signal Ref.1
Chain34 – 376343Copper-containing nitrite reductase
PRO_0000002987

Regions

Domain34 – 211178Plastocyanin-like 1
Domain212 – 376165Plastocyanin-like 2

Sites

Metal binding1311Copper 1; type 1 Ref.2
Metal binding1361Copper 2; type 2
Metal binding1711Copper 2; type 2
Metal binding1721Copper 1; type 1
Metal binding1811Copper 1; type 1
Metal binding1861Copper 1; type 1
Metal binding3421Copper 2; type 2 Ref.2

Amino acid modifications

Modified residue341Pyrrolidone carboxylic acid

Experimental info

Mutagenesis1711H → K: Loses nitrite-reducing activity.
Mutagenesis1861M → E: Contains only a type II copper atom and fails to catalyze the reduction of nitrite.

Secondary structure

.......................................................... 376
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P38501 [UniParc].

Last modified October 1, 1994. Version 1.
Checksum: 0AD918988301BF29

FASTA37640,332
        10         20         30         40         50         60 
MAEQMQISRR TILAGAALAG ALAPVLATTS AWGQGAVRKA TAAEIAALPR QKVELVDPPF 

        70         80         90        100        110        120 
VHAHSQVAEG GPKVVEFTMV IEEKKIVIDD AGTEVHAMAF NGTVPGPLMV VHQDDYLELT 

       130        140        150        160        170        180 
LINPETNTLM HNIDFHAATG ALGGGGLTEI NPGEKTILRF KATKPGVFVY HCAPPGMVPW 

       190        200        210        220        230        240 
HVVSGMNGAI MVLPREGLHD GKGKALTYDK IYYVGEQDFY VPRDENGKYK KYEAPGDAYE 

       250        260        270        280        290        300 
DTVKVMRTLT PTHVVFNGAV GALTGDKAMT AAVGEKVLIV HSQANRDTRP HLIGGHGDYV 

       310        320        330        340        350        360 
WATGKFNTPP DVDQETWFIP GGAAGAAFYT FQQPGIYAYV NHNLIEAFEL GAAAHFKVTG 

       370 
EWNDDLMTSV LAPSGT 

« Hide

References

[1]"Cloning and characterization of a nitrite reductase gene from Alcaligenes faecalis and its expression in Escherichia coli."
Nishiyama M., Suzuki J., Kukimoto M., Ohnuki T., Horinouchi S., Beppu T.
J. Gen. Microbiol. 139:725-733(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 34-48 AND 192-240.
Strain: S-6.
[2]"X-ray structure and site-directed mutagenesis of a nitrite reductase from Alcaligenes faecalis S-6: roles of two copper atoms in nitrite reduction."
Kukimoto M., Nishiyama M., Murphy M.E.P., Turley S., Adman E.T., Horinouchi S., Beppu T.
Biochemistry 33:5246-5252(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS), MUTAGENESIS.
Strain: S-6.
[3]"Structure of Alcaligenes faecalis nitrite reductase and a copper site mutant, M150E, that contains zinc."
Murphy M.E., Turley S., Kukimoto M., Nishiyama M., Horinouchi S., Sasaki H., Tanokura M., Adman E.T.
Biochemistry 34:12107-12117(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
[4]"Structure of nitrite bound to copper-containing nitrite reductase from Alcaligenes faecalis. Mechanistic implications."
Murphy M.E., Turley S., Adman E.T.
J. Biol. Chem. 272:28455-28460(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
D13155 Genomic DNA. Translation: BAA02440.1.
PIRI39582.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1AQ8X-ray2.00A/B/C34-376[»]
1AS6X-ray1.80A/B/C34-376[»]
1AS7X-ray2.00A/B/C34-376[»]
1AS8X-ray1.85A/B/C34-376[»]
1ET5X-ray1.90A40-376[»]
1ET7X-ray1.70A40-376[»]
1ET8X-ray1.80A40-376[»]
1J9QX-ray1.65A/B/C40-376[»]
1J9RX-ray2.00A/B/C40-376[»]
1J9SX-ray1.90A/B/C40-376[»]
1J9TX-ray1.95A/B/C40-376[»]
1L9OX-ray1.70A/B/C40-376[»]
1L9PX-ray1.75A/B/C40-376[»]
1L9QX-ray1.70A/B/C40-376[»]
1L9RX-ray1.78A/B/C40-376[»]
1L9SX-ray1.78A/B/C40-376[»]
1L9TX-ray1.75A/B/C40-376[»]
1NPJX-ray1.90A/B/C34-376[»]
1NPNX-ray1.80A/B/C34-376[»]
1NTDX-ray2.30A34-376[»]
1SJMX-ray1.40A/B/C40-376[»]
1SNRX-ray1.31A/B/C40-376[»]
1ZDQX-ray1.80A/B/C40-375[»]
1ZDSX-ray1.55A/B/C40-375[»]
2AFNX-ray2.00A/B/C34-376[»]
2B08X-ray1.90A/B/C37-376[»]
2E86X-ray1.50A/B/C40-376[»]
2FJSX-ray1.85A/B/C40-376[»]
2P80NMR-A/B/C40-376[»]
2PP7X-ray1.65A/B/C40-376[»]
2PP8X-ray1.50A/B/C40-376[»]
2PP9X-ray1.80A/B/C40-376[»]
2PPAX-ray1.69A/B/C40-376[»]
2PPCX-ray1.58A/B/C40-376[»]
2PPDX-ray1.80A/B/C34-376[»]
2PPEX-ray1.75A/B/C34-376[»]
2PPFX-ray1.65A/B/C40-376[»]
3H4FX-ray2.10A/B/C40-375[»]
3H4HX-ray1.60A/B/C41-375[»]
3H56X-ray1.50A40-375[»]
ProteinModelPortalP38501.
SMRP38501. Positions 40-376.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Enzyme and pathway databases

SABIO-RKP38501.
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

EvolutionaryTraceP38501.

Entry information

Entry nameNIR_ALCFA
AccessionPrimary (citable) accession number: P38501
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: October 16, 2013
This is version 98 of the entry and version 1 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