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P25006

- NIR_ACHCY

UniProt

P25006 - NIR_ACHCY

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Protein

Copper-containing nitrite reductase

Gene

nirK

Organism
Achromobacter cycloclastes
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Catalytic activityi

Nitric oxide + H2O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H+.

Cofactori

Binds 1 Cu+ ion.
Binds 1 Cu2+ ion.
FAD.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi133 – 1331Copper 1; type 1
Metal bindingi138 – 1381Copper 2; type 2
Metal bindingi173 – 1731Copper 2; type 2
Metal bindingi174 – 1741Copper 1; type 1
Metal bindingi183 – 1831Copper 1; type 1
Metal bindingi188 – 1881Copper 1; type 1
Metal bindingi344 – 3441Copper 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-RKP25006.
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
OrganismiAchromobacter cycloclastes
Taxonomic identifieri223 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesAlcaligenaceaeAchromobacter

Subcellular locationi

GO - Cellular componenti

  1. periplasmic space Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3838Tat-type signal1 PublicationPROSITE-ProRule annotationAdd
BLAST
Chaini39 – 378340Copper-containing nitrite reductasePRO_0000002986Add
BLAST

Post-translational modificationi

Predicted to be exported by the Tat system. The position of the signal peptide cleavage has been experimentally proven.

Interactioni

Subunit structurei

Homotrimer.

Structurei

Secondary structure

1
378
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi47 – 493
Beta strandi52 – 543
Beta strandi71 – 733
Beta strandi76 – 8914
Beta strandi96 – 1027
Beta strandi105 – 1073
Beta strandi110 – 1145
Beta strandi118 – 1258
Beta strandi135 – 1406
Helixi143 – 1497
Beta strandi156 – 1638
Beta strandi168 – 1736
Turni177 – 1793
Helixi180 – 1856
Beta strandi189 – 1957
Beta strandi211 – 22111
Beta strandi227 – 2293
Helixi237 – 24913
Beta strandi254 – 2585
Turni262 – 2654
Helixi267 – 2693
Beta strandi271 – 2744
Beta strandi278 – 28811
Beta strandi292 – 2954
Beta strandi299 – 3035
Beta strandi313 – 3175
Beta strandi325 – 3328
Beta strandi337 – 3459
Helixi346 – 3505
Beta strandi355 – 3628
Turni366 – 3683
Beta strandi369 – 3713

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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[»]
ProteinModelPortaliP25006.
SMRiP25006. Positions 45-378.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP25006.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini39 – 213175Plastocyanin-like 1Add
BLAST
Domaini214 – 378165Plastocyanin-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.

P25006-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MTEQLQMTRR TMLAGAALAG AVAPLLHTAQ AHAAGAAAAA GAAPVDISTL
60 70 80 90 100
PRVKVDLVKP PFVHAHDQVA KTGPRVVEFT MTIEEKKLVI DREGTEIHAM
110 120 130 140 150
TFNGSVPGPL MVVHENDYVE LRLINPDTNT LLHNIDFHAA TGALGGGALT
160 170 180 190 200
QVNPGEETTL RFKATKPGVF VYHCAPEGMV PWHVTSGMNG AIMVLPRDGL
210 220 230 240 250
KDEKGQPLTY DKIYYVGEQD FYVPKDEAGN YKKYETPGEA YEDAVKAMRT
260 270 280 290 300
LTPTHIVFNG AVGALTGDHA LTAAVGERVL VVHSQANRDT RPHLIGGHGD
310 320 330 340 350
YVWATGKFRN PPDLDQETWL IPGGTAGAAF YTFRQPGVYA YVNHNLIEAF
360 370
ELGAAGHFKV TGEWNDDLMT SVVKPASM
Length:378
Mass (Da):40,771
Last modified:November 1, 1997 - v2
Checksum:iA70B52B814090EA5
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
Z48635 Genomic DNA. Translation: CAA88564.1.
PIRiJC4648.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
Z48635 Genomic DNA. Translation: CAA88564.1 .
PIRi JC4648.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1KCB X-ray 1.65 A 39-378 [» ]
1NIA X-ray 2.50 A/B/C 39-378 [» ]
1NIB X-ray 2.70 A/B/C 39-378 [» ]
1NIC X-ray 1.90 A 39-378 [» ]
1NID X-ray 2.20 A 39-378 [» ]
1NIE X-ray 1.90 A 39-378 [» ]
1NIF X-ray 1.70 A 39-378 [» ]
1RZP X-ray 1.90 A/B/C 39-373 [» ]
1RZQ X-ray 2.20 A/B/C 39-373 [» ]
2AVF X-ray 2.60 A/B/C/D/E/F 39-367 [» ]
2BW4 X-ray 0.90 A 39-378 [» ]
2BW5 X-ray 1.12 A 39-378 [» ]
2BWD X-ray 1.15 A 39-378 [» ]
2BWI X-ray 1.10 A 39-378 [» ]
2NRD X-ray 2.10 A 39-378 [» ]
2Y1A X-ray 1.95 A 39-378 [» ]
ProteinModelPortali P25006.
SMRi P25006. Positions 45-378.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Enzyme and pathway databases

UniPathwayi UPA00652 ; UER00707 .
SABIO-RK P25006.

Miscellaneous databases

EvolutionaryTracei P25006.

Family and domain databases

Gene3Di 2.60.40.420. 2 hits.
InterProi IPR001117. Cu-oxidase.
IPR011707. Cu-oxidase_3.
IPR008972. Cupredoxin.
IPR001287. NO2-reductase_Cu.
IPR006311. TAT_signal.
[Graphical view ]
Pfami PF00394. Cu-oxidase. 1 hit.
PF07732. Cu-oxidase_3. 1 hit.
[Graphical view ]
PRINTSi PR00695. CUNO2RDTASE.
SUPFAMi SSF49503. SSF49503. 2 hits.
TIGRFAMsi TIGR02376. Cu_nitrite_red. 1 hit.
PROSITEi PS51318. TAT. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  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).

Entry informationi

Entry nameiNIR_ACHCY
AccessioniPrimary (citable) accession number: P25006
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 1992
Last sequence update: November 1, 1997
Last modified: October 29, 2014
This is version 100 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, Direct protein sequencing

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