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P25006

- NIR_ACHCY

UniProt

P25006 - NIR_ACHCY

Protein

Copper-containing nitrite reductase

Gene

nirK

Organism
Achromobacter cycloclastes
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 99 (01 Oct 2014)
      Sequence version 2 (01 Nov 1997)
      Previous versions | rss
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    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

    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-SubCell

    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

    MTEQLQMTRR TMLAGAALAG AVAPLLHTAQ AHAAGAAAAA GAAPVDISTL    50
    PRVKVDLVKP PFVHAHDQVA KTGPRVVEFT MTIEEKKLVI DREGTEIHAM 100
    TFNGSVPGPL MVVHENDYVE LRLINPDTNT LLHNIDFHAA TGALGGGALT 150
    QVNPGEETTL RFKATKPGVF VYHCAPEGMV PWHVTSGMNG AIMVLPRDGL 200
    KDEKGQPLTY DKIYYVGEQD FYVPKDEAGN YKKYETPGEA YEDAVKAMRT 250
    LTPTHIVFNG AVGALTGDHA LTAAVGERVL VVHSQANRDT RPHLIGGHGD 300
    YVWATGKFRN PPDLDQETWL IPGGTAGAAF YTFRQPGVYA YVNHNLIEAF 350
    ELGAAGHFKV TGEWNDDLMT SVVKPASM 378
    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 1, 2014
    This is version 99 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