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Q53239

- NIR_RHOS5

UniProt

Q53239 - NIR_RHOS5

Protein

Copper-containing nitrite reductase

Gene

nirK

Organism
Rhodobacter sphaeroides (strain ATCC 17025 / ATH 2.4.3)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 97 (01 Oct 2014)
      Sequence version 2 (23 Oct 2007)
      Previous versions | rss
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    Functioni

    Catalytic activityi

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

    Cofactori

    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.By similarity
    Binds 1 Cu+ ion. The Cu+ ion is bound within a single monomer By similarity.By similarity
    FAD.By similarity

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi126 – 1261Copper 1; type 1By similarity
    Metal bindingi131 – 1311Copper 2; type 2By similarity
    Metal bindingi166 – 1661Copper 2; type 2By similarity
    Metal bindingi167 – 1671Copper 1; type 1By similarity
    Metal bindingi177 – 1771Copper 1; type 1By similarity
    Metal bindingi182 – 1821Copper 1; type 1By similarity
    Metal bindingi338 – 3381Copper 2; type 2By similarity

    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

    BioCyciRSPH349102:GHE1-2922-MONOMER.
    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
    Ordered Locus Names:Rsph17025_1595
    OrganismiRhodobacter sphaeroides (strain ATCC 17025 / ATH 2.4.3)
    Taxonomic identifieri349102 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaeRhodobacter
    ProteomesiUP000000234: Chromosome

    Subcellular locationi

    Periplasm By similarity

    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 – 3131Tat-type signalPROSITE-ProRule annotationAdd
    BLAST
    Chaini32 – 374343Copper-containing nitrite reductasePRO_0000002992Add
    BLAST

    Post-translational modificationi

    Predicted to be exported by the Tat system. The position of the signal peptide cleavage has not been experimentally proven.

    Interactioni

    Subunit structurei

    Homotrimer.By similarity

    Protein-protein interaction databases

    STRINGi349102.Rsph17025_1595.

    Structurei

    Secondary structure

    1
    374
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi46 – 483
    Beta strandi65 – 673
    Beta strandi70 – 8516
    Beta strandi88 – 958
    Beta strandi98 – 1003
    Beta strandi103 – 1075
    Beta strandi111 – 1188
    Helixi136 – 1427
    Beta strandi149 – 1568
    Beta strandi161 – 1666
    Helixi173 – 1797
    Beta strandi183 – 1897
    Beta strandi205 – 21511
    Beta strandi223 – 2253
    Helixi231 – 24212
    Turni243 – 2453
    Beta strandi248 – 2525
    Turni256 – 2594
    Helixi261 – 2633
    Beta strandi265 – 2684
    Beta strandi272 – 28211
    Beta strandi286 – 2894
    Beta strandi293 – 2975
    Beta strandi307 – 3126
    Beta strandi319 – 3268
    Beta strandi331 – 3399
    Helixi340 – 3445
    Beta strandi349 – 3568
    Turni360 – 3623
    Beta strandi363 – 3719

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1MZYX-ray1.46A39-371[»]
    1MZZX-ray2.00A/B/C39-371[»]
    1N70X-ray1.60A41-374[»]
    1ZV2X-ray1.74A44-371[»]
    2A3TX-ray1.85A44-371[»]
    2DWSX-ray1.85A44-371[»]
    2DWTX-ray1.90A44-372[»]
    2DY2X-ray2.26A44-372[»]
    ProteinModelPortaliQ53239.
    SMRiQ53239. Positions 44-372.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ53239.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini93 – 18997Plastocyanin-like 1Add
    BLAST
    Domaini254 – 355102Plastocyanin-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

    Phylogenomic databases

    eggNOGiCOG2132.
    HOGENOMiHOG000217143.
    KOiK00368.
    OMAiNIDFHSA.
    OrthoDBiEOG66B40C.

    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.

    Q53239-1 [UniParc]FASTAAdd to Basket

    « Hide

    MFTRRAALVG AAALASAPLV IRTAGAEEAP AQLASAAPVD LSNLPRVKHT    50
    LVPPPFAHAH EQVAASGPVI NEFEMRIIEK EVQLDEDAYL QAMTFDGSIP 100
    GPLMIVHEGD YVELTLINPP ENTMPHNIDF HAATGALGGG GLTLINPGEK 150
    VVLRFKATRA GAFVYHCAPG GPMIPWHVVS GMAGCIMVLP RDGLKDHEGK 200
    PVRYDTVYYI GESDHYIPKD EDGTYMRFSD PSEGYEDMVA VMDTLIPSHI 250
    VFNGAVGALT GEGALKAKVG DNVLFVHSQP NRDSRPHLIG GHGDLVWETG 300
    KFHNAPERDL ETWFIRGGSA GAALYKFLQP GVYAYVNHNL IEAVHKGATA 350
    HVLVEGEWDN DLMEQVVAPV GLTG 374
    Length:374
    Mass (Da):40,232
    Last modified:October 23, 2007 - v2
    Checksum:iBD0FACA94A991F3B
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti27 – 271E → Q in AAB05767. (PubMed:9023188)Curated
    Sequence conflicti230 – 2301D → T in AAB05767. (PubMed:9023188)Curated
    Sequence conflicti281 – 2811N → K in AAB05767. (PubMed:9023188)Curated
    Sequence conflicti319 – 3191S → T in AAB05767. (PubMed:9023188)Curated
    Sequence conflicti351 – 3511H → S in AAB05767. (PubMed:9023188)Curated
    Sequence conflicti367 – 3682VA → WP in AAB05767. (PubMed:9023188)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U62291 Genomic DNA. Translation: AAB05767.1.
    CP000661 Genomic DNA. Translation: ABP70488.1.
    RefSeqiYP_001167793.1. NC_009428.1.

    Genome annotation databases

    EnsemblBacteriaiABP70488; ABP70488; Rsph17025_1595.
    GeneIDi5082406.
    KEGGirsq:Rsph17025_1595.
    PATRICi23161440. VBIRhoSph94549_1644.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U62291 Genomic DNA. Translation: AAB05767.1 .
    CP000661 Genomic DNA. Translation: ABP70488.1 .
    RefSeqi YP_001167793.1. NC_009428.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1MZY X-ray 1.46 A 39-371 [» ]
    1MZZ X-ray 2.00 A/B/C 39-371 [» ]
    1N70 X-ray 1.60 A 41-374 [» ]
    1ZV2 X-ray 1.74 A 44-371 [» ]
    2A3T X-ray 1.85 A 44-371 [» ]
    2DWS X-ray 1.85 A 44-371 [» ]
    2DWT X-ray 1.90 A 44-372 [» ]
    2DY2 X-ray 2.26 A 44-372 [» ]
    ProteinModelPortali Q53239.
    SMRi Q53239. Positions 44-372.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 349102.Rsph17025_1595.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ABP70488 ; ABP70488 ; Rsph17025_1595 .
    GeneIDi 5082406.
    KEGGi rsq:Rsph17025_1595.
    PATRICi 23161440. VBIRhoSph94549_1644.

    Phylogenomic databases

    eggNOGi COG2132.
    HOGENOMi HOG000217143.
    KOi K00368.
    OMAi NIDFHSA.
    OrthoDBi EOG66B40C.

    Enzyme and pathway databases

    UniPathwayi UPA00652 ; UER00707 .
    BioCyci RSPH349102:GHE1-2922-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q53239.

    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. "Characterization and regulation of the gene encoding nitrite reductase in Rhodobacter sphaeroides 2.4.3."
      Tosques I.E., Kwiatkowski A.V., Shi J., Shapleigh J.P.
      J. Bacteriol. 179:1090-1095(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 17025 / ATH 2.4.3.

    Entry informationi

    Entry nameiNIR_RHOS5
    AccessioniPrimary (citable) accession number: Q53239
    Secondary accession number(s): A4WSX4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: October 23, 2007
    Last modified: October 1, 2014
    This is version 97 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, Complete proteome

    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