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Q53176

- NAPA_RHOS4

UniProt

Q53176 - NAPA_RHOS4

Protein

Periplasmic nitrate reductase

Gene

napA

Organism
Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 114 (01 Oct 2014)
      Sequence version 2 (24 Jan 2006)
      Previous versions | rss
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    Functioni

    Catalytic subunit of the periplasmic nitrate reductase (NAP). Only expressed at high levels during aerobic growth. NapAB complex receives electrons from the membrane-anchored tetraheme protein NapC, thus allowing electron flow between membrane and periplasm. Essential function for nitrate assimilation and may have a role in anaerobic metabolism.

    Catalytic activityi

    Nitrite + acceptor = nitrate + reduced acceptor.UniRule annotation

    Cofactori

    Binds 1 4Fe-4S cluster.UniRule annotation
    Binds 1 molybdenum-bis(molybdopterin guanine dinucleotide) (Mo-bis-MGD) cofactor per subunit.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi48 – 481Iron-sulfur (4Fe-4S)UniRule annotation
    Metal bindingi51 – 511Iron-sulfur (4Fe-4S)UniRule annotation
    Metal bindingi55 – 551Iron-sulfur (4Fe-4S)UniRule annotation
    Metal bindingi83 – 831Iron-sulfur (4Fe-4S)UniRule annotation

    GO - Molecular functioni

    1. 4 iron, 4 sulfur cluster binding Source: UniProtKB-HAMAP
    2. electron carrier activity Source: UniProtKB-HAMAP
    3. iron ion binding Source: UniProtKB-HAMAP
    4. molybdenum ion binding Source: InterPro
    5. nitrate reductase activity Source: UniProtKB-HAMAP

    GO - Biological processi

    1. Mo-molybdopterin cofactor biosynthetic process Source: UniProtKB-HAMAP
    2. nitrate assimilation Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Electron transport, Nitrate assimilation, Transport

    Keywords - Ligandi

    4Fe-4S, Iron, Iron-sulfur, Metal-binding, Molybdenum

    Enzyme and pathway databases

    BioCyciRSPH272943:GJAS-4224-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Periplasmic nitrate reductaseUniRule annotation (EC:1.7.99.4UniRule annotation)
    Gene namesi
    Name:napAUniRule annotation
    Ordered Locus Names:RHOS4_40230
    ORF Names:RSP_4116
    Encoded oniPlasmid pRS241c1 Publication
    OrganismiRhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
    Taxonomic identifieri272943 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaeRhodobacter
    ProteomesiUP000002703: Plasmid pRS241c

    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 – 2929Tat-type signalUniRule annotationAdd
    BLAST
    Chaini30 – 831802Periplasmic nitrate reductasePRO_0000019171Add
    BLAST

    Post-translational modificationi

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

    Expressioni

    Inductioni

    Nitrate reductase activity can be induced by nitrate and not repressed by ammonium or oxygen.

    Interactioni

    Subunit structurei

    Interacts with NapB.1 PublicationUniRule annotation

    Protein-protein interaction databases

    IntActiQ53176. 1 interaction.
    STRINGi272943.RSP_4116.

    Structurei

    Secondary structure

    1
    831
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi42 – 476
    Beta strandi56 – 627
    Beta strandi65 – 717
    Turni76 – 783
    Helixi84 – 874
    Helixi88 – 914
    Beta strandi103 – 1053
    Beta strandi107 – 1093
    Helixi122 – 13918
    Helixi142 – 1443
    Beta strandi145 – 1495
    Helixi155 – 16612
    Beta strandi174 – 1763
    Helixi178 – 1814
    Helixi183 – 19311
    Helixi204 – 2074
    Beta strandi209 – 2157
    Helixi218 – 2214
    Helixi223 – 23513
    Beta strandi240 – 2489
    Helixi250 – 2534
    Beta strandi256 – 2605
    Turni263 – 2653
    Helixi266 – 27914
    Helixi285 – 2917
    Beta strandi292 – 2965
    Helixi310 – 3134
    Helixi329 – 3379
    Helixi341 – 3488
    Helixi352 – 36110
    Beta strandi369 – 3746
    Helixi375 – 3784
    Helixi383 – 39715
    Beta strandi405 – 4095
    Turni414 – 4196
    Helixi420 – 4234
    Turni431 – 4333
    Beta strandi434 – 4374
    Helixi439 – 44810
    Helixi464 – 4729
    Beta strandi478 – 4836
    Helixi486 – 4894
    Turni491 – 4977
    Helixi498 – 5025
    Beta strandi507 – 5148
    Helixi517 – 5204
    Beta strandi522 – 5287
    Helixi531 – 5333
    Beta strandi536 – 5394
    Beta strandi543 – 5486
    Helixi561 – 5699
    Helixi574 – 5774
    Helixi580 – 5856
    Beta strandi587 – 5915
    Turni594 – 5996
    Beta strandi601 – 6055
    Beta strandi607 – 6126
    Beta strandi614 – 6174
    Helixi619 – 6224
    Beta strandi623 – 6264
    Helixi628 – 63710
    Beta strandi640 – 6445
    Helixi652 – 6554
    Beta strandi659 – 6613
    Beta strandi670 – 6756
    Beta strandi692 – 6943
    Beta strandi697 – 7015
    Beta strandi713 – 7153
    Beta strandi717 – 7226
    Helixi734 – 7363
    Helixi738 – 7436
    Beta strandi748 – 7503
    Helixi753 – 7586
    Beta strandi766 – 7705
    Beta strandi775 – 78713
    Beta strandi792 – 7965
    Beta strandi800 – 8023
    Helixi804 – 8063
    Turni814 – 8163
    Beta strandi825 – 8295

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1OGYX-ray3.20A/C/E/G/I/K/M/O30-831[»]
    ProteinModelPortaliQ53176.
    SMRiQ53176. Positions 41-829.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ53176.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini41 – 97574Fe-4S Mo/W bis-MGD-typeUniRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the prokaryotic molybdopterin-containing oxidoreductase family. NasA/NapA/NarB subfamily.UniRule annotation
    Contains 1 4Fe-4S Mo/W bis-MGD-type domain.UniRule annotation

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiCOG0243.
    HOGENOMiHOG000031441.
    KOiK02567.
    OMAiHQLVEAP.
    OrthoDBiEOG6CVV7G.
    PhylomeDBiQ53176.

    Family and domain databases

    HAMAPiMF_01630. Nitrate_reduct.
    InterProiIPR009010. Asp_de-COase-like_dom.
    IPR006657. MoPterin_dinucl-bd_dom.
    IPR006656. Mopterin_OxRdtase.
    IPR006963. Mopterin_OxRdtase_4Fe-4S_dom.
    IPR027467. MopterinOxRdtase_cofactor_BS.
    IPR010051. Periplasm_NO3_reductase_lsu.
    IPR006311. TAT_signal.
    IPR019546. TAT_signal_bac_arc.
    [Graphical view]
    PfamiPF04879. Molybdop_Fe4S4. 1 hit.
    PF00384. Molybdopterin. 1 hit.
    PF01568. Molydop_binding. 1 hit.
    [Graphical view]
    SMARTiSM00926. Molybdop_Fe4S4. 1 hit.
    [Graphical view]
    SUPFAMiSSF50692. SSF50692. 1 hit.
    TIGRFAMsiTIGR01706. NAPA. 1 hit.
    TIGR01409. TAT_signal_seq. 1 hit.
    PROSITEiPS51669. 4FE4S_MOW_BIS_MGD. 1 hit.
    PS00551. MOLYBDOPTERIN_PROK_1. 1 hit.
    PS51318. TAT. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q53176-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTLTRRDLIK AQAAATAAAA AGLPVSALAQ PVTGGAEALR IRWSKAPCRF    50
    CGTGCGVMVG TRDGQVVATH GDTQAEVNRG LNCVKGYFLS KIMYGEDRLT 100
    TPLLRMKDGV YHKEGEFAPV SWDEAFDVMA AQAKRVLKEK GPKAVGMFGS 150
    GQWTIWEGYA ASKLMRAGFR SNNLDPNARH CMASAATAFM RTFGMDEPMG 200
    CYDDFEAADA FVLWGSNMAE MHPILWSRLT DRRLSHEHVR VAVLSTFTHR 250
    SMDLADTPII FRPGTDLAIL NYIAHHIIST GRVNRDFVDR HTNFALGATD 300
    IGYGLRPEHQ LQLAAKGAAD AGAMTPTDFE TFAALVSEYT LEKAAEISGV 350
    EPALLEELAE LYADPDRKVM SLWTMGFNQH VRGVWANHMV YNLHLLTGKI 400
    SEPGNSPFSL TGQPSACGTA REVGTFAHRL PADMVVTNPE HRAHAEEIWK 450
    LPAGLLPDWV GAHAVEQDRK LHDGEINFYW VQVNNNMQAA PNIDQETYPG 500
    YRNPENFIVV SDAYPTVTGR CADLVLPAAM WVEKEGAYGN AERRTHFWHQ 550
    LVEAPGEARS DLWQLMEFSK RFTTDEVWPE EILSAAPAYR GKTLFEVLFA 600
    NGSVDRFPAS DVNPDHANHE AALFGFYPQK GLFEEYAAFG RGHGHDLAPF 650
    DTYHEVRGLR WPVVEGEETR WRYREGFDPY VKPGEGLRFY GKPDGRAVIL 700
    GVPYEPPAES PDEEFGFWLV TGRVLEHWHS GSMTLRVPEL YKAFPGAVCF 750
    MHPEDARSRG LNRGSEVRVI SRRGEIRTRL ETRGRNRMPR GVVFVPWFDA 800
    SQLINKVTLD ANDPISRQTD FKKCAVKIEA V 831
    Length:831
    Mass (Da):92,637
    Last modified:January 24, 2006 - v2
    Checksum:i74B35640749CC906
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti135 – 1351R → L in CAA86827. (PubMed:8730872)Curated
    Sequence conflicti141 – 1411G → A(PubMed:8730872)Curated
    Sequence conflicti143 – 1431K → E(PubMed:8730872)Curated
    Sequence conflicti252 – 2521M → S in CAA86827. (PubMed:8730872)Curated
    Sequence conflicti255 – 2551A → S in CAA86827. (PubMed:8730872)Curated
    Sequence conflicti267 – 2671L → R in CAA86827. (PubMed:8730872)Curated
    Sequence conflicti369 – 3691V → W in CAA86827. (PubMed:8730872)Curated
    Sequence conflicti415 – 4151S → F in CAA86827. (PubMed:8730872)Curated
    Sequence conflicti521 – 5211C → A in CAA86827. (PubMed:8730872)Curated
    Sequence conflicti660 – 6601R → H in CAA86827. (PubMed:8730872)Curated
    Sequence conflicti737 – 7371V → W in CAA86827. (PubMed:8730872)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z46806 Genomic DNA. Translation: CAA86827.1.
    CP000146 Genomic DNA. Translation: ABA81591.1.
    RefSeqiYP_345332.1. NC_007489.1.

    Genome annotation databases

    EnsemblBacteriaiABA81591; ABA81591; RSP_4116.
    GeneIDi3711832.
    KEGGirsp:RSP_4116.
    PATRICi23149531. VBIRhoSph57909_0178.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z46806 Genomic DNA. Translation: CAA86827.1 .
    CP000146 Genomic DNA. Translation: ABA81591.1 .
    RefSeqi YP_345332.1. NC_007489.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1OGY X-ray 3.20 A/C/E/G/I/K/M/O 30-831 [» ]
    ProteinModelPortali Q53176.
    SMRi Q53176. Positions 41-829.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi Q53176. 1 interaction.
    STRINGi 272943.RSP_4116.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ABA81591 ; ABA81591 ; RSP_4116 .
    GeneIDi 3711832.
    KEGGi rsp:RSP_4116.
    PATRICi 23149531. VBIRhoSph57909_0178.

    Phylogenomic databases

    eggNOGi COG0243.
    HOGENOMi HOG000031441.
    KOi K02567.
    OMAi HQLVEAP.
    OrthoDBi EOG6CVV7G.
    PhylomeDBi Q53176.

    Enzyme and pathway databases

    BioCyci RSPH272943:GJAS-4224-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q53176.

    Family and domain databases

    HAMAPi MF_01630. Nitrate_reduct.
    InterProi IPR009010. Asp_de-COase-like_dom.
    IPR006657. MoPterin_dinucl-bd_dom.
    IPR006656. Mopterin_OxRdtase.
    IPR006963. Mopterin_OxRdtase_4Fe-4S_dom.
    IPR027467. MopterinOxRdtase_cofactor_BS.
    IPR010051. Periplasm_NO3_reductase_lsu.
    IPR006311. TAT_signal.
    IPR019546. TAT_signal_bac_arc.
    [Graphical view ]
    Pfami PF04879. Molybdop_Fe4S4. 1 hit.
    PF00384. Molybdopterin. 1 hit.
    PF01568. Molydop_binding. 1 hit.
    [Graphical view ]
    SMARTi SM00926. Molybdop_Fe4S4. 1 hit.
    [Graphical view ]
    SUPFAMi SSF50692. SSF50692. 1 hit.
    TIGRFAMsi TIGR01706. NAPA. 1 hit.
    TIGR01409. TAT_signal_seq. 1 hit.
    PROSITEi PS51669. 4FE4S_MOW_BIS_MGD. 1 hit.
    PS00551. MOLYBDOPTERIN_PROK_1. 1 hit.
    PS51318. TAT. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Isolation of periplasmic nitrate reductase genes from Rhodobacter sphaeroides DSM 158: structural and functional differences among prokaryotic nitrate reductases."
      Reyes F., Roldan M.D., Klipp W., Castillo F., Moreno-Vivian C.
      Mol. Microbiol. 19:1307-1318(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Complete sequence of plasmid C of Rhodobacter sphaeroides 2.4.1."
      Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T., Hammon N., Israni S., Pitluck S., Richardson P., Mackenzie C., Choudhary M., Larimer F., Hauser L.J., Land M., Donohue T.J., Kaplan S.
      Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158.
      Plasmid: pRS241c
    3. "Structural and redox plasticity in the heterodimeric periplasmic nitrate reductase."
      Arnoux P., Sabaty M., Alric J., Frangioni B., Guigliarelli B., Adriano J.-M., Pignol D.
      Nat. Struct. Biol. 10:928-934(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) IN COMPLEX WITH NAPB.

    Entry informationi

    Entry nameiNAPA_RHOS4
    AccessioniPrimary (citable) accession number: Q53176
    Secondary accession number(s): Q3IV43
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: January 24, 2006
    Last modified: October 1, 2014
    This is version 114 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, Plasmid, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3