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P81186

- NAPA_DESDA

UniProt

P81186 - NAPA_DESDA

Protein

Periplasmic nitrate reductase

Gene

napA

Organism
Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 110 (01 Oct 2014)
      Sequence version 2 (30 May 2000)
      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.

    Cofactori

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

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi45 – 451Iron-sulfur (4Fe-4S)
    Metal bindingi48 – 481Iron-sulfur (4Fe-4S)
    Metal bindingi52 – 521Iron-sulfur (4Fe-4S)
    Metal bindingi79 – 791Iron-sulfur (4Fe-4S)

    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

    BioCyciDDES525146:GIWF-637-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Periplasmic nitrate reductase (EC:1.7.99.4)
    Gene namesi
    Name:napA
    Synonyms:nap
    Ordered Locus Names:Ddes_0616
    OrganismiDesulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949)
    Taxonomic identifieri525146 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
    ProteomesiUP000002598: Chromosome

    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 – 3232Tat-type signal1 PublicationAdd
    BLAST
    Chaini33 – 755723Periplasmic nitrate reductasePRO_0000019169Add
    BLAST

    Post-translational modificationi

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

    Expressioni

    Inductioni

    Nitrate reductase activity is induced by potassium and sodium and inhibited by magnesium and calcium.

    Interactioni

    Subunit structurei

    Monomer.

    Protein-protein interaction databases

    STRINGi525146.Ddes_0616.

    Structurei

    Secondary structure

    1
    755
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi38 – 447
    Beta strandi53 – 597
    Beta strandi62 – 687
    Turni73 – 764
    Helixi80 – 834
    Helixi86 – 894
    Beta strandi99 – 1035
    Beta strandi108 – 1103
    Helixi113 – 13119
    Helixi133 – 1353
    Beta strandi136 – 1405
    Helixi146 – 15813
    Beta strandi165 – 1673
    Helixi168 – 1703
    Turni171 – 1733
    Helixi174 – 18411
    Helixi193 – 1975
    Beta strandi200 – 2067
    Helixi209 – 2124
    Helixi214 – 22613
    Beta strandi231 – 2355
    Helixi241 – 2455
    Beta strandi247 – 2504
    Turni254 – 2563
    Helixi257 – 27014
    Helixi276 – 2827
    Beta strandi283 – 2864
    Helixi295 – 3028
    Helixi303 – 3053
    Helixi307 – 3148
    Helixi318 – 33013
    Beta strandi331 – 3388
    Turni340 – 3423
    Beta strandi343 – 3453
    Helixi348 – 36215
    Beta strandi370 – 3745
    Beta strandi378 – 3803
    Helixi381 – 3844
    Turni385 – 3895
    Turni396 – 3983
    Helixi404 – 41411
    Helixi429 – 43810
    Beta strandi443 – 4486
    Helixi451 – 4544
    Beta strandi455 – 4573
    Helixi458 – 4658
    Beta strandi471 – 4755
    Helixi482 – 4854
    Beta strandi488 – 4914
    Helixi496 – 4983
    Beta strandi501 – 5044
    Beta strandi508 – 5136
    Helixi526 – 53712
    Turni541 – 5444
    Helixi549 – 56012
    Helixi572 – 5776
    Beta strandi581 – 5833
    Turni599 – 6013
    Beta strandi610 – 6134
    Beta strandi623 – 6264
    Beta strandi639 – 6413
    Beta strandi643 – 6486
    Beta strandi657 – 6593
    Helixi660 – 6623
    Helixi664 – 6674
    Beta strandi675 – 6784
    Helixi679 – 6857
    Beta strandi692 – 6976
    Beta strandi700 – 71213
    Beta strandi716 – 7205
    Helixi728 – 7303
    Turni738 – 7403
    Beta strandi748 – 7547

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2JIMX-ray2.45A33-755[»]
    2JIOX-ray2.20A33-755[»]
    2JIPX-ray2.30A33-755[»]
    2JIQX-ray2.44A33-755[»]
    2JIRX-ray2.35A33-755[»]
    2NAPX-ray1.90A33-755[»]
    2V3VX-ray1.99A33-755[»]
    2V45X-ray2.40A33-755[»]
    ProteinModelPortaliP81186.
    SMRiP81186. Positions 35-755.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP81186.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini38 – 93564Fe-4S Mo/W bis-MGD-typeAdd
    BLAST

    Sequence similaritiesi

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiCOG0243.
    HOGENOMiHOG000031441.
    KOiK02567.
    OrthoDBiEOG6CVV7G.

    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.
    IPR010051. Periplasm_NO3_reductase_lsu.
    IPR006311. TAT_signal.
    [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.
    PROSITEiPS51669. 4FE4S_MOW_BIS_MGD. 1 hit.
    PS51318. TAT. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P81186-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSTSRRDFLK YFAMSAAVAA ASGAGFGSLA LAADNRPEKW VKGVCRYCGT    50
    GCGVLVGVKD GKAVAIQGDP NNHNAGLLCL KGSLLIPVLN SKERVTQPLV 100
    RRHKGGKLEP VSWDEALDLM ASRFRSSIDM YGPNSVAWYG SGQCLTEESY 150
    VANKIFKGGF GTNNVDGNPR LCMASAVGGY VTSFGKDEPM GTYADIDQAT 200
    CFFIIGSNTS EAHPVLFRRI ARRKQVEPGV KIIVADPRRT NTSRIADMHV 250
    AFRPGTDLAF MHSMAWVIIN EELDNPRFWQ RYVNFMDAEG KPSDFEGYKA 300
    FLENYRPEKV AEICRVPVEQ IYGAARAFAE SAATMSLWCM GINQRVQGVF 350
    ANNLIHNLHL ITGQICRPGA TSFSLTGQPN ACGGVRDGGA LSHLLPAGRA 400
    IPNAKHRAEM EKLWGLPEGR IAPEPGYHTV ALFEALGRGD VKCMIICETN 450
    PAHTLPNLNK VHKAMSHPES FIVCIEAFPD AVTLEYADLV LPPAFWCERD 500
    GVYGCGERRY SLTEKAVDPP GQCRPTVNTL VEFARRAGVD PQLVNFRNAE 550
    DVWNEWRMVS KGTTYDFWGM TRERLRKESG LIWPCPSEDH PGTSLRYVRG 600
    QDPCVPADHP DRFFFYGKPD GRAVIWMRPA KGAAEEPDAE YPLYLTSMRV 650
    IDHWHTATMT GKVPELQKAN PIAFVEINEE DAARTGIKHG DSVIVETRRD 700
    AMELPARVSD VCRPGLIAVP FFDPKKLVNK LFLDATDPVS REPEYKICAA 750
    RVRKA 755
    Length:755
    Mass (Da):83,497
    Last modified:May 30, 2000 - v2
    Checksum:iD54BDB9D1FE21DC2
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Y18045 Genomic DNA. Translation: CAA77019.1.
    AJ920046 Genomic DNA. Translation: CAI72603.1.
    CP001358 Genomic DNA. Translation: ACL48525.1.
    PIRiPC4422.
    RefSeqiWP_012624252.1. NC_011883.1.
    YP_002479203.1. NC_011883.1.

    Genome annotation databases

    EnsemblBacteriaiACL48525; ACL48525; Ddes_0616.
    GeneIDi7284288.
    KEGGidds:Ddes_0616.
    PATRICi21734702. VBIDesDes50650_0720.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Y18045 Genomic DNA. Translation: CAA77019.1 .
    AJ920046 Genomic DNA. Translation: CAI72603.1 .
    CP001358 Genomic DNA. Translation: ACL48525.1 .
    PIRi PC4422.
    RefSeqi WP_012624252.1. NC_011883.1.
    YP_002479203.1. NC_011883.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2JIM X-ray 2.45 A 33-755 [» ]
    2JIO X-ray 2.20 A 33-755 [» ]
    2JIP X-ray 2.30 A 33-755 [» ]
    2JIQ X-ray 2.44 A 33-755 [» ]
    2JIR X-ray 2.35 A 33-755 [» ]
    2NAP X-ray 1.90 A 33-755 [» ]
    2V3V X-ray 1.99 A 33-755 [» ]
    2V45 X-ray 2.40 A 33-755 [» ]
    ProteinModelPortali P81186.
    SMRi P81186. Positions 35-755.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 525146.Ddes_0616.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ACL48525 ; ACL48525 ; Ddes_0616 .
    GeneIDi 7284288.
    KEGGi dds:Ddes_0616.
    PATRICi 21734702. VBIDesDes50650_0720.

    Phylogenomic databases

    eggNOGi COG0243.
    HOGENOMi HOG000031441.
    KOi K02567.
    OrthoDBi EOG6CVV7G.

    Enzyme and pathway databases

    BioCyci DDES525146:GIWF-637-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P81186.

    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.
    IPR010051. Periplasm_NO3_reductase_lsu.
    IPR006311. TAT_signal.
    [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.
    PROSITEi PS51669. 4FE4S_MOW_BIS_MGD. 1 hit.
    PS51318. TAT. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Crystal structure of the first dissimilatory nitrate reductase at 1.9 A solved by MAD methods."
      Dias J.M., Than M.E., Humm A., Huber R., Bourenkov G.P., Bartunik H.D., Bursakov S., Calvete J.J., Caldeira J., Carneiro C., Moura J.J.G., Moura I., Romao M.J.
      Structure 7:65-79(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
    2. "Nitrate reduction by Desulfovibrio desulfuricans: a periplasmic nitrate reductase system that lacks NapB, but includes a unique tetraheme c-type cytochrome, NapM."
      Marietou A., Richardson D., Cole J., Mohan S.
      FEMS Microbiol. Lett. 248:217-225(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    3. "Complete sequence of Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774."
      US DOE Joint Genome Institute
      Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Lu M., Kiss H., Meineke L., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L.
      , Kyrpides N., Ovchinnikova G., Hazen T.C.
      Submitted (JAN-2009) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 27774 / DSM 6949.
    4. "Enzymatic properties and effect of ionic strength on periplasmic nitrate reductase (NAP) from Desulfovibrio desulfuricans ATCC 27774."
      Bursakov S.A., Carneiro C., Almendra M.J., Duarte R.O., Caldeira J., Moura I., Moura J.J.G.
      Biochem. Biophys. Res. Commun. 239:816-822(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 33-73.
    5. "Isolation and preliminary characterization of a soluble nitrate reductase from the sulfate-reducing bacterium Desulfovibrio desulfuricans 27774."
      Bursakov S., Liu M.-Y., Payne W.J., Legall J., Moura I., Moura J.J.G.
      Anaerobe 1:55-60(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.

    Entry informationi

    Entry nameiNAPA_DESDA
    AccessioniPrimary (citable) accession number: P81186
    Secondary accession number(s): B8IYC9, Q599G8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 15, 1998
    Last sequence update: May 30, 2000
    Last modified: October 1, 2014
    This is version 110 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, Direct protein sequencing, 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