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Protein

Periplasmic nitrate reductase

Gene

napA

Organism
Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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.2 Publications

Catalytic activityi

Nitrite + acceptor = nitrate + reduced acceptor.2 Publications

Cofactori

Protein has several cofactor binding sites:

Enzyme regulationi

Activated by potassium and sodium ions and inhibited by magnesium and calcium ions.1 Publication

Kineticsi

  1. KM=12 µM for nitrate (in the presence of NaCl)1 Publication
  2. KM=20 µM for nitrate1 Publication
  3. KM=32 µM for nitrate1 Publication

    pH dependencei

    Optimum pH is between 8 and 9.5.2 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi45 – 451Iron-sulfur (4Fe-4S)2 Publications
    Metal bindingi48 – 481Iron-sulfur (4Fe-4S)2 Publications
    Metal bindingi52 – 521Iron-sulfur (4Fe-4S)2 Publications
    Metal bindingi79 – 791Iron-sulfur (4Fe-4S)2 Publications
    Binding sitei81 – 811Molybdopterin guanine dinucleotide 12 Publications
    Binding sitei143 – 1431Molybdopterin guanine dinucleotide 22 Publications
    Binding sitei168 – 1681Molybdopterin guanine dinucleotide 22 Publications
    Binding sitei170 – 1701Substrate1 Publication
    Metal bindingi172 – 1721Molybdenum2 Publications
    Binding sitei172 – 1721Molybdopterin guanine dinucleotide 12 Publications
    Binding sitei340 – 3401Molybdopterin guanine dinucleotide 12 Publications
    Binding sitei344 – 3441Molybdopterin guanine dinucleotide 22 Publications
    Binding sitei618 – 6181Substrate1 Publication
    Binding sitei628 – 6281Substrate1 Publication
    Binding sitei650 – 6501Substrate; via amide nitrogen1 Publication
    Binding sitei721 – 7211Substrate; via amide nitrogen1 Publication
    Binding sitei729 – 7291Molybdopterin guanine dinucleotide 22 Publications
    Binding sitei746 – 7461Molybdopterin guanine dinucleotide 12 Publications

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    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:1.7.99.42 Publications)
    Gene namesi
    Name:napA
    Synonyms:nap
    Ordered Locus Names:Ddes_0616
    OrganismiDesulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949)
    Taxonomic identifieri525146 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
    Proteomesi
    • UP000002598 Componenti: Chromosome

    Subcellular locationi

    • Periplasm 1 Publication

    GO - Cellular componenti

    Complete GO annotation...

    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.

    Interactioni

    Subunit structurei

    Monomer.1 Publication

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

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    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

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni208 – 2114Molybdopterin guanine dinucleotide 1 binding2 Publications
    Regioni236 – 2383Molybdopterin guanine dinucleotide 1 binding2 Publications
    Regioni255 – 2573Molybdopterin guanine dinucleotide 1 binding2 Publications
    Regioni450 – 4545Molybdopterin guanine dinucleotide 2 binding2 Publications
    Regioni475 – 4773Molybdopterin guanine dinucleotide 2 binding2 Publications
    Regioni647 – 6493Molybdopterin guanine dinucleotide 2 binding2 Publications
    Regioni649 – 6557Molybdopterin guanine dinucleotide 1 binding2 Publications
    Regioni654 – 6585Molybdopterin guanine dinucleotide 2 binding2 Publications

    Sequence similaritiesi

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiENOG4107QIW. Bacteria.
    COG0243. LUCA.
    HOGENOMiHOG000031441.
    KOiK02567.
    OMAiMNMERRV.
    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

            10         20         30         40         50
    MSTSRRDFLK YFAMSAAVAA ASGAGFGSLA LAADNRPEKW VKGVCRYCGT
    60 70 80 90 100
    GCGVLVGVKD GKAVAIQGDP NNHNAGLLCL KGSLLIPVLN SKERVTQPLV
    110 120 130 140 150
    RRHKGGKLEP VSWDEALDLM ASRFRSSIDM YGPNSVAWYG SGQCLTEESY
    160 170 180 190 200
    VANKIFKGGF GTNNVDGNPR LCMASAVGGY VTSFGKDEPM GTYADIDQAT
    210 220 230 240 250
    CFFIIGSNTS EAHPVLFRRI ARRKQVEPGV KIIVADPRRT NTSRIADMHV
    260 270 280 290 300
    AFRPGTDLAF MHSMAWVIIN EELDNPRFWQ RYVNFMDAEG KPSDFEGYKA
    310 320 330 340 350
    FLENYRPEKV AEICRVPVEQ IYGAARAFAE SAATMSLWCM GINQRVQGVF
    360 370 380 390 400
    ANNLIHNLHL ITGQICRPGA TSFSLTGQPN ACGGVRDGGA LSHLLPAGRA
    410 420 430 440 450
    IPNAKHRAEM EKLWGLPEGR IAPEPGYHTV ALFEALGRGD VKCMIICETN
    460 470 480 490 500
    PAHTLPNLNK VHKAMSHPES FIVCIEAFPD AVTLEYADLV LPPAFWCERD
    510 520 530 540 550
    GVYGCGERRY SLTEKAVDPP GQCRPTVNTL VEFARRAGVD PQLVNFRNAE
    560 570 580 590 600
    DVWNEWRMVS KGTTYDFWGM TRERLRKESG LIWPCPSEDH PGTSLRYVRG
    610 620 630 640 650
    QDPCVPADHP DRFFFYGKPD GRAVIWMRPA KGAAEEPDAE YPLYLTSMRV
    660 670 680 690 700
    IDHWHTATMT GKVPELQKAN PIAFVEINEE DAARTGIKHG DSVIVETRRD
    710 720 730 740 750
    AMELPARVSD VCRPGLIAVP FFDPKKLVNK LFLDATDPVS REPEYKICAA

    RVRKA
    Length:755
    Mass (Da):83,497
    Last modified:May 30, 2000 - v2
    Checksum:iD54BDB9D1FE21DC2
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    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.

    Genome annotation databases

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

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    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.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    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...

    Protein-protein interaction databases

    STRINGi525146.Ddes_0616.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

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

    Phylogenomic databases

    eggNOGiENOG4107QIW. Bacteria.
    COG0243. LUCA.
    HOGENOMiHOG000031441.
    KOiK02567.
    OMAiMNMERRV.
    OrthoDBiEOG6CVV7G.

    Enzyme and pathway databases

    BioCyciDDES525146:GIWF-637-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiP81186.

    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]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    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) IN COMPLEX WITH IRON-SULFUR (4FE-4S); MOLYBDENUM ION AND MOLYBDOPTERIN, COFACTOR.
      Strain: ATCC 27774 / DSM 6949.
    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, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, COFACTOR.
      Strain: ATCC 27774 / DSM 6949.
    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: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBCELLULAR LOCATION, COFACTOR, SUBUNIT.
      Strain: ATCC 27774 / DSM 6949.
    6. "Periplasmic nitrate reductase revisited: a sulfur atom completes the sixth coordination of the catalytic molybdenum."
      Najmudin S., Gonzalez P.J., Trincao J., Coelho C., Mukhopadhyay A., Cerqueira N.M., Romao C.C., Moura I., Moura J.J., Brondino C.D., Romao M.J.
      J. Biol. Inorg. Chem. 13:737-753(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.99 ANGSTROMS) OF 33-755 IN COMPLEX WITH IRON-SULFUR (4FE-4S); MOLYBDENUM ION; MOLYBDOPTERIN AND SUBSTRATE, COFACTOR.

    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: January 20, 2016
    This is version 120 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

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.