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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)DescriptionActionsGraphical viewLength
    Metal bindingi45Iron-sulfur (4Fe-4S)2 Publications1
    Metal bindingi48Iron-sulfur (4Fe-4S)2 Publications1
    Metal bindingi52Iron-sulfur (4Fe-4S)2 Publications1
    Metal bindingi79Iron-sulfur (4Fe-4S)2 Publications1
    Binding sitei81Molybdopterin guanine dinucleotide 12 Publications1
    Binding sitei143Molybdopterin guanine dinucleotide 22 Publications1
    Binding sitei168Molybdopterin guanine dinucleotide 22 Publications1
    Binding sitei170Substrate1 Publication1
    Metal bindingi172Molybdenum2 Publications1
    Binding sitei172Molybdopterin guanine dinucleotide 12 Publications1
    Binding sitei340Molybdopterin guanine dinucleotide 12 Publications1
    Binding sitei344Molybdopterin guanine dinucleotide 22 Publications1
    Binding sitei618Substrate1 Publication1
    Binding sitei628Substrate1 Publication1
    Binding sitei650Substrate; via amide nitrogen1 Publication1
    Binding sitei721Substrate; via amide nitrogen1 Publication1
    Binding sitei729Molybdopterin guanine dinucleotide 22 Publications1
    Binding sitei746Molybdopterin guanine dinucleotide 12 Publications1

    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

    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)DescriptionActionsGraphical viewLength
    Signal peptidei1 – 32Tat-type signal1 PublicationAdd BLAST32
    ChainiPRO_000001916933 – 755Periplasmic nitrate reductaseAdd BLAST723

    Post-translational modificationi

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

    Proteomic databases

    PRIDEiP81186.

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Protein-protein interaction databases

    STRINGi525146.Ddes_0616.

    Structurei

    Secondary structure

    1755
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi38 – 44Combined sources7
    Beta strandi53 – 59Combined sources7
    Beta strandi62 – 68Combined sources7
    Turni73 – 76Combined sources4
    Helixi80 – 83Combined sources4
    Helixi86 – 89Combined sources4
    Beta strandi99 – 103Combined sources5
    Beta strandi108 – 110Combined sources3
    Helixi113 – 131Combined sources19
    Helixi133 – 135Combined sources3
    Beta strandi136 – 140Combined sources5
    Helixi146 – 158Combined sources13
    Beta strandi165 – 167Combined sources3
    Helixi168 – 170Combined sources3
    Turni171 – 173Combined sources3
    Helixi174 – 184Combined sources11
    Helixi193 – 197Combined sources5
    Beta strandi200 – 206Combined sources7
    Helixi209 – 212Combined sources4
    Helixi214 – 226Combined sources13
    Beta strandi231 – 235Combined sources5
    Helixi241 – 245Combined sources5
    Beta strandi247 – 250Combined sources4
    Turni254 – 256Combined sources3
    Helixi257 – 270Combined sources14
    Helixi276 – 282Combined sources7
    Beta strandi283 – 286Combined sources4
    Helixi295 – 302Combined sources8
    Helixi303 – 305Combined sources3
    Helixi307 – 314Combined sources8
    Helixi318 – 330Combined sources13
    Beta strandi331 – 338Combined sources8
    Turni340 – 342Combined sources3
    Beta strandi343 – 345Combined sources3
    Helixi348 – 362Combined sources15
    Beta strandi370 – 374Combined sources5
    Beta strandi378 – 380Combined sources3
    Helixi381 – 384Combined sources4
    Turni385 – 389Combined sources5
    Turni396 – 398Combined sources3
    Helixi404 – 414Combined sources11
    Helixi429 – 438Combined sources10
    Beta strandi443 – 448Combined sources6
    Helixi451 – 454Combined sources4
    Beta strandi455 – 457Combined sources3
    Helixi458 – 465Combined sources8
    Beta strandi471 – 475Combined sources5
    Helixi482 – 485Combined sources4
    Beta strandi488 – 491Combined sources4
    Helixi496 – 498Combined sources3
    Beta strandi501 – 504Combined sources4
    Beta strandi508 – 513Combined sources6
    Helixi526 – 537Combined sources12
    Turni541 – 544Combined sources4
    Helixi549 – 560Combined sources12
    Helixi572 – 577Combined sources6
    Beta strandi581 – 583Combined sources3
    Turni599 – 601Combined sources3
    Beta strandi610 – 613Combined sources4
    Beta strandi623 – 626Combined sources4
    Beta strandi639 – 641Combined sources3
    Beta strandi643 – 648Combined sources6
    Beta strandi657 – 659Combined sources3
    Helixi660 – 662Combined sources3
    Helixi664 – 667Combined sources4
    Beta strandi675 – 678Combined sources4
    Helixi679 – 685Combined sources7
    Beta strandi692 – 697Combined sources6
    Beta strandi700 – 712Combined sources13
    Beta strandi716 – 720Combined sources5
    Helixi728 – 730Combined sources3
    Turni738 – 740Combined sources3
    Beta strandi748 – 754Combined sources7

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP81186.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini38 – 934Fe-4S Mo/W bis-MGD-typeAdd BLAST56

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni208 – 211Molybdopterin guanine dinucleotide 1 binding2 Publications4
    Regioni236 – 238Molybdopterin guanine dinucleotide 1 binding2 Publications3
    Regioni255 – 257Molybdopterin guanine dinucleotide 1 binding2 Publications3
    Regioni450 – 454Molybdopterin guanine dinucleotide 2 binding2 Publications5
    Regioni475 – 477Molybdopterin guanine dinucleotide 2 binding2 Publications3
    Regioni647 – 649Molybdopterin guanine dinucleotide 2 binding2 Publications3
    Regioni649 – 655Molybdopterin guanine dinucleotide 1 binding2 Publications7
    Regioni654 – 658Molybdopterin guanine dinucleotide 2 binding2 Publications5

    Sequence similaritiesi

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiENOG4107QIW. Bacteria.
    COG0243. LUCA.
    HOGENOMiHOG000031441.
    KOiK02567.
    OMAiMNMERRV.
    OrthoDBiPOG091H04T5.

    Family and domain databases

    HAMAPiMF_01630. Nitrate_reduct. 1 hit.
    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
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi525146.Ddes_0616.

    Proteomic databases

    PRIDEiP81186.

    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.
    OrthoDBiPOG091H04T5.

    Miscellaneous databases

    EvolutionaryTraceiP81186.

    Family and domain databases

    HAMAPiMF_01630. Nitrate_reduct. 1 hit.
    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...

    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: November 2, 2016
    This is version 123 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.