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Protein

Periplasmic nitrate reductase

Gene

napA

Organism
Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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.UniRule annotation

Catalytic activityi

Nitrite + acceptor = nitrate + reduced acceptor.UniRule annotation

Cofactori

Protein has several cofactor binding sites:
  • [4Fe-4S] clusterUniRule annotationNote: Binds 1 [4Fe-4S] cluster.UniRule annotation
  • Mo-bis(molybdopterin guanine dinucleotide)UniRule annotationNote: Binds 1 molybdenum-bis(molybdopterin guanine dinucleotide) (Mo-bis-MGD) cofactor per subunit.UniRule annotation

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
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

BioCyciVPAR223926:GHK4-4439-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:VPA1199
OrganismiVibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Taxonomic identifieri223926 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
ProteomesiUP000002493 Componenti: Chromosome 2

Subcellular locationi

Periplasm UniRule annotation

GO - Cellular componenti

  1. periplasmic space Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3030Tat-type signalUniRule annotationAdd
BLAST
Chaini31 – 829799Periplasmic nitrate reductasePRO_0000046011Add
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

Interacts with NapB.UniRule annotation

Protein-protein interaction databases

STRINGi223926.VPA1199.

Structurei

3D structure databases

ProteinModelPortaliQ87GW6.
SMRiQ87GW6. Positions 41-827.
ModBaseiSearch...
MobiDBiSearch...

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.
OMAiKITWDKA.
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.
IPR027467. MopterinOxRdtase_cofactor_BS.
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.
TIGRFAMsiTIGR01706. NAPA. 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.

Q87GW6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKMTRRAFVK ANAAASAAAV AGITLPASAA NLIASSDQTK ITWDKAPCRF
60 70 80 90 100
CGTGCSVLVG TQNGKVVATQ GDPEAPVNKG LNCIKGYFLS KIMYGQDRLT
110 120 130 140 150
QPLLRMKDGK YHKDGEFTPV SWDVAFDTMA EKWKASLEKK GPTSVGMFGS
160 170 180 190 200
GQWTVMEGYA AAKMMKAGFR SNNIDPNARH CMASAVVGFM RAFGIDEPMG
210 220 230 240 250
CYDDFENADA FVLWGSNMAE MHPVLWTRIT DRRLSHPHVR VNVLSTYYHR
260 270 280 290 300
SFELADHGYI FNPQSDLAIA NFIANYIIEN DAVNWDFVNK HTNFTQADTD
310 320 330 340 350
IGYGLRDDDP LQKAAKNPNS GKLTSISFEE YKKSVAPYTV EKASEISGVE
360 370 380 390 400
KEKLIELAKQ YADPNTKVMS LWTMGMNQHT RGVWMNNLVY NIHLLTGKIA
410 420 430 440 450
TPGNSPFSLT GQPSACGTAR EVGTFAHRLP ADMVVANPKH RQIAEKIWKL
460 470 480 490 500
PEGTIPPKPG FHAVLQDRML NDGVLNCYWV QCNNNMQAGP NINTERLPGY
510 520 530 540 550
RNPENFIVVS DPYPTATAQA ADLILPTAMW IEKEGAYGNA ERRTQAWYQQ
560 570 580 590 600
VGTVGDAKSD LWQVMEFSKR FKMEEVWPEE LLAKAPQYRG KTMYDMLFKN
610 620 630 640 650
GQVDKFPLEE ARELNDDSHH FGFYVQKGLF EEYATFGRGH GHDLAPYDVY
660 670 680 690 700
HTVRGLRWPV VDGKETQWRF KEGSDPYAKA GSGWDFYGNA DGKAKIISAP
710 720 730 740 750
YEAPPEVPDS EFDLWLCTGR VLEHWHTGTM TRRVPELYKA VPDAVCYMHP
760 770 780 790 800
EDAKARNVRR GEEVVIANKR GEVRVRVETR GRNRPPKGLV FVPFFDARIL
810 820
INKLILDATD PLSKQTDFKK CPVKITKVA
Length:829
Mass (Da):92,961
Last modified:May 31, 2003 - v1
Checksum:i9E42579656BA0C13
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000032 Genomic DNA. Translation: BAC62542.1.
RefSeqiNP_800709.1. NC_004605.1.

Genome annotation databases

EnsemblBacteriaiBAC62542; BAC62542; BAC62542.
GeneIDi1191895.
KEGGivpa:VPA1199.
PATRICi20146797. VBIVibPar50997_4125.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000032 Genomic DNA. Translation: BAC62542.1.
RefSeqiNP_800709.1. NC_004605.1.

3D structure databases

ProteinModelPortaliQ87GW6.
SMRiQ87GW6. Positions 41-827.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi223926.VPA1199.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC62542; BAC62542; BAC62542.
GeneIDi1191895.
KEGGivpa:VPA1199.
PATRICi20146797. VBIVibPar50997_4125.

Phylogenomic databases

eggNOGiCOG0243.
HOGENOMiHOG000031441.
KOiK02567.
OMAiKITWDKA.
OrthoDBiEOG6CVV7G.

Enzyme and pathway databases

BioCyciVPAR223926:GHK4-4439-MONOMER.

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.
[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.
PROSITEiPS51669. 4FE4S_MOW_BIS_MGD. 1 hit.
PS00551. MOLYBDOPTERIN_PROK_1. 1 hit.
PS51318. TAT. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V. cholerae."
    Makino K., Oshima K., Kurokawa K., Yokoyama K., Uda T., Tagomori K., Iijima Y., Najima M., Nakano M., Yamashita A., Kubota Y., Kimura S., Yasunaga T., Honda T., Shinagawa H., Hattori M., Iida T.
    Lancet 361:743-749(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: RIMD 2210633.

Entry informationi

Entry nameiNAPA_VIBPA
AccessioniPrimary (citable) accession number: Q87GW6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 6, 2006
Last sequence update: May 31, 2003
Last modified: January 6, 2015
This is version 80 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.