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P81186

- NAPA_DESDA

UniProt

P81186 - NAPA_DESDA

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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

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

Protein has several cofactor binding sites:

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
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:1.7.99.4)
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-HAMAP
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.

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 – 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

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

        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.
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
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

« 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).
  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: November 26, 2014
This is version 112 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