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P81186

- NAPA_DESDA

UniProt

P81186 - NAPA_DESDA

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Protein
Periplasmic nitrate reductase
Gene
napA, nap, Ddes_0616
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.UniRule annotation

Catalytic activityi

Nitrite + acceptor = nitrate + reduced acceptor.UniRule annotation

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
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

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 – 3232Tat-type signal1 Publication
Add
BLAST
Chaini33 – 755723Periplasmic nitrate reductaseUniRule annotation
PRO_0000019169Add
BLAST

Post-translational modificationi

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

Expressioni

Inductioni

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

Interactioni

Subunit structurei

Monomer.

Protein-protein interaction databases

STRINGi525146.Ddes_0616.

Structurei

Secondary structure

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.

Miscellaneous databases

EvolutionaryTraceiP81186.

Family & Domainsi

Domains and Repeats

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

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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

« 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: September 3, 2014
This is version 109 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

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

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