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Protein

5'-deoxynucleotidase VP0926

Gene

VP0926

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

Functioni

Catalyzes the strictly specific dephosphorylation of 2'-deoxyribonucleoside 5'-monophosphates.UniRule annotation

Catalytic activityi

A 2'-deoxyribonucleoside 5'-monophosphate + H2O = a 2'-deoxyribonucleoside + phosphate.UniRule annotation

Cofactori

a divalent metal cationUniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei18 – 181Appears to be important in orienting the phosphate for catalysisUniRule annotation
Metal bindingi33 – 331Divalent metal cation; via tele nitrogenUniRule annotation
Binding sitei33 – 331SubstrateUniRule annotation
Metal bindingi68 – 681Divalent metal cation; via tele nitrogenUniRule annotation
Metal bindingi69 – 691Divalent metal cationUniRule annotation
Binding sitei69 – 691SubstrateUniRule annotation
Metal bindingi137 – 1371Divalent metal cationUniRule annotation
Binding sitei137 – 1371SubstrateUniRule annotation

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciVPAR223926:GHK4-968-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
5'-deoxynucleotidase VP0926UniRule annotation (EC:3.1.3.89UniRule annotation)
Alternative name(s):
5'-deoxyribonucleotidaseUniRule annotation
Nucleoside 5'-monophosphate phosphohydrolaseUniRule annotation
Gene namesi
Ordered Locus Names:VP0926
OrganismiVibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Taxonomic identifieri223926 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
Proteomesi
  • UP000002493 Componenti: Chromosome 1

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 1941945'-deoxynucleotidase VP0926PRO_0000095062Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi223926.VP0926.

Structurei

3D structure databases

ProteinModelPortaliQ87R72.
SMRiQ87R72. Positions 4-186.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni18 – 192Substrate bindingUniRule annotation
Regioni77 – 804Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the 5DNU family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105DK2. Bacteria.
COG1896. LUCA.
HOGENOMiHOG000276964.
KOiK08722.
OMAiMPTPIKY.
OrthoDBiEOG696C17.

Family and domain databases

Gene3Di1.10.3210.10. 1 hit.
HAMAPiMF_01100. 5DNU.
InterProiIPR003607. HD/PDEase_dom.
IPR006674. HD_domain.
IPR022971. YfbR.
[Graphical view]
PfamiPF13023. HD_3. 1 hit.
[Graphical view]
SMARTiSM00471. HDc. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q87R72-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKESHFFAHL ARMKLIQRWP LMRSVSPENV SEHSLQVAFV AHALALIKNK
60 70 80 90 100
KFGGTLNPER IALLAMYHDS SEVLTGDLPT PVKYYNPEIA KEYKKIEAAA
110 120 130 140 150
EHKLLSMLPE EFQEDFAPFL LSHSSHEEDS QIVKQADSIC AYLKCLEELS
160 170 180 190
AGNHEFALAK KRLDVTLQER KTPEMEYFLN TFAPSFELSL DEIS
Length:194
Mass (Da):22,153
Last modified:November 21, 2003 - v2
Checksum:i24BD02A15C12C9D7
GO

Sequence cautioni

The sequence BAC59189.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000031 Genomic DNA. Translation: BAC59189.1. Different initiation.
RefSeqiNP_797305.1. NC_004603.1.

Genome annotation databases

EnsemblBacteriaiBAC59189; BAC59189; BAC59189.
GeneIDi1188424.
KEGGivpa:VP0926.
PATRICi20140068. VBIVibPar50997_0878.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000031 Genomic DNA. Translation: BAC59189.1. Different initiation.
RefSeqiNP_797305.1. NC_004603.1.

3D structure databases

ProteinModelPortaliQ87R72.
SMRiQ87R72. Positions 4-186.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi223926.VP0926.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC59189; BAC59189; BAC59189.
GeneIDi1188424.
KEGGivpa:VP0926.
PATRICi20140068. VBIVibPar50997_0878.

Phylogenomic databases

eggNOGiENOG4105DK2. Bacteria.
COG1896. LUCA.
HOGENOMiHOG000276964.
KOiK08722.
OMAiMPTPIKY.
OrthoDBiEOG696C17.

Enzyme and pathway databases

BioCyciVPAR223926:GHK4-968-MONOMER.

Family and domain databases

Gene3Di1.10.3210.10. 1 hit.
HAMAPiMF_01100. 5DNU.
InterProiIPR003607. HD/PDEase_dom.
IPR006674. HD_domain.
IPR022971. YfbR.
[Graphical view]
PfamiPF13023. HD_3. 1 hit.
[Graphical view]
SMARTiSM00471. HDc. 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(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: RIMD 2210633.

Entry informationi

Entry namei5DNU_VIBPA
AccessioniPrimary (citable) accession number: Q87R72
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 21, 2003
Last sequence update: November 21, 2003
Last modified: July 6, 2016
This is version 71 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

Complete proteome, Reference proteome

Documents

  1. 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.