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Protein

5'-deoxynucleotidase YfbR

Gene

yfbR

Organism
Salmonella enteritidis PT4 (strain P125109)
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

BioCyciSENT550537:GJFI-2343-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
5'-deoxynucleotidase YfbRUniRule annotation (EC:3.1.3.89UniRule annotation)
Alternative name(s):
5'-deoxyribonucleotidaseUniRule annotation
Nucleoside 5'-monophosphate phosphohydrolaseUniRule annotation
Gene namesi
Name:yfbRUniRule annotation
Ordered Locus Names:SEN2314
OrganismiSalmonella enteritidis PT4 (strain P125109)
Taxonomic identifieri550537 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella

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 – 1991995'-deoxynucleotidase YfbRPRO_1000136973Add
BLAST

Proteomic databases

PRIDEiB5R313.

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Structurei

3D structure databases

ProteinModelPortaliB5R313.
SMRiB5R313. Positions 2-187.
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

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.

B5R313-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKQSHFFAHL SRMKLINRWP LMRNVRTENV SEHSLQVAMV AHALAAIKNR
60 70 80 90 100
KFGGQLNAER IALLAMYHDA SEVLTGDLPT PVKYFNSQIA QEYKAIEKIA
110 120 130 140 150
QQKLVDMAPD ELRDIFAPLI DENAWSEEEQ AIVKQADALC AYLKCLEELS
160 170 180 190
AGNNEFGLAK TRLEKTLELR RSQEMDYFMA VFVPSFHLSL DEISQDSPL
Length:199
Mass (Da):22,697
Last modified:November 4, 2008 - v1
Checksum:i7193B30D8B30167E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM933172 Genomic DNA. Translation: CAR33898.1.
RefSeqiWP_000813882.1. NC_011294.1.

Genome annotation databases

EnsemblBacteriaiCAR33898; CAR33898; SEN2314.
KEGGiset:SEN2314.
PATRICi32335155. VBISalEnt14964_2351.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM933172 Genomic DNA. Translation: CAR33898.1.
RefSeqiWP_000813882.1. NC_011294.1.

3D structure databases

ProteinModelPortaliB5R313.
SMRiB5R313. Positions 2-187.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiB5R313.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAR33898; CAR33898; SEN2314.
KEGGiset:SEN2314.
PATRICi32335155. VBISalEnt14964_2351.

Phylogenomic databases

HOGENOMiHOG000276964.
KOiK08722.
OMAiMPTPIKY.
OrthoDBiEOG696C17.

Enzyme and pathway databases

BioCyciSENT550537:GJFI-2343-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: P125109.

Entry informationi

Entry namei5DNU_SALEP
AccessioniPrimary (citable) accession number: B5R313
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: November 4, 2008
Last modified: November 11, 2015
This is version 52 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.