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Protein

5'-deoxynucleotidase YfbR

Gene

yfbR

Organism
Escherichia coli (strain K12 / MC4100 / BW2952)
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

BioCyciECOL595496:GI18-2135-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:BWG_2065
OrganismiEscherichia coli (strain K12 / MC4100 / BW2952)
Taxonomic identifieri595496 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

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_1000213543Add
BLAST

Proteomic databases

PRIDEiC4ZVI4.

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Structurei

3D structure databases

ProteinModelPortaliC4ZVI4.
SMRiC4ZVI4. Positions 2-187.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini31 – 139109HDUniRule annotationAdd
BLAST

Region

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

Sequence similaritiesi

Belongs to the 5DNU family.UniRule annotation
Contains 1 HD domain.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.

C4ZVI4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKQSHFFAHL SRLKLINRWP LMRNVRTENV SEHSLQVAMV AHALAAIKNR
60 70 80 90 100
KFGGNVNAER IALLAMYHDA SEVLTGDLPT PVKYFNSQIA QEYKAIEKIA
110 120 130 140 150
QQKLVDMVPE ELRDIFAPLI DEHAYSDEEK SLVKQADALC AYLKCLEELA
160 170 180 190
AGNNEFLLAK TRLEATLEAR RSQEMDYFME IFVPSFHLSL DEISQDSPL
Length:199
Mass (Da):22,708
Last modified:July 28, 2009 - v1
Checksum:i895E9A06130DA057
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001396 Genomic DNA. Translation: ACR62745.1.
RefSeqiWP_000813859.1. NC_012759.1.

Genome annotation databases

EnsemblBacteriaiACR62745; ACR62745; BWG_2065.
KEGGiebw:BWG_2065.
PATRICi18273486. VBIEscCol60876_2267.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001396 Genomic DNA. Translation: ACR62745.1.
RefSeqiWP_000813859.1. NC_012759.1.

3D structure databases

ProteinModelPortaliC4ZVI4.
SMRiC4ZVI4. Positions 2-187.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiC4ZVI4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACR62745; ACR62745; BWG_2065.
KEGGiebw:BWG_2065.
PATRICi18273486. VBIEscCol60876_2267.

Phylogenomic databases

HOGENOMiHOG000276964.
KOiK08722.
OMAiMPTPIKY.
OrthoDBiEOG696C17.

Enzyme and pathway databases

BioCyciECOL595496:GI18-2135-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. "Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12."
    Ferenci T., Zhou Z., Betteridge T., Ren Y., Liu Y., Feng L., Reeves P.R., Wang L.
    J. Bacteriol. 191:4025-4029(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MC4100 / BW2952.

Entry informationi

Entry namei5DNU_ECOBW
AccessioniPrimary (citable) accession number: C4ZVI4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 22, 2009
Last sequence update: July 28, 2009
Last modified: November 11, 2015
This is version 48 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.