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Protein

5'-deoxynucleotidase YfbR

Gene

yfbR

Organism
Shigella flexneri
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

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:SF2367, S2502
OrganismiShigella flexneri
Taxonomic identifieri623 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeShigella
Proteomesi
  • UP000002673 Componenti: Chromosome
  • UP000001006 Componenti: Chromosome

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_0000095060Add
BLAST

Proteomic databases

PaxDbiQ83QS4.

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi198214.SF2367.

Structurei

3D structure databases

ProteinModelPortaliQ83QS4.
SMRiQ83QS4. 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

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.

Q83QS4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKQSHFFAHL SRLKLINRWP LMRNVRTENV SEHSLQVAMV AHALAAIKNR
60 70 80 90 100
KFGGNVNAER IALLAMYHDA SEVLTGDLPT PVKYFNAQIA QEYKAIEKIA
110 120 130 140 150
QQKLVDMVPE ELRDIFAPLI DEHAYSDEEK SLVKQADALC AYLKCLEELA
160 170 180 190
AGNNEFLLAK TRLEATLEAR RSQEMDYFME VFVPSFHLSL DEISQDSPL
Length:199
Mass (Da):22,678
Last modified:June 1, 2003 - v1
Checksum:i14A16C6AC30DBFA8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE005674 Genomic DNA. Translation: AAN43880.1.
AE014073 Genomic DNA. Translation: AAP17698.1.
RefSeqiNP_708173.1. NC_004337.2.
WP_000813851.1. NZ_LM651928.1.

Genome annotation databases

EnsemblBacteriaiAAN43880; AAN43880; SF2367.
AAP17698; AAP17698; S2502.
GeneIDi1025547.
KEGGisfl:SF2367.
sft:NCTC1_02602.
sfx:S2502.
PATRICi18706597. VBIShiFle31049_2774.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE005674 Genomic DNA. Translation: AAN43880.1.
AE014073 Genomic DNA. Translation: AAP17698.1.
RefSeqiNP_708173.1. NC_004337.2.
WP_000813851.1. NZ_LM651928.1.

3D structure databases

ProteinModelPortaliQ83QS4.
SMRiQ83QS4. Positions 2-187.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi198214.SF2367.

Proteomic databases

PaxDbiQ83QS4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAN43880; AAN43880; SF2367.
AAP17698; AAP17698; S2502.
GeneIDi1025547.
KEGGisfl:SF2367.
sft:NCTC1_02602.
sfx:S2502.
PATRICi18706597. VBIShiFle31049_2774.

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]
ProtoNetiSearch...

Publicationsi

  1. "Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157."
    Jin Q., Yuan Z., Xu J., Wang Y., Shen Y., Lu W., Wang J., Liu H., Yang J., Yang F., Zhang X., Zhang J., Yang G., Wu H., Qu D., Dong J., Sun L., Xue Y.
    , Zhao A., Gao Y., Zhu J., Kan B., Ding K., Chen S., Cheng H., Yao Z., He B., Chen R., Ma D., Qiang B., Wen Y., Hou Y., Yu J.
    Nucleic Acids Res. 30:4432-4441(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 301 / Serotype 2a.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700930 / 2457T / Serotype 2a.

Entry informationi

Entry namei5DNU_SHIFL
AccessioniPrimary (citable) accession number: Q83QS4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 10, 2004
Last sequence update: June 1, 2003
Last modified: July 6, 2016
This is version 83 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete 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.