5DNU_ECO5E
ID 5DNU_ECO5E Reviewed; 199 AA.
AC B5YXT1;
DT 14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT 25-NOV-2008, sequence version 1.
DT 03-AUG-2022, entry version 75.
DE RecName: Full=5'-deoxynucleotidase YfbR {ECO:0000255|HAMAP-Rule:MF_01100};
DE EC=3.1.3.89 {ECO:0000255|HAMAP-Rule:MF_01100};
DE AltName: Full=5'-deoxyribonucleotidase {ECO:0000255|HAMAP-Rule:MF_01100};
DE AltName: Full=Nucleoside 5'-monophosphate phosphohydrolase {ECO:0000255|HAMAP-Rule:MF_01100};
GN Name=yfbR {ECO:0000255|HAMAP-Rule:MF_01100};
GN OrderedLocusNames=ECH74115_3430;
OS Escherichia coli O157:H7 (strain EC4115 / EHEC).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=444450;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=EC4115 / EHEC;
RX PubMed=22135463; DOI=10.1073/pnas.1107176108;
RA Eppinger M., Mammel M.K., Leclerc J.E., Ravel J., Cebula T.A.;
RT "Genomic anatomy of Escherichia coli O157:H7 outbreaks.";
RL Proc. Natl. Acad. Sci. U.S.A. 108:20142-20147(2011).
CC -!- FUNCTION: Catalyzes the strictly specific dephosphorylation of 2'-
CC deoxyribonucleoside 5'-monophosphates. {ECO:0000255|HAMAP-
CC Rule:MF_01100}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxyribonucleoside 5'-phosphate + H2O = a 2'-
CC deoxyribonucleoside + phosphate; Xref=Rhea:RHEA:36167,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:18274, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:65317; EC=3.1.3.89; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01100};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01100};
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_01100}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01100}.
CC -!- SIMILARITY: Belongs to the 5DNU family. {ECO:0000255|HAMAP-
CC Rule:MF_01100}.
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DR EMBL; CP001164; ACI36668.1; -; Genomic_DNA.
DR RefSeq; WP_000813860.1; NC_011353.1.
DR AlphaFoldDB; B5YXT1; -.
DR SMR; B5YXT1; -.
DR KEGG; ecf:ECH74115_3430; -.
DR HOGENOM; CLU_084784_0_0_6; -.
DR OMA; NQSHFFA; -.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0002953; F:5'-deoxynucleotidase activity; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR CDD; cd00077; HDc; 1.
DR HAMAP; MF_01100; 5DNU; 1.
DR InterPro; IPR003607; HD/PDEase_dom.
DR InterPro; IPR006674; HD_domain.
DR InterPro; IPR022971; YfbR.
DR InterPro; IPR039356; YfbR/HDDC2.
DR PANTHER; PTHR11845; PTHR11845; 1.
DR SMART; SM00471; HDc; 1.
DR PROSITE; PS51831; HD; 1.
PE 3: Inferred from homology;
KW Cytoplasm; Hydrolase; Metal-binding; Nucleotide-binding.
FT CHAIN 1..199
FT /note="5'-deoxynucleotidase YfbR"
FT /id="PRO_1000136962"
FT DOMAIN 30..142
FT /note="HD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01175"
FT BINDING 18..19
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01100"
FT BINDING 33
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01100"
FT BINDING 33
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01100"
FT BINDING 68
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01100"
FT BINDING 69
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01100"
FT BINDING 69
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01100"
FT BINDING 77..80
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01100"
FT BINDING 137
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01100"
FT BINDING 137
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01100"
FT SITE 18
FT /note="Appears to be important in orienting the phosphate
FT for catalysis"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01100"
SQ SEQUENCE 199 AA; 22694 MW; 895E8C6AC30DA057 CRC64;
MKQSHFFAHL SRLKLINRWP LMRNVRTENV SEHSLQVAMV AHALAAIKNR KFGGNVNAER
IALLAMYHDA SEVLTGDLPT PVKYFNSQIA QEYKAIEKIA QQKLVDMVPE ELRDIFAPLI
DEHAYSDEEK SLVKQADALC AYLKCLEELA AGNNEFLLAK TRLEATLEAR RSQEMDYFME
VFVPSFHLSL DEISQDSPL
