5DNU_ECODH
ID 5DNU_ECODH Reviewed; 199 AA.
AC B1X903;
DT 14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT 20-MAY-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=ECDH10B_2453;
OS Escherichia coli (strain K12 / DH10B).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=316385;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / DH10B;
RX PubMed=18245285; DOI=10.1128/jb.01695-07;
RA Durfee T., Nelson R., Baldwin S., Plunkett G. III, Burland V., Mau B.,
RA Petrosino J.F., Qin X., Muzny D.M., Ayele M., Gibbs R.A., Csorgo B.,
RA Posfai G., Weinstock G.M., Blattner F.R.;
RT "The complete genome sequence of Escherichia coli DH10B: insights into the
RT biology of a laboratory workhorse.";
RL J. Bacteriol. 190:2597-2606(2008).
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; CP000948; ACB03450.1; -; Genomic_DNA.
DR RefSeq; WP_000813859.1; NC_010473.1.
DR AlphaFoldDB; B1X903; -.
DR SMR; B1X903; -.
DR KEGG; ecd:ECDH10B_2453; -.
DR HOGENOM; CLU_084784_0_0_6; -.
DR OMA; NQSHFFA; -.
DR BioCyc; ECOL316385:ECDH10B_RS12475-MON; -.
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_1000136965"
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; 22708 MW; 895E9A06130DA057 CRC64;
MKQSHFFAHL SRLKLINRWP LMRNVRTENV SEHSLQVAMV AHALAAIKNR KFGGNVNAER
IALLAMYHDA SEVLTGDLPT PVKYFNSQIA QEYKAIEKIA QQKLVDMVPE ELRDIFAPLI
DEHAYSDEEK SLVKQADALC AYLKCLEELA AGNNEFLLAK TRLEATLEAR RSQEMDYFME
IFVPSFHLSL DEISQDSPL
