5DNU_ECO45
ID 5DNU_ECO45 Reviewed; 199 AA.
AC B7MG55;
DT 14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT 10-FEB-2009, sequence version 1.
DT 03-AUG-2022, entry version 76.
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}; OrderedLocusNames=ECS88_2438;
OS Escherichia coli O45:K1 (strain S88 / ExPEC).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=585035;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=S88 / ExPEC;
RX PubMed=19165319; DOI=10.1371/journal.pgen.1000344;
RA Touchon M., Hoede C., Tenaillon O., Barbe V., Baeriswyl S., Bidet P.,
RA Bingen E., Bonacorsi S., Bouchier C., Bouvet O., Calteau A., Chiapello H.,
RA Clermont O., Cruveiller S., Danchin A., Diard M., Dossat C., Karoui M.E.,
RA Frapy E., Garry L., Ghigo J.M., Gilles A.M., Johnson J., Le Bouguenec C.,
RA Lescat M., Mangenot S., Martinez-Jehanne V., Matic I., Nassif X., Oztas S.,
RA Petit M.A., Pichon C., Rouy Z., Ruf C.S., Schneider D., Tourret J.,
RA Vacherie B., Vallenet D., Medigue C., Rocha E.P.C., Denamur E.;
RT "Organised genome dynamics in the Escherichia coli species results in
RT highly diverse adaptive paths.";
RL PLoS Genet. 5:E1000344-E1000344(2009).
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; CU928161; CAR03717.1; -; Genomic_DNA.
DR RefSeq; WP_000813854.1; NC_011742.1.
DR AlphaFoldDB; B7MG55; -.
DR SMR; B7MG55; -.
DR EnsemblBacteria; CAR03717; CAR03717; ECS88_2438.
DR KEGG; ecz:ECS88_2438; -.
DR HOGENOM; CLU_084784_0_0_6; -.
DR OMA; NQSHFFA; -.
DR Proteomes; UP000000747; Chromosome.
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_1000136961"
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; 22666 MW; 1A6EBF69F00DA238 CRC64;
MKQSHFFAHL SRLKLINRWP LMRNVRTENV SEHSLQVAMV AHALAAIKNR KFGGNVNAER
IALLAMYHDA SEVLTGDLPT PVKYFNSQIA QEYKAIEKIA QQKLVDMVPE ELQDIFAPLI
DEHAYSDEEK SLVKQADALC AYLKCLEELA AGNNEFLLAK TRLEATLEAR RSQEMDYFME
VFVPSFHLSL DEISQDSPL
