5DNU_PHOTE
ID 5DNU_PHOTE Reviewed; 197 AA.
AC Q8GLH5;
DT 24-MAY-2004, integrated into UniProtKB/Swiss-Prot.
DT 24-MAY-2004, sequence version 2.
DT 03-AUG-2022, entry version 64.
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};
OS Photorhabdus temperata.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Morganellaceae; Photorhabdus.
OX NCBI_TaxID=574560;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K122;
RX PubMed=12603747; DOI=10.1046/j.1365-2958.2003.03389.x;
RA Joyce S.A., Clarke D.J.;
RT "A hexA homologue from Photorhabdus regulates pathogenicity, symbiosis and
RT phenotypic variation.";
RL Mol. Microbiol. 47:1445-1457(2003).
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAN08356.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AY137386; AAN08356.1; ALT_INIT; Genomic_DNA.
DR AlphaFoldDB; Q8GLH5; -.
DR SMR; Q8GLH5; -.
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 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..197
FT /note="5'-deoxynucleotidase yfbR"
FT /id="PRO_0000095056"
FT DOMAIN 28..140
FT /note="HD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01175"
FT BINDING 16..17
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01100"
FT BINDING 31
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01100"
FT BINDING 31
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01100"
FT BINDING 66
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01100"
FT BINDING 67
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01100"
FT BINDING 67
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01100"
FT BINDING 75..78
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01100"
FT BINDING 135
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01100"
FT BINDING 135
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01100"
FT SITE 16
FT /note="Appears to be important in orienting the phosphate
FT for catalysis"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01100"
SQ SEQUENCE 197 AA; 22516 MW; EEB9B8D33842EE4D CRC64;
MSHFFAHLSR LKLINRWPLM RNVRTENVSE HSLQVAFVAH ALAIIKNRKF SGNVNAERIA
LLAMYHDASE VITGDLPTPI KYHNPHIARE YKKIEKIAQK KLLEMLPAEL QEDFRPILDD
SQHTEEEISI VKQADALCAY LKCLEELSAG NSEFNLAKAR LEKTLAARHS QEMDYFMTVF
VPGFSLSLDE ISLDIPD
