ID A0A0T9PTR9_9GAMM Unreviewed; 197 AA.
AC A0A0T9PTR9;
DT 17-FEB-2016, integrated into UniProtKB/TrEMBL.
DT 17-FEB-2016, sequence version 1.
DT 27-MAR-2024, entry version 35.
DE RecName: Full=5'-deoxynucleotidase {ECO:0000256|ARBA:ARBA00012964};
DE EC=3.1.3.89 {ECO:0000256|ARBA:ARBA00012964};
GN Name=yfbR {ECO:0000313|EMBL:CNH79965.1};
GN ORFNames=ERS008529_02150 {ECO:0000313|EMBL:CNH79965.1};
OS Yersinia pekkanenii.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Yersiniaceae; Yersinia.
OX NCBI_TaxID=1288385 {ECO:0000313|EMBL:CNH79965.1, ECO:0000313|Proteomes:UP000045840};
RN [1] {ECO:0000313|Proteomes:UP000045840}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=A125KOH2 {ECO:0000313|Proteomes:UP000045840};
RG Pathogen Informatics;
RL Submitted (MAR-2015) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Catalyzes the strictly specific dephosphorylation of 2'-
CC deoxyribonucleoside 5'-monophosphates. {ECO:0000256|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;
CC Evidence={ECO:0000256|ARBA:ARBA00001638, ECO:0000256|HAMAP-
CC Rule:MF_01100};
CC -!- COFACTOR:
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000256|ARBA:ARBA00001941};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|ARBA:ARBA00001936};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01100};
CC -!- SUBUNIT: Homodimer. {ECO:0000256|ARBA:ARBA00011738, ECO:0000256|HAMAP-
CC Rule:MF_01100}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_01100}.
CC -!- SIMILARITY: Belongs to the 5DNU family. {ECO:0000256|HAMAP-
CC Rule:MF_01100}.
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DR EMBL; CQAZ01000017; CNH79965.1; -; Genomic_DNA.
DR RefSeq; WP_049613055.1; NZ_CWJL01000011.1.
DR AlphaFoldDB; A0A0T9PTR9; -.
DR STRING; 1288385.ERS137968_02467; -.
DR OrthoDB; 9812744at2; -.
DR Proteomes; UP000045840; Unassembled WGS sequence.
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 Gene3D; 1.10.3210.10; Hypothetical protein af1432; 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:SF13; 5'-DEOXYNUCLEOTIDASE HDDC2; 1.
DR PANTHER; PTHR11845; UNCHARACTERIZED; 1.
DR Pfam; PF12917; YfbR-like; 1.
DR SMART; SM00471; HDc; 1.
DR SUPFAM; SSF109604; HD-domain/PDEase-like; 1.
DR PROSITE; PS51831; HD; 1.
PE 3: Inferred from homology;
KW Cytoplasm {ECO:0000256|ARBA:ARBA00022490, ECO:0000256|HAMAP-Rule:MF_01100};
KW Hydrolase {ECO:0000256|HAMAP-Rule:MF_01100, ECO:0000313|EMBL:CNH79965.1};
KW Metal-binding {ECO:0000256|HAMAP-Rule:MF_01100};
KW Nucleotide-binding {ECO:0000256|HAMAP-Rule:MF_01100}.
FT DOMAIN 28..140
FT /note="HD"
FT /evidence="ECO:0000259|PROSITE:PS51831"
FT BINDING 16..17
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01100"
FT BINDING 31
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01100"
FT BINDING 31
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01100"
FT BINDING 66
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01100"
FT BINDING 67
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01100"
FT BINDING 67
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01100"
FT BINDING 75..78
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01100"
FT BINDING 135
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01100"
FT BINDING 135
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01100"
FT SITE 16
FT /note="Appears to be important in orienting the phosphate
FT for catalysis"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01100"
SQ SEQUENCE 197 AA; 22696 MW; 41DF37626A7B8B57 CRC64;
MSHFFAHLSR LKLINRWPLM RNVRTENVSE HSLQVAFVAH ALAIIKNRKF KGNLNADRIA
LLAMYHDASE VITGDLPTPI KYYNPQIAHE YKKIEKVAQQ KLIEMLPAEL QHDFRCLLDE
HYYSDEEKAL VKQADALCAY LKCLEELSAG NNEFIQAKAR LEKTLALRQS PEMDYFMVVF
VPSFSLSLDE ISLDSPD
//
