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5DNU_YERPE
ID   5DNU_YERPE              Reviewed;         197 AA.
AC   Q8ZDK3; Q0WDW8;
DT   30-AUG-2002, integrated into UniProtKB/Swiss-Prot.
DT   01-MAR-2002, sequence version 1.
DT   03-AUG-2022, entry version 125.
DE   RecName: Full=5'-deoxynucleotidase YPO2559 {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   OrderedLocusNames=YPO2559, y1627, YP_2370;
OS   Yersinia pestis.
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC   Yersiniaceae; Yersinia.
OX   NCBI_TaxID=632;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=CO-92 / Biovar Orientalis;
RX   PubMed=11586360; DOI=10.1038/35097083;
RA   Parkhill J., Wren B.W., Thomson N.R., Titball R.W., Holden M.T.G.,
RA   Prentice M.B., Sebaihia M., James K.D., Churcher C.M., Mungall K.L.,
RA   Baker S., Basham D., Bentley S.D., Brooks K., Cerdeno-Tarraga A.-M.,
RA   Chillingworth T., Cronin A., Davies R.M., Davis P., Dougan G., Feltwell T.,
RA   Hamlin N., Holroyd S., Jagels K., Karlyshev A.V., Leather S., Moule S.,
RA   Oyston P.C.F., Quail M.A., Rutherford K.M., Simmonds M., Skelton J.,
RA   Stevens K., Whitehead S., Barrell B.G.;
RT   "Genome sequence of Yersinia pestis, the causative agent of plague.";
RL   Nature 413:523-527(2001).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=KIM10+ / Biovar Mediaevalis;
RX   PubMed=12142430; DOI=10.1128/jb.184.16.4601-4611.2002;
RA   Deng W., Burland V., Plunkett G. III, Boutin A., Mayhew G.F., Liss P.,
RA   Perna N.T., Rose D.J., Mau B., Zhou S., Schwartz D.C., Fetherston J.D.,
RA   Lindler L.E., Brubaker R.R., Plano G.V., Straley S.C., McDonough K.A.,
RA   Nilles M.L., Matson J.S., Blattner F.R., Perry R.D.;
RT   "Genome sequence of Yersinia pestis KIM.";
RL   J. Bacteriol. 184:4601-4611(2002).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=91001 / Biovar Mediaevalis;
RX   PubMed=15368893; DOI=10.1093/dnares/11.3.179;
RA   Song Y., Tong Z., Wang J., Wang L., Guo Z., Han Y., Zhang J., Pei D.,
RA   Zhou D., Qin H., Pang X., Han Y., Zhai J., Li M., Cui B., Qi Z., Jin L.,
RA   Dai R., Chen F., Li S., Ye C., Du Z., Lin W., Wang J., Yu J., Yang H.,
RA   Wang J., Huang P., Yang R.;
RT   "Complete genome sequence of Yersinia pestis strain 91001, an isolate
RT   avirulent to humans.";
RL   DNA Res. 11:179-197(2004).
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; AL590842; CAL21184.1; -; Genomic_DNA.
DR   EMBL; AE009952; AAM85196.1; -; Genomic_DNA.
DR   EMBL; AE017042; AAS62575.1; -; Genomic_DNA.
DR   PIR; AE0312; AE0312.
DR   RefSeq; WP_002210283.1; NZ_WUCM01000021.1.
DR   RefSeq; YP_002347520.1; NC_003143.1.
DR   AlphaFoldDB; Q8ZDK3; -.
DR   SMR; Q8ZDK3; -.
DR   STRING; 214092.YPO2559; -.
DR   PaxDb; Q8ZDK3; -.
DR   DNASU; 1146574; -.
DR   EnsemblBacteria; AAM85196; AAM85196; y1627.
DR   EnsemblBacteria; AAS62575; AAS62575; YP_2370.
DR   GeneID; 57976131; -.
DR   KEGG; ype:YPO2559; -.
DR   KEGG; ypk:y1627; -.
DR   KEGG; ypm:YP_2370; -.
DR   PATRIC; fig|214092.21.peg.2983; -.
DR   eggNOG; COG1896; Bacteria.
DR   HOGENOM; CLU_084784_0_0_6; -.
DR   OMA; NQSHFFA; -.
DR   Proteomes; UP000000815; Chromosome.
DR   Proteomes; UP000001019; Chromosome.
DR   Proteomes; UP000002490; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0002953; F:5'-deoxynucleotidase activity; IBA:GO_Central.
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;
KW   Reference proteome.
FT   CHAIN           1..197
FT                   /note="5'-deoxynucleotidase YPO2559"
FT                   /id="PRO_0000095065"
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;  22729 MW;  B3AC752101903423 CRC64;
     MSHFFAHLSR LKLINRWPLM RNVRTENVSE HSLQVAFVAH ALAIIKNRKF NGNLNAERIA
     LLAMYHDASE VITGDLPTPI KYHNPKIAHE YKKIEKVAQQ KLIEMLPKEL QHDFRCLLDE
     HYYSEEEKAL VKQADALCAY LKCLEELSAG NNEFIQAKAR LEKTLAIRQS PEMDYFMAVF
     VPSFSLSLDE ISLDSLD
 
 
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