5DNU_SHIFL
ID 5DNU_SHIFL Reviewed; 199 AA.
AC Q83QS4;
DT 10-MAY-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 116.
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=SF2367, S2502;
OS Shigella flexneri.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Shigella.
OX NCBI_TaxID=623;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=301 / Serotype 2a;
RX PubMed=12384590; DOI=10.1093/nar/gkf566;
RA Jin Q., Yuan Z., Xu J., Wang Y., Shen Y., Lu W., Wang J., Liu H., Yang J.,
RA Yang F., Zhang X., Zhang J., Yang G., Wu H., Qu D., Dong J., Sun L.,
RA Xue Y., Zhao A., Gao Y., Zhu J., Kan B., Ding K., Chen S., Cheng H.,
RA Yao Z., He B., Chen R., Ma D., Qiang B., Wen Y., Hou Y., Yu J.;
RT "Genome sequence of Shigella flexneri 2a: insights into pathogenicity
RT through comparison with genomes of Escherichia coli K12 and O157.";
RL Nucleic Acids Res. 30:4432-4441(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700930 / 2457T / Serotype 2a;
RX PubMed=12704152; DOI=10.1128/iai.71.5.2775-2786.2003;
RA Wei J., Goldberg M.B., Burland V., Venkatesan M.M., Deng W., Fournier G.,
RA Mayhew G.F., Plunkett G. III, Rose D.J., Darling A., Mau B., Perna N.T.,
RA Payne S.M., Runyen-Janecky L.J., Zhou S., Schwartz D.C., Blattner F.R.;
RT "Complete genome sequence and comparative genomics of Shigella flexneri
RT serotype 2a strain 2457T.";
RL Infect. Immun. 71:2775-2786(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}.
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DR EMBL; AE005674; AAN43880.1; -; Genomic_DNA.
DR EMBL; AE014073; AAP17698.1; -; Genomic_DNA.
DR RefSeq; NP_708173.1; NC_004337.2.
DR RefSeq; WP_000813851.1; NZ_WPGW01000016.1.
DR AlphaFoldDB; Q83QS4; -.
DR SMR; Q83QS4; -.
DR STRING; 198214.SF2367; -.
DR EnsemblBacteria; AAN43880; AAN43880; SF2367.
DR EnsemblBacteria; AAP17698; AAP17698; S2502.
DR GeneID; 1025547; -.
DR GeneID; 58388089; -.
DR KEGG; sfl:SF2367; -.
DR KEGG; sfx:S2502; -.
DR PATRIC; fig|198214.7.peg.2833; -.
DR HOGENOM; CLU_084784_0_0_6; -.
DR OMA; NQSHFFA; -.
DR OrthoDB; 1508841at2; -.
DR Proteomes; UP000001006; Chromosome.
DR Proteomes; UP000002673; 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;
KW Reference proteome.
FT CHAIN 1..199
FT /note="5'-deoxynucleotidase YfbR"
FT /id="PRO_0000095060"
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; 22678 MW; 14A16C6AC30DBFA8 CRC64;
MKQSHFFAHL SRLKLINRWP LMRNVRTENV SEHSLQVAMV AHALAAIKNR KFGGNVNAER
IALLAMYHDA SEVLTGDLPT PVKYFNAQIA QEYKAIEKIA QQKLVDMVPE ELRDIFAPLI
DEHAYSDEEK SLVKQADALC AYLKCLEELA AGNNEFLLAK TRLEATLEAR RSQEMDYFME
VFVPSFHLSL DEISQDSPL
