5DNU_VIBPA
ID 5DNU_VIBPA Reviewed; 194 AA.
AC Q87R72;
DT 21-NOV-2003, integrated into UniProtKB/Swiss-Prot.
DT 21-NOV-2003, sequence version 2.
DT 03-AUG-2022, entry version 100.
DE RecName: Full=5'-deoxynucleotidase VP0926 {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=VP0926;
OS Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Vibrio.
OX NCBI_TaxID=223926;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=RIMD 2210633;
RX PubMed=12620739; DOI=10.1016/s0140-6736(03)12659-1;
RA Makino K., Oshima K., Kurokawa K., Yokoyama K., Uda T., Tagomori K.,
RA Iijima Y., Najima M., Nakano M., Yamashita A., Kubota Y., Kimura S.,
RA Yasunaga T., Honda T., Shinagawa H., Hattori M., Iida T.;
RT "Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism
RT distinct from that of V. cholerae.";
RL Lancet 361:743-749(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=BAC59189.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; BA000031; BAC59189.1; ALT_INIT; Genomic_DNA.
DR RefSeq; NP_797305.1; NC_004603.1.
DR RefSeq; WP_005482513.1; NC_004603.1.
DR AlphaFoldDB; Q87R72; -.
DR SMR; Q87R72; -.
DR STRING; 223926.28805913; -.
DR EnsemblBacteria; BAC59189; BAC59189; BAC59189.
DR GeneID; 1188424; -.
DR KEGG; vpa:VP0926; -.
DR PATRIC; fig|223926.6.peg.878; -.
DR eggNOG; COG1896; Bacteria.
DR HOGENOM; CLU_084784_0_0_6; -.
DR OMA; NQSHFFA; -.
DR Proteomes; UP000002493; Chromosome 1.
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..194
FT /note="5'-deoxynucleotidase VP0926"
FT /id="PRO_0000095062"
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 194 AA; 22153 MW; 24BD02A15C12C9D7 CRC64;
MKESHFFAHL ARMKLIQRWP LMRSVSPENV SEHSLQVAFV AHALALIKNK KFGGTLNPER
IALLAMYHDS SEVLTGDLPT PVKYYNPEIA KEYKKIEAAA EHKLLSMLPE EFQEDFAPFL
LSHSSHEEDS QIVKQADSIC AYLKCLEELS AGNHEFALAK KRLDVTLQER KTPEMEYFLN
TFAPSFELSL DEIS
