ID I0QUE5_9GAMM Unreviewed; 199 AA.
AC I0QUE5;
DT 13-JUN-2012, integrated into UniProtKB/TrEMBL.
DT 13-JUN-2012, sequence version 1.
DT 27-MAR-2024, entry version 53.
DE RecName: Full=5'-deoxynucleotidase {ECO:0000256|ARBA:ARBA00012964};
DE EC=3.1.3.89 {ECO:0000256|ARBA:ARBA00012964};
GN ORFNames=SPM24T3_09244 {ECO:0000313|EMBL:EIC84918.1};
OS Serratia sp. M24T3.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Yersiniaceae; Serratia.
OX NCBI_TaxID=932213 {ECO:0000313|EMBL:EIC84918.1, ECO:0000313|Proteomes:UP000011072};
RN [1] {ECO:0000313|EMBL:EIC84918.1, ECO:0000313|Proteomes:UP000011072}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=M24T3 {ECO:0000313|EMBL:EIC84918.1,
RC ECO:0000313|Proteomes:UP000011072};
RX PubMed=22740681; DOI=10.1128/JB.00670-12;
RA Proenca D.N., Espirito Santo C., Grass G., Morais P.V.;
RT "Draft Genome Sequence of Serratia sp. Strain M24T3, Isolated from Pinewood
RT Disease Nematode Bursaphelenchus xylophilus.";
RL J. Bacteriol. 194:3764-3764(2012).
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}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:EIC84918.1}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AJHJ01000008; EIC84918.1; -; Genomic_DNA.
DR RefSeq; WP_009636453.1; NZ_AJHJ01000008.1.
DR AlphaFoldDB; I0QUE5; -.
DR STRING; 932213.SPM24T3_09244; -.
DR PATRIC; fig|932213.3.peg.1869; -.
DR eggNOG; COG1896; Bacteria.
DR OrthoDB; 9812744at2; -.
DR Proteomes; UP000011072; 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 CDD; cd00077; HDc; 1.
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};
KW Metal-binding {ECO:0000256|HAMAP-Rule:MF_01100};
KW Nucleotide-binding {ECO:0000256|HAMAP-Rule:MF_01100}.
FT DOMAIN 30..142
FT /note="HD"
FT /evidence="ECO:0000259|PROSITE:PS51831"
FT BINDING 18..19
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01100"
FT BINDING 33
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01100"
FT BINDING 33
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01100"
FT BINDING 68
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01100"
FT BINDING 69
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01100"
FT BINDING 69
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01100"
FT BINDING 77..80
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01100"
FT BINDING 137
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01100"
FT BINDING 137
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01100"
FT SITE 18
FT /note="Appears to be important in orienting the phosphate
FT for catalysis"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01100"
SQ SEQUENCE 199 AA; 22840 MW; 0AA31795354C3BD4 CRC64;
MSQSHFFAHL SRLKLIGRWP LMRNVRTENV SEHSLQVAFV AHALALIKNR KFGGTLNAER
VALLAMYHDA SEVLTGDMPT PIKYYNPQIA HEYKKIEKIA QQKLIEMLPE EFQDDYRSLI
DEHHFSDDEK KTVKQADALC AYLKCLEELS AGNTEFAMAK TRLEKTLAER NSPEMDYFMA
VFIPSFSLSL DEISQDSPL
//
