ID D3DIR6_HYDTT Unreviewed; 580 AA.
AC D3DIR6;
DT 23-MAR-2010, integrated into UniProtKB/TrEMBL.
DT 23-MAR-2010, sequence version 1.
DT 24-JAN-2024, entry version 79.
DE RecName: Full=DNA polymerase beta {ECO:0000256|ARBA:ARBA00020020};
DE EC=2.7.7.7 {ECO:0000256|ARBA:ARBA00012417};
DE EC=4.2.99.18 {ECO:0000256|ARBA:ARBA00012720};
DE AltName: Full=5'-deoxyribose-phosphate lyase {ECO:0000256|ARBA:ARBA00035717};
DE AltName: Full=AP lyase {ECO:0000256|ARBA:ARBA00035726};
GN OrderedLocusNames=HTH_1265 {ECO:0000313|EMBL:BAI69718.1};
OS Hydrogenobacter thermophilus (strain DSM 6534 / IAM 12695 / TK-6).
OC Bacteria; Aquificota; Aquificae; Aquificales; Aquificaceae;
OC Hydrogenobacter.
OX NCBI_TaxID=608538 {ECO:0000313|EMBL:BAI69718.1, ECO:0000313|Proteomes:UP000002574};
RN [1] {ECO:0000313|EMBL:BAI69718.1, ECO:0000313|Proteomes:UP000002574}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 6534 / IAM 12695 / TK-6 [Tokyo]
RC {ECO:0000313|Proteomes:UP000002574};
RX PubMed=20348262; DOI=10.1128/JB.00158-10;
RA Arai H., Kanbe H., Ishii M., Igarashi Y.;
RT "Complete genome sequence of the thermophilic, obligately
RT chemolithoautotrophic hydrogen-oxidizing bacterium Hydrogenobacter
RT thermophilus TK-6.";
RL J. Bacteriol. 192:2651-2652(2010).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)-2'-
CC deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3-
CC dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-monophospho-
CC 2'-deoxyribonucleoside-DNA + H(+); Xref=Rhea:RHEA:66592, Rhea:RHEA-
CC COMP:13180, Rhea:RHEA-COMP:16897, Rhea:RHEA-COMP:17067,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:136412, ChEBI:CHEBI:157695,
CC ChEBI:CHEBI:167181; EC=4.2.99.18;
CC Evidence={ECO:0000256|ARBA:ARBA00024490};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) =
CC diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339,
CC Rhea:RHEA-COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560,
CC ChEBI:CHEBI:173112; EC=2.7.7.7;
CC Evidence={ECO:0000256|ARBA:ARBA00024632};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5'-end 2'-deoxyribose-2'-deoxyribonucleotide-DNA = (2E,4S)-
CC 4-hydroxypenten-2-al-5-phosphate + a 5'-end 5'-monophospho-2'-
CC deoxyribonucleoside-DNA + H(+); Xref=Rhea:RHEA:76255, Rhea:RHEA-
CC COMP:13180, Rhea:RHEA-COMP:18657, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:136412, ChEBI:CHEBI:195194, ChEBI:CHEBI:195195;
CC Evidence={ECO:0000256|ARBA:ARBA00035582};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|ARBA:ARBA00001946};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|ARBA:ARBA00004496}.
CC Nucleus {ECO:0000256|ARBA:ARBA00004123}.
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DR EMBL; AP011112; BAI69718.1; -; Genomic_DNA.
DR RefSeq; WP_012963898.1; NC_017161.1.
DR AlphaFoldDB; D3DIR6; -.
DR STRING; 608538.HTH_1265; -.
DR KEGG; hth:HTH_1265; -.
DR PATRIC; fig|608538.5.peg.1283; -.
DR eggNOG; COG1387; Bacteria.
DR eggNOG; COG1796; Bacteria.
DR OMA; HNVRMRQ; -.
DR OrthoDB; 9808747at2; -.
DR Proteomes; UP000002574; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
DR GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR CDD; cd00141; NT_POLXc; 1.
DR CDD; cd07436; PHP_PolX; 1.
DR Gene3D; 1.10.150.20; 5' to 3' exonuclease, C-terminal subdomain; 1.
DR Gene3D; 3.30.460.10; Beta Polymerase, domain 2; 1.
DR Gene3D; 1.10.150.110; DNA polymerase beta, N-terminal domain-like; 1.
DR Gene3D; 3.30.210.10; DNA polymerase, thumb domain; 1.
DR Gene3D; 3.20.20.140; Metal-dependent hydrolases; 1.
DR InterPro; IPR002054; DNA-dir_DNA_pol_X.
DR InterPro; IPR010996; DNA_pol_b-like_N.
DR InterPro; IPR027421; DNA_pol_lamdba_lyase_dom_sf.
DR InterPro; IPR037160; DNA_Pol_thumb_sf.
DR InterPro; IPR002008; DNA_pol_X_beta-like.
DR InterPro; IPR003583; Hlx-hairpin-Hlx_DNA-bd_motif.
DR InterPro; IPR043519; NT_sf.
DR InterPro; IPR004013; PHP_dom.
DR InterPro; IPR003141; Pol/His_phosphatase_N.
DR InterPro; IPR016195; Pol/histidinol_Pase-like.
DR InterPro; IPR029398; PolB_thumb.
DR InterPro; IPR022311; PolX-like.
DR InterPro; IPR047967; PolX_PHP.
DR PANTHER; PTHR36928; PHOSPHATASE YCDX-RELATED; 1.
DR PANTHER; PTHR36928:SF1; PHOSPHATASE YCDX-RELATED; 1.
DR Pfam; PF14791; DNA_pol_B_thumb; 1.
DR Pfam; PF14520; HHH_5; 1.
DR Pfam; PF14716; HHH_8; 1.
DR Pfam; PF02811; PHP; 1.
DR PIRSF; PIRSF005047; UCP005047_YshC; 1.
DR PRINTS; PR00870; DNAPOLXBETA.
DR SMART; SM00278; HhH1; 3.
DR SMART; SM00481; POLIIIAc; 1.
DR SMART; SM00483; POLXc; 1.
DR SUPFAM; SSF47802; DNA polymerase beta, N-terminal domain-like; 1.
DR SUPFAM; SSF81301; Nucleotidyltransferase; 1.
DR SUPFAM; SSF89550; PHP domain-like; 1.
PE 4: Predicted;
KW DNA damage {ECO:0000256|ARBA:ARBA00022763};
KW DNA repair {ECO:0000256|ARBA:ARBA00023204};
KW DNA synthesis {ECO:0000256|ARBA:ARBA00022634};
KW DNA-directed DNA polymerase {ECO:0000256|ARBA:ARBA00022932};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723};
KW Methylation {ECO:0000256|ARBA:ARBA00022481};
KW Nucleotidyltransferase {ECO:0000256|ARBA:ARBA00022695};
KW Reference proteome {ECO:0000313|Proteomes:UP000002574};
KW Sodium {ECO:0000256|ARBA:ARBA00023053};
KW Transferase {ECO:0000256|ARBA:ARBA00022679};
KW Ubl conjugation {ECO:0000256|ARBA:ARBA00022843}.
FT DOMAIN 2..319
FT /note="DNA-directed DNA polymerase X"
FT /evidence="ECO:0000259|SMART:SM00483"
FT DOMAIN 52..71
FT /note="Helix-hairpin-helix DNA-binding motif class 1"
FT /evidence="ECO:0000259|SMART:SM00278"
FT DOMAIN 92..111
FT /note="Helix-hairpin-helix DNA-binding motif class 1"
FT /evidence="ECO:0000259|SMART:SM00278"
FT DOMAIN 127..146
FT /note="Helix-hairpin-helix DNA-binding motif class 1"
FT /evidence="ECO:0000259|SMART:SM00278"
FT DOMAIN 343..424
FT /note="Polymerase/histidinol phosphatase N-terminal"
FT /evidence="ECO:0000259|SMART:SM00481"
SQ SEQUENCE 580 AA; 66049 MW; AF15DC7954B3A583 CRC64;
MSKNKEIAEI FERMADILEF LGDNPYRIST YRRVANILSE LNVDVEDLVK SGKIHHIPGI
GASSVEKILE YLRTGKISKY EELKGKVPED LLELMNVPSI GPKTLKLAYE RLGIRTKDDF
IRAVRSGMLA TLPGFGEKKL QNIMRGIELW EKSKERMTLI EAFEIGQEYL SYMKRLGDII
ERIELAGSLR RRKETVGDID MLVSAMHENW SKIHEHFVSF PDVKDVLLKG ETKSSVVLKN
ARQVDLRTVE PHQWGAALQY FTGSKEHNIR VRDIAKMKGL KVSEYGVFRA DTDQWIGGKS
EEEVYALIGM QTPPPEIREN AGEIELALEG KLPKLLSLED VKGDFHIHTN WSDGIGSLEQ
MVETAYHMGH RYVVIGDHSL SSKVAKGLDM ERYKQQWKEI DRLRKRYEPL GFYILKGCEV
DILPDGSLDL PDEFLAEFDF VVASIHTRFS QDNTYRILKA IENPYVNLIG HPTGKSYGTR
EGYPLDMDRV IQLAKETGTA LELNTFRADL SPENVRKCMQ KGVFIAIVTD AHAPAHLRYI
ELGVGLARRG WAMPELVLNT KDVEGIREFV YKKRKLLAAT
//