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Database: UniProt
Entry: D3DIR6_HYDTT
LinkDB: D3DIR6_HYDTT
Original site: D3DIR6_HYDTT 
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
//
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