ID I7LLQ2_METBM Unreviewed; 577 AA.
AC I7LLQ2;
DT 03-OCT-2012, integrated into UniProtKB/TrEMBL.
DT 03-OCT-2012, sequence version 1.
DT 27-MAR-2024, entry version 62.
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=BN140_0626 {ECO:0000313|EMBL:CCJ35549.1};
OS Methanoculleus bourgensis (strain ATCC 43281 / DSM 3045 / OCM 15 / MS2)
OS (Methanogenium bourgense).
OC Archaea; Euryarchaeota; Stenosarchaea group; Methanomicrobia;
OC Methanomicrobiales; Methanomicrobiaceae; Methanoculleus.
OX NCBI_TaxID=1201294 {ECO:0000313|EMBL:CCJ35549.1, ECO:0000313|Proteomes:UP000009007};
RN [1] {ECO:0000313|Proteomes:UP000009007}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43281 / DSM 3045 / OCM 15 / MS2
RC {ECO:0000313|Proteomes:UP000009007};
RX PubMed=22965103; DOI=10.1128/JB.01292-12;
RA Maus I., Wibberg D., Stantscheff R., Eikmeyer F.G., Seffner A., Boelter J.,
RA Szczepanowski R., Blom J., Jaenicke S., Konig H., Puhler A., Schluter A.;
RT "Complete genome sequence of the hydrogenotrophic, methanogenic archaeon
RT Methanoculleus bourgensis strain MS2T, isolated from a sewage sludge
RT digester.";
RL J. Bacteriol. 194:5487-5488(2012).
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; HE964772; CCJ35549.1; -; Genomic_DNA.
DR RefSeq; WP_014866526.1; NC_018227.2.
DR AlphaFoldDB; I7LLQ2; -.
DR STRING; 1201294.BN140_0626; -.
DR GeneID; 13355096; -.
DR KEGG; mbg:BN140_0626; -.
DR PATRIC; fig|1201294.9.peg.683; -.
DR HOGENOM; CLU_017729_1_0_2; -.
DR BioCyc; MBOU1201294:BN140_RS03150-MONOMER; -.
DR Proteomes; UP000009007; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0140078; F:class I DNA-(apurinic or apyrimidinic site) endonuclease activity; IEA:RHEA.
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:0046872; F:metal ion binding; 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.
DR SUPFAM; SSF158702; Sec63 N-terminal 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 Methylation {ECO:0000256|ARBA:ARBA00022481};
KW Nucleotidyltransferase {ECO:0000256|ARBA:ARBA00022695,
KW ECO:0000313|EMBL:CCJ35549.1};
KW Reference proteome {ECO:0000313|Proteomes:UP000009007};
KW Sodium {ECO:0000256|ARBA:ARBA00023053};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000313|EMBL:CCJ35549.1};
KW Ubl conjugation {ECO:0000256|ARBA:ARBA00022843}.
FT DOMAIN 7..320
FT /note="DNA-directed DNA polymerase X"
FT /evidence="ECO:0000259|SMART:SM00483"
FT DOMAIN 56..75
FT /note="Helix-hairpin-helix DNA-binding motif class 1"
FT /evidence="ECO:0000259|SMART:SM00278"
FT DOMAIN 96..115
FT /note="Helix-hairpin-helix DNA-binding motif class 1"
FT /evidence="ECO:0000259|SMART:SM00278"
FT DOMAIN 131..150
FT /note="Helix-hairpin-helix DNA-binding motif class 1"
FT /evidence="ECO:0000259|SMART:SM00278"
FT DOMAIN 344..424
FT /note="Polymerase/histidinol phosphatase N-terminal"
FT /evidence="ECO:0000259|SMART:SM00481"
SQ SEQUENCE 577 AA; 63306 MW; DB5C60B871F5CE60 CRC64;
MERLARLTNI EVAAVLYEVA DLLEIKGVRF KPHAYRRAAQ AIETLPEDIA DVAREGRLGE
IPGVGKGIAG KVMEVVETGS LGYLESLREE LPEGVQELTR IEGIGPKKAL VLSRELGIRT
IDDLEAAATA GRIRDLPGFG EKTEQNILAG IQMSRMAGKR HLLGYILPTA RVIERRLSSL
GSVGQVSLAG SIRRRKETIG DLDLLATSTR PEEVMEVFAT LPGVSRVLAR GTTKTSVVLE
TGLQVDLRVV EEKHYGAALQ YFTGSKEHNI ALRKLAIARN WRLNEYGLVD LADGRMIAGE
DEAGVYRALG LSWIEPELRE DRGEIEAART GTLPDLVGYG SIRGDLHVHT RWSEGAHSIE
EMAEAAQGLG YEYIAICDHA ETLHIARGLS PERLADQVRE IERLNREFDG EFTILAGTEC
NIDMDGRIDL PDSILADLDV VVASVHSGFK QPEREMTDRV IAAMQNDHVD IIGHPTGRIL
LSREPCQIDL ATIFEAAAAL GVLMEINAFP GRLDLSDVNC RLAQGFGVRF SLGSDAHNRG
NLRYMEFGVA TARRGWLAAD DIANTRSLED LRGFLRS
//
