ID A0A919V1H2_9ACTN Unreviewed; 561 AA.
AC A0A919V1H2;
DT 22-FEB-2023, integrated into UniProtKB/TrEMBL.
DT 22-FEB-2023, sequence version 1.
DT 28-JAN-2026, entry version 16.
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 ORFNames=Sru01_35790 {ECO:0000313|EMBL:GII78597.1};
OS Sphaerisporangium rufum.
OC Bacteria; Bacillati; Actinomycetota; Actinomycetes; Streptosporangiales;
OC Streptosporangiaceae; Sphaerisporangium.
OX NCBI_TaxID=1381558 {ECO:0000313|EMBL:GII78597.1, ECO:0000313|Proteomes:UP000655287};
RN [1] {ECO:0000313|EMBL:GII78597.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=NBRC 109079 {ECO:0000313|EMBL:GII78597.1};
RA Komaki H., Tamura T.;
RT "Whole genome shotgun sequence of Sphaerisporangium rufum NBRC 109079.";
RL Submitted (JAN-2021) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Repair polymerase that plays a key role in base-excision
CC repair. During this process, the damaged base is excised by specific
CC DNA glycosylases, the DNA backbone is nicked at the abasic site by an
CC apurinic/apyrimidic (AP) endonuclease, and POLB removes 5'-deoxyribose-
CC phosphate from the preincised AP site acting as a 5'-deoxyribose-
CC phosphate lyase (5'-dRP lyase); through its DNA polymerase activity, it
CC adds one nucleotide to the 3' end of the arising single-nucleotide gap.
CC Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion
CC rather than in a processive fashion as for other DNA polymerases. It is
CC also able to cleave sugar-phosphate bonds 3' to an intact AP site,
CC acting as an AP lyase. {ECO:0000256|ARBA:ARBA00045548}.
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'-phospho-2'-
CC 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:ARBA00044632};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) +
CC diphosphate; Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339, Rhea:RHEA-
CC COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560, ChEBI:CHEBI:173112;
CC EC=2.7.7.7; Evidence={ECO:0000256|ARBA:ARBA00049244};
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'-phospho-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:ARBA00044678};
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 -!- 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:GII78597.1}.
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DR EMBL; BOOU01000051; GII78597.1; -; Genomic_DNA.
DR RefSeq; WP_203986960.1; NZ_BOOU01000051.1.
DR AlphaFoldDB; A0A919V1H2; -.
DR Proteomes; UP000655287; Unassembled WGS sequence.
DR GO; GO:0005829; C:cytosol; IEA:TreeGrafter.
DR GO; GO:0140078; F:class I DNA-(apurinic or apyrimidinic site) endonuclease activity; IEA:UniProtKB-EC.
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:0004527; F:exonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0042578; F:phosphoric ester hydrolase activity; IEA:TreeGrafter.
DR GO; GO:0008270; F:zinc ion binding; IEA:TreeGrafter.
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; IPR027421; DNA_pol_lamdba_lyase_dom_sf.
DR InterPro; IPR037160; DNA_Pol_thumb_sf.
DR InterPro; IPR002008; DNA_pol_X_beta-like.
DR InterPro; IPR010996; HHH_MUS81.
DR InterPro; IPR003583; Hlx-hairpin-Hlx_DNA-bd_motif.
DR InterPro; IPR043519; NT_sf.
DR InterPro; IPR004013; PHP_dom.
DR InterPro; IPR050243; PHP_phosphatase.
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 NCBIfam; NF006375; PRK08609.1; 1.
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 replication {ECO:0000256|ARBA:ARBA00022705};
KW DNA synthesis {ECO:0000256|ARBA:ARBA00022634};
KW DNA-directed DNA polymerase {ECO:0000256|ARBA:ARBA00022932};
KW Exonuclease {ECO:0000313|EMBL:GII78597.1};
KW Hydrolase {ECO:0000313|EMBL:GII78597.1};
KW Methylation {ECO:0000256|ARBA:ARBA00022481};
KW Nuclease {ECO:0000313|EMBL:GII78597.1};
KW Nucleotidyltransferase {ECO:0000256|ARBA:ARBA00022695};
KW Reference proteome {ECO:0000313|Proteomes:UP000655287};
KW Sodium {ECO:0000256|ARBA:ARBA00023053};
KW Transferase {ECO:0000256|ARBA:ARBA00022679};
KW Ubl conjugation {ECO:0000256|ARBA:ARBA00022843}.
FT DOMAIN 3..305
FT /note="DNA-directed DNA polymerase X"
FT /evidence="ECO:0000259|SMART:SM00483"
FT DOMAIN 49..68
FT /note="Helix-hairpin-helix DNA-binding motif class 1"
FT /evidence="ECO:0000259|SMART:SM00278"
FT DOMAIN 89..108
FT /note="Helix-hairpin-helix DNA-binding motif class 1"
FT /evidence="ECO:0000259|SMART:SM00278"
FT DOMAIN 124..143
FT /note="Helix-hairpin-helix DNA-binding motif class 1"
FT /evidence="ECO:0000259|SMART:SM00278"
FT DOMAIN 329..407
FT /note="Polymerase/histidinol phosphatase N-terminal"
FT /evidence="ECO:0000259|SMART:SM00481"
SQ SEQUENCE 561 AA; 61122 MW; 13015286AAF2E8BC CRC64;
MGRANDEVAA ALTEYADLFA MTGGDAFRVR SYQKAAKAIA GHPEDISQVN VRRVPGVGEA
IAKKVEEFLS RGGFRQLDDL RAEVPEGVRR LTRVPSLGPK RAIFLYRELG IDSPEALAAA
IGAGRLAGVR GFGAKSEENL LKGVEQLRQA GGRVHLGVAM DLAERVIASL PAERVACAGS
VRRMKETVGD IDILAVGPPS LMEHFRRQPY VAEVIASGER KTSVRTREGM QVDLRLVPAG
SWGAAMQYFT GSKEHNVRLR EMCVKRGWKL SEYGLFEGDR VIAAATEEEI YQALGMPWIP
PPLREDTGEV AAALRGELPD LVTLDDLRGD LHTHTNLTDG IAPLADMVAA AARLGYAYYA
VTDHAPDLVM QRMTLDKALE QRAALAELQP AYPGMRLLHG TELNIGPDGA VDWPAEVLAG
FDVTVASVHS HFTQPRAEMT RRFVAACENP HVHVIGHPTT RKIGRREPVD ADWDAVFAAA
ARTGTALEID AYPDRADLPS DLVRRARHHG VKFSIDSDSH AVPHLANLRF GVGVAQRGWL
TAEDVINAWP VERLLAFLNR A
//
