ID A0A3M8PCM9_9BACL Unreviewed; 567 AA.
AC A0A3M8PCM9;
DT 13-FEB-2019, integrated into UniProtKB/TrEMBL.
DT 13-FEB-2019, sequence version 1.
DT 27-MAR-2024, entry version 22.
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 Name=polX {ECO:0000313|EMBL:RNF40890.1};
GN ORFNames=EEX84_00610 {ECO:0000313|EMBL:RNF40890.1};
OS Planococcus salinus.
OC Bacteria; Bacillota; Bacilli; Bacillales; Planococcaceae; Planococcus.
OX NCBI_TaxID=1848460 {ECO:0000313|EMBL:RNF40890.1, ECO:0000313|Proteomes:UP000275473};
RN [1] {ECO:0000313|EMBL:RNF40890.1, ECO:0000313|Proteomes:UP000275473}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LCB217 {ECO:0000313|EMBL:RNF40890.1,
RC ECO:0000313|Proteomes:UP000275473};
RX PubMed=29300160; DOI=10.1099/ijsem.0.002548;
RA Gan L.;
RT "Planococcus salinus sp. nov., a moderately halophilic bacterium isolated
RT from a saline-alkali soil.";
RL Int. J. Syst. Evol. Microbiol. 68:589-595(2018).
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}.
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:RNF40890.1}.
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DR EMBL; RIAX01000001; RNF40890.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A3M8PCM9; -.
DR OrthoDB; 9808747at2; -.
DR Proteomes; UP000275473; Unassembled WGS sequence.
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:0004527; F:exonuclease 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; IPR028207; DNA_pol_B_palm_palm.
DR InterPro; IPR027421; DNA_pol_lamdba_lyase_dom_sf.
DR InterPro; IPR037160; DNA_Pol_thumb_sf.
DR InterPro; IPR022312; DNA_pol_X.
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; PF14792; DNA_pol_B_palm; 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; PR00869; DNAPOLX.
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 Exonuclease {ECO:0000313|EMBL:RNF40890.1};
KW Hydrolase {ECO:0000313|EMBL:RNF40890.1};
KW Methylation {ECO:0000256|ARBA:ARBA00022481};
KW Nuclease {ECO:0000313|EMBL:RNF40890.1};
KW Nucleotidyltransferase {ECO:0000256|ARBA:ARBA00022695};
KW Reference proteome {ECO:0000313|Proteomes:UP000275473};
KW Sodium {ECO:0000256|ARBA:ARBA00023053};
KW Transferase {ECO:0000256|ARBA:ARBA00022679};
KW Ubl conjugation {ECO:0000256|ARBA:ARBA00022843}.
FT DOMAIN 1..313
FT /note="DNA-directed DNA polymerase X"
FT /evidence="ECO:0000259|SMART:SM00483"
FT DOMAIN 48..67
FT /note="Helix-hairpin-helix DNA-binding motif class 1"
FT /evidence="ECO:0000259|SMART:SM00278"
FT DOMAIN 88..107
FT /note="Helix-hairpin-helix DNA-binding motif class 1"
FT /evidence="ECO:0000259|SMART:SM00278"
FT DOMAIN 123..142
FT /note="Helix-hairpin-helix DNA-binding motif class 1"
FT /evidence="ECO:0000259|SMART:SM00278"
FT DOMAIN 335..414
FT /note="Polymerase/histidinol phosphatase N-terminal"
FT /evidence="ECO:0000259|SMART:SM00481"
SQ SEQUENCE 567 AA; 63590 MW; CD8D411CEFC58778 CRC64;
MNKKVIIRTL EKIALYMELK GDNPFKVSAF RKAAQALELD PRSLDELEDV TKLKGIGKGT
GDVIVELMET GKSSVLEELQ AAVPKGLVPL MKLQGMGGKK IAKLYKELGI DSAEALKQAC
IDHEIQKLPG FGPKSEEKIL KELMEFESKP GRLPIWKTEE TVAFVEDVLQ NIQEVSEFSV
AGSYRRVKET SKDLDFIVAT SEPAAVKEQL LAALPVQETI ASGDTKVSVT VELQELVDVD
FRLVAPEEFV TALHHFTGSK DHNVKMRQLA KSQNKKISEY GVEQEDGTIK TFASETDFYA
HFGLPFIPPT VREDGREFDR LDDLPKLIEL QDIKGDLHMH TTASDGANSL KEMIEACRAK
SYDYMVITDH SQYLKVANGL TPERLLEQNA KIRQLNEEYT DLEILSGTEM DILPDATLDF
DDEVLKQLDF VIASIHSSFQ QPREQIMERL LTAMKNPYVH MIAHPTGRIV GQRNGYDPDV
EQLLDWAKQY GKIVELNASP YRLDLAVEFL EMAQEKGVPV AINTDAHAID GLGVMATGVH
HAQKAWLKKD TVVNTWPLSK LKDYLKR
//
