DPOLB_DANRE
ID DPOLB_DANRE Reviewed; 336 AA.
AC Q6DRD3;
DT 13-SEP-2005, integrated into UniProtKB/Swiss-Prot.
DT 13-SEP-2005, sequence version 2.
DT 03-AUG-2022, entry version 110.
DE RecName: Full=DNA polymerase beta;
DE EC=2.7.7.7;
DE EC=4.2.99.-;
GN Name=polb;
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX PubMed=15256591; DOI=10.1073/pnas.0403929101;
RA Amsterdam A., Nissen R.M., Sun Z., Swindell E.C., Farrington S.,
RA Hopkins N.;
RT "Identification of 315 genes essential for early zebrafish development.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:12792-12797(2004).
CC -!- FUNCTION: Repair polymerase that plays a key role in base-excision
CC repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that
CC removes the 5' sugar phosphate and also acts as a DNA polymerase that
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 (By
CC similarity). {ECO:0000250}.
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 -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Note=Binds 2 magnesium ions per subunit. {ECO:0000250};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}. Cytoplasm {ECO:0000250}.
CC Note=Cytoplasmic in normal conditions. Translocates to the nucleus
CC following DNA damage (By similarity). {ECO:0000250}.
CC -!- PTM: Methylation by PRMT6 stimulates the polymerase activity by
CC enhancing DNA binding and processivity. {ECO:0000250}.
CC -!- PTM: Ubiquitinated: monoubiquitinated by huwe1/arf-bp1.
CC Monoubiquitinated protein is then the target of stub1/chip, which
CC catalyzes polyubiquitination from monoubiquitin, leading to degradation
CC by the proteasome. usp47 mediates the deubiquitination of
CC monoubiquitinated protein, preventing polyubiquitination by STUB1/CHIP
CC and its subsequent degradation (By similarity). {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the DNA polymerase type-X family. {ECO:0000305}.
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DR EMBL; AY648826; AAT68144.1; -; mRNA.
DR AlphaFoldDB; Q6DRD3; -.
DR SMR; Q6DRD3; -.
DR STRING; 7955.ENSDARP00000017489; -.
DR PaxDb; Q6DRD3; -.
DR PeptideAtlas; Q6DRD3; -.
DR ZFIN; ZDB-GENE-040830-1; polb.
DR eggNOG; KOG2534; Eukaryota.
DR InParanoid; Q6DRD3; -.
DR BRENDA; 2.7.7.7; 928.
DR Reactome; R-DRE-110362; POLB-Dependent Long Patch Base Excision Repair.
DR Reactome; R-DRE-110373; Resolution of AP sites via the multiple-nucleotide patch replacement pathway.
DR Reactome; R-DRE-110381; Resolution of AP sites via the single-nucleotide replacement pathway.
DR Reactome; R-DRE-5649702; APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway.
DR Reactome; R-DRE-5651801; PCNA-Dependent Long Patch Base Excision Repair.
DR Reactome; R-DRE-5689880; Ub-specific processing proteases.
DR Reactome; R-DRE-73930; Abasic sugar-phosphate removal via the single-nucleotide replacement pathway.
DR PRO; PR:Q6DRD3; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Unplaced.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IDA:ZFIN.
DR GO; GO:0016829; F:lyase activity; ISS:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006284; P:base-excision repair; ISS:UniProtKB.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; ISS:UniProtKB.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR GO; GO:0006303; P:double-strand break repair via nonhomologous end joining; IBA:GO_Central.
DR CDD; cd00141; NT_POLXc; 1.
DR Gene3D; 1.10.150.110; -; 1.
DR Gene3D; 3.30.210.10; -; 1.
DR Gene3D; 3.30.460.10; -; 1.
DR InterPro; IPR002054; DNA-dir_DNA_pol_X.
DR InterPro; IPR019843; DNA_pol-X_BS.
DR InterPro; IPR010996; DNA_pol_b-like_N.
DR InterPro; IPR028207; DNA_pol_B_palm_palm.
DR InterPro; IPR018944; DNA_pol_lambd_fingers_domain.
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; IPR029398; PolB_thumb.
DR PANTHER; PTHR11276; PTHR11276; 1.
DR Pfam; PF14792; DNA_pol_B_palm; 1.
DR Pfam; PF14791; DNA_pol_B_thumb; 1.
DR Pfam; PF10391; DNA_pol_lambd_f; 1.
DR Pfam; PF14716; HHH_8; 1.
DR PRINTS; PR00869; DNAPOLX.
DR PRINTS; PR00870; DNAPOLXBETA.
DR SMART; SM00278; HhH1; 2.
DR SMART; SM00483; POLXc; 1.
DR SUPFAM; SSF47802; SSF47802; 1.
DR SUPFAM; SSF81301; SSF81301; 1.
DR PROSITE; PS00522; DNA_POLYMERASE_X; 1.
PE 2: Evidence at transcript level;
KW Cytoplasm; DNA damage; DNA repair; DNA replication; DNA synthesis;
KW DNA-binding; DNA-directed DNA polymerase; Lyase; Magnesium; Metal-binding;
KW Methylation; Nucleotidyltransferase; Nucleus; Reference proteome; Sodium;
KW Transferase; Ubl conjugation.
FT CHAIN 1..336
FT /note="DNA polymerase beta"
FT /id="PRO_0000218781"
FT REGION 182..191
FT /note="DNA-binding"
FT /evidence="ECO:0000250"
FT ACT_SITE 71
FT /note="Schiff-base intermediate with DNA"
FT /evidence="ECO:0000250"
FT BINDING 100
FT /ligand="Na(+)"
FT /ligand_id="ChEBI:CHEBI:29101"
FT /evidence="ECO:0000250"
FT BINDING 102
FT /ligand="Na(+)"
FT /ligand_id="ChEBI:CHEBI:29101"
FT /evidence="ECO:0000250"
FT BINDING 105
FT /ligand="Na(+)"
FT /ligand_id="ChEBI:CHEBI:29101"
FT /evidence="ECO:0000250"
FT BINDING 189
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 189
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 191
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 191
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 257
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT MOD_RES 82
FT /note="Omega-N-methylarginine; by PRMT6"
FT /evidence="ECO:0000250"
FT MOD_RES 151
FT /note="Omega-N-methylarginine; by PRMT6"
FT /evidence="ECO:0000250"
SQ SEQUENCE 336 AA; 38566 MW; FDF6EA3088354973 CRC64;
SKRKAPQESL NEGITDFLVE LANYERNVNR AIHKYNAYRK AASVIAKYPQ KIKSGTEAKK
LDGVGAKIAE KIDEFLTTGK LRKLEKIRND DTSSSINFLT RVTGIGPAAA RKFFDEGVRN
LEDLKKIEHK LNHHQQIGLK YFEEFEKRIP RSEMQKMEAL ILKELDIVDP EYIGTICGSY
RRGAESSGDI DILLTHPDFT SQSEKQPKLL HAVVDHLESI GFITDTLSKG DTKFMGVCQL
QKEKEEEEEE SLHRRIDIRL IPKDQYYCGV LYFTGSDIFN KNMRTHALEK GFTLNEYTIR
PLGVTGVAGE PLLVDSEKDI FEYIQWKYRE PKDRSE
