DPOD1_CAEEL
ID DPOD1_CAEEL Reviewed; 1081 AA.
AC P90829;
DT 21-FEB-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1997, sequence version 1.
DT 03-AUG-2022, entry version 154.
DE RecName: Full=DNA polymerase delta catalytic subunit;
DE EC=2.7.7.7;
GN ORFNames=F10C2.4;
OS Caenorhabditis elegans.
OC Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
OC Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae;
OC Caenorhabditis.
OX NCBI_TaxID=6239;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Bristol N2;
RX PubMed=9851916; DOI=10.1126/science.282.5396.2012;
RG The C. elegans sequencing consortium;
RT "Genome sequence of the nematode C. elegans: a platform for investigating
RT biology.";
RL Science 282:2012-2018(1998).
CC -!- FUNCTION: Possesses two enzymatic activities: DNA synthesis
CC (polymerase) and an exonucleolytic activity that degrades single
CC stranded DNA in the 3'- to 5'-direction. Required with its accessory
CC proteins (proliferating cell nuclear antigen (PCNA) and replication
CC factor C (RFC) or activator 1) for leading strand synthesis. Also
CC involved in completing Okazaki fragments initiated by the DNA
CC polymerase alpha/primase complex (By 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=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; Evidence={ECO:0000250};
CC Note=Binds 1 [4Fe-4S] cluster. {ECO:0000250};
CC -!- SUBUNIT: Heterodimer with subunits of 125 kDa and 50 kDa. The 125 kDa
CC subunit contains the polymerase active site and most likely the active
CC site for the 3'-5' exonuclease activity (By similarity). {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- DOMAIN: The CysB motif binds 1 4Fe-4S cluster and is required for the
CC formation of polymerase complexes. {ECO:0000250}.
CC -!- MISCELLANEOUS: In eukaryotes there are five DNA polymerases: alpha,
CC beta, gamma, delta, and epsilon which are responsible for different
CC reactions of DNA synthesis.
CC -!- SIMILARITY: Belongs to the DNA polymerase type-B family. {ECO:0000305}.
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DR EMBL; Z81497; CAB04077.1; -; Genomic_DNA.
DR PIR; T20698; T20698.
DR RefSeq; NP_506017.1; NM_073616.3.
DR AlphaFoldDB; P90829; -.
DR SMR; P90829; -.
DR BioGRID; 44675; 19.
DR STRING; 6239.F10C2.4; -.
DR iPTMnet; P90829; -.
DR EPD; P90829; -.
DR PaxDb; P90829; -.
DR PeptideAtlas; P90829; -.
DR EnsemblMetazoa; F10C2.4.1; F10C2.4.1; WBGene00008645.
DR GeneID; 179652; -.
DR KEGG; cel:CELE_F10C2.4; -.
DR UCSC; F10C2.4; c. elegans.
DR CTD; 179652; -.
DR WormBase; F10C2.4; CE09308; WBGene00008645; -.
DR eggNOG; KOG0969; Eukaryota.
DR GeneTree; ENSGT00560000077365; -.
DR HOGENOM; CLU_000203_2_0_1; -.
DR InParanoid; P90829; -.
DR OMA; GNQKSPY; -.
DR OrthoDB; 20210at2759; -.
DR PhylomeDB; P90829; -.
DR Reactome; R-CEL-110314; Recognition of DNA damage by PCNA-containing replication complex.
DR Reactome; R-CEL-5651801; PCNA-Dependent Long Patch Base Excision Repair.
DR Reactome; R-CEL-5656169; Termination of translesion DNA synthesis.
DR Reactome; R-CEL-5696397; Gap-filling DNA repair synthesis and ligation in GG-NER.
DR Reactome; R-CEL-5696400; Dual Incision in GG-NER.
DR Reactome; R-CEL-6782135; Dual incision in TC-NER.
DR Reactome; R-CEL-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
DR Reactome; R-CEL-69091; Polymerase switching.
DR Reactome; R-CEL-69166; Removal of the Flap Intermediate.
DR Reactome; R-CEL-69183; Processive synthesis on the lagging strand.
DR PRO; PR:P90829; -.
DR Proteomes; UP000001940; Chromosome V.
DR Bgee; WBGene00008645; Expressed in germ line (C elegans) and 4 other tissues.
DR GO; GO:0043625; C:delta DNA polymerase complex; IBA:GO_Central.
DR GO; GO:0008296; F:3'-5'-exodeoxyribonuclease activity; IBA:GO_Central.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000166; F:nucleotide binding; IEA:InterPro.
DR GO; GO:0006287; P:base-excision repair, gap-filling; IBA:GO_Central.
DR GO; GO:0045004; P:DNA replication proofreading; IBA:GO_Central.
DR GO; GO:0006261; P:DNA-templated DNA replication; IBA:GO_Central.
DR GO; GO:0006297; P:nucleotide-excision repair, DNA gap filling; IBA:GO_Central.
DR Gene3D; 1.10.132.60; -; 1.
DR Gene3D; 3.30.420.10; -; 1.
DR Gene3D; 3.90.1600.10; -; 1.
DR InterPro; IPR006172; DNA-dir_DNA_pol_B.
DR InterPro; IPR017964; DNA-dir_DNA_pol_B_CS.
DR InterPro; IPR006133; DNA-dir_DNA_pol_B_exonuc.
DR InterPro; IPR006134; DNA-dir_DNA_pol_B_multi_dom.
DR InterPro; IPR043502; DNA/RNA_pol_sf.
DR InterPro; IPR042087; DNA_pol_B_thumb.
DR InterPro; IPR023211; DNA_pol_palm_dom_sf.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR InterPro; IPR025687; Znf-C4pol.
DR Pfam; PF00136; DNA_pol_B; 1.
DR Pfam; PF03104; DNA_pol_B_exo1; 1.
DR Pfam; PF14260; zf-C4pol; 1.
DR PRINTS; PR00106; DNAPOLB.
DR SMART; SM00486; POLBc; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
DR SUPFAM; SSF56672; SSF56672; 1.
DR PROSITE; PS00116; DNA_POLYMERASE_B; 1.
PE 3: Inferred from homology;
KW 4Fe-4S; DNA replication; DNA-binding; DNA-directed DNA polymerase;
KW Exonuclease; Hydrolase; Iron; Iron-sulfur; Metal-binding; Nuclease;
KW Nucleotidyltransferase; Nucleus; Reference proteome; Transferase; Zinc;
KW Zinc-finger.
FT CHAIN 1..1081
FT /note="DNA polymerase delta catalytic subunit"
FT /id="PRO_0000046446"
FT ZN_FING 981..1001
FT /note="CysA-type"
FT REGION 1..22
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 1030..1048
FT /note="CysB motif"
FT BINDING 981
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 984
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 998
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 1001
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 1030
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 1033
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 1043
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 1048
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1081 AA; 120830 MW; 405954DDCC61F07E CRC64;
MTSKRPGGSS FQPEVKRKRE SDEFEQCYVS RFENELPSVP TIDKTGWARP AVDKDLGISK
SIACQILEVE TYHEDGSATS YDRTNVKLYG VTKSGNSICV IVTDYFPHFY FQAPQGFGVE
HIGTAQSAIC NMVAAAKRRG GSGQAQLPGK VVDNLVHVEI VHGENLYYFR GADTKVPFVK
VSGSTEALHK ARMELKNGVN LMGKGPVNVG NLYESNINVI VMFLAKTNIV GCGWIEIPAG
KCRILSNSEK SSRCQIEVTV PVKNLIVHES DGEWAGIAPI RTLSLDIECI GRRGVFPEAI
KDPIIQIANL VKIEGEAEPF VRNCFVLGTC APVVGSNIIQ CVNEKVLLEK WAEFVREVDP
DIITGYNILN FDLPYILDRA KVLSLPQVSH LGRQKEKGSV VRDAAISSKQ MGSRVNKSID
IHGRIIFDVL QVVLRDYKLR SYTLNSVSYQ FLSEQKEDVE HNIIPDLQRG DEQTRRRLAQ
YCLKDAYLPL RLLDKLMSII NYIEMARVTG VPMNFLLTKG QQIKILSMML RRCKQNNFFL
PVIEANSGDG EGYEGATVID PIRGFYNEPI ATLDFASLYP SIMIAHNLCY TTLLKSPQGV
ENEDYIRTPS GQYFATKSKR RGLLPEILED ILAARKRAKN DMKNEKDEFK RMVYNGRQLA
LKISANSVYG FTGATVGKLP CLEISQSVTA FGRKMIDMTK LEVERIYKKG ALDGKCPADA
KVIYGDTDSV MVKFGVETVA QAMEIGLDAA KEVSKIFTPP IKLEFEKVYS PYLLINKKRY
AGLYFTKPDV HDKMDCKGLE TVRRDNCPLV AKVLGVCLEK LLIERDQQSA LDFAKRTISD
LLCNKIDISL LIISKELTKS GDKYQAKQAH VELAARMKKR DAGSAPRLGD RVPYVFVAAA
KNVPAYERAE DPTFVLQNNI PLDTKHYLTN QLAKPLARIF EPILGDRAEK ILVEGEHTRV
RTVVQSKVGG LAAFTTKSAT CLGCKSVLPR AESENAVCKH CEPKLPTIFA SRMNTMHELE
NHFGRLWTEC QNCAKTMQDK VNCSARDCPI YYMREKVRNE LSEASAVIER FGDPCFQAPT
K
