DPOD_SCHPO
ID DPOD_SCHPO Reviewed; 1086 AA.
AC P30316; Q10016; Q9USU0; Q9UU61;
DT 01-APR-1993, integrated into UniProtKB/Swiss-Prot.
DT 11-JAN-2001, sequence version 2.
DT 03-AUG-2022, entry version 191.
DE RecName: Full=DNA polymerase delta catalytic subunit;
DE EC=2.7.7.7 {ECO:0000250|UniProtKB:P15436};
DE AltName: Full=3'-5' exodeoxyribonuclease {ECO:0000305};
DE EC=3.1.11.- {ECO:0000250|UniProtKB:P15436};
DE AltName: Full=DNA polymerase III;
GN Name=pol3; Synonyms=pold; ORFNames=SPBC336.04;
OS Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina;
OC Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae;
OC Schizosaccharomyces.
OX NCBI_TaxID=284812;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1960723; DOI=10.1016/0022-2836(91)90207-m;
RA Pignede G., Bouvier D., de Recondo A.-M., Baldacci G.;
RT "Characterization of the POL3 gene product from Schizosaccharomyces pombe
RT indicates inter-species conservation of the catalytic subunit of DNA
RT polymerase delta.";
RL J. Mol. Biol. 222:209-218(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=8443413; DOI=10.1091/mbc.4.2.145;
RA Park H., Francesconi S., Wang T.S.F.;
RT "Cell cycle expression of two replicative DNA polymerases alpha and delta
RT from Schizosaccharomyces pombe.";
RL Mol. Biol. Cell 4:145-157(1993).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=972 / ATCC 24843;
RX PubMed=11859360; DOI=10.1038/nature724;
RA Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A.,
RA Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S.,
RA Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.,
RA Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S.,
RA Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S.,
RA Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D.,
RA Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P.,
RA Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K.,
RA O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M.,
RA Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N.,
RA Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A.,
RA Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R.,
RA Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M.,
RA Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A.,
RA Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A.,
RA Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H.,
RA Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S.,
RA Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C.,
RA Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A.,
RA Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M.,
RA del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S.,
RA Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R.,
RA Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G.,
RA Nurse P.;
RT "The genome sequence of Schizosaccharomyces pombe.";
RL Nature 415:871-880(2002).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] OF 272-455.
RC STRAIN=ATCC 38364 / 968;
RX PubMed=10759889; DOI=10.1046/j.1365-2443.2000.00317.x;
RA Ding D.-Q., Tomita Y., Yamamoto A., Chikashige Y., Haraguchi T.,
RA Hiraoka Y.;
RT "Large-scale screening of intracellular protein localization in living
RT fission yeast cells by the use of a GFP-fusion genomic DNA library.";
RL Genes Cells 5:169-190(2000).
RN [5]
RP FUNCTION.
RX PubMed=31488849; DOI=10.1038/s41467-019-11995-z;
RA Zhou Z.X., Lujan S.A., Burkholder A.B., Garbacz M.A., Kunkel T.A.;
RT "Roles for DNA polymerase delta in initiating and terminating leading
RT strand DNA replication.";
RL Nat. Commun. 10:3992-3992(2019).
CC -!- FUNCTION: Catalytic component of DNA polymerase delta (DNA polymerase
CC III) which participates in chromosomal DNA replication
CC (PubMed:31488849). Required during synthesis of the lagging DNA strands
CC at the replication fork, binds at/or near replication origins and moves
CC along DNA with the replication fork (PubMed:31488849). Participates in
CC leading strand synthesis during replication initiation and termination
CC (PubMed:31488849). Has 3'-5' proofreading exonuclease activity that
CC corrects errors arising during DNA replication (By similarity).
CC {ECO:0000250|UniProtKB:P15436, ECO:0000269|PubMed:31488849}.
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:0000250|UniProtKB:P15436};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000250|UniProtKB:P15436};
CC Note=Binds 1 [4Fe-4S] cluster. {ECO:0000250|UniProtKB:P15436};
CC -!- SUBUNIT: Heterotetramer that consist of the pol3, cdc1, cdc27 and cdm1
CC subunits. The pol3 subunit contains the polymerase active site and most
CC likely the active site for the 3'-5' exonuclease activity.
CC -!- INTERACTION:
CC P30316; P87324: cdc1; NbExp=2; IntAct=EBI-865207, EBI-865227;
CC -!- SUBCELLULAR LOCATION: Nucleus.
CC -!- DOMAIN: The CysB motif binds 1 4Fe-4S cluster and is required for the
CC formation of polymerase complexes. {ECO:0000250|UniProtKB:P15436}.
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; X59278; CAA41968.1; -; Genomic_DNA.
DR EMBL; L07734; AAA35303.1; -; Genomic_DNA.
DR EMBL; CU329671; CAB58156.1; -; Genomic_DNA.
DR EMBL; AB027796; BAA87100.1; -; Genomic_DNA.
DR PIR; S19661; S19661.
DR PIR; T40242; T40242.
DR PIR; T43266; T43266.
DR RefSeq; NP_596124.1; NM_001022042.2.
DR AlphaFoldDB; P30316; -.
DR SMR; P30316; -.
DR BioGRID; 276786; 38.
DR ComplexPortal; CPX-2100; DNA polymerase delta complex.
DR IntAct; P30316; 1.
DR STRING; 4896.SPBC336.04.1; -.
DR iPTMnet; P30316; -.
DR MaxQB; P30316; -.
DR PaxDb; P30316; -.
DR PRIDE; P30316; -.
DR EnsemblFungi; SPBC336.04.1; SPBC336.04.1:pep; SPBC336.04.
DR GeneID; 2540255; -.
DR KEGG; spo:SPBC336.04; -.
DR PomBase; SPBC336.04; -.
DR VEuPathDB; FungiDB:SPBC336.04; -.
DR eggNOG; KOG0969; Eukaryota.
DR HOGENOM; CLU_000203_2_0_1; -.
DR InParanoid; P30316; -.
DR OMA; GNQKSPY; -.
DR PhylomeDB; P30316; -.
DR Reactome; R-SPO-110314; Recognition of DNA damage by PCNA-containing replication complex.
DR Reactome; R-SPO-174437; Removal of the Flap Intermediate from the C-strand.
DR Reactome; R-SPO-5358565; Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha).
DR Reactome; R-SPO-5358606; Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta).
DR Reactome; R-SPO-5651801; PCNA-Dependent Long Patch Base Excision Repair.
DR Reactome; R-SPO-5656169; Termination of translesion DNA synthesis.
DR Reactome; R-SPO-5696397; Gap-filling DNA repair synthesis and ligation in GG-NER.
DR Reactome; R-SPO-5696400; Dual Incision in GG-NER.
DR Reactome; R-SPO-6782135; Dual incision in TC-NER.
DR Reactome; R-SPO-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
DR Reactome; R-SPO-69091; Polymerase switching.
DR Reactome; R-SPO-69166; Removal of the Flap Intermediate.
DR Reactome; R-SPO-69183; Processive synthesis on the lagging strand.
DR PRO; PR:P30316; -.
DR Proteomes; UP000002485; Chromosome II.
DR GO; GO:0140445; C:chromosome, telomeric repeat region; IDA:PomBase.
DR GO; GO:0043625; C:delta DNA polymerase complex; IDA:PomBase.
DR GO; GO:0005634; C:nucleus; IDA:PomBase.
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; ISM:PomBase.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IDA:PomBase.
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:0006271; P:DNA strand elongation involved in DNA replication; IDA:PomBase.
DR GO; GO:1904161; P:DNA synthesis involved in UV-damage excision repair; IDA:PomBase.
DR GO; GO:0006261; P:DNA-templated DNA replication; IBA:GO_Central.
DR GO; GO:1903459; P:mitotic DNA replication lagging strand elongation; IMP:PomBase.
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 1: Evidence at protein level;
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..1086
FT /note="DNA polymerase delta catalytic subunit"
FT /id="PRO_0000046453"
FT ZN_FING 993..1011
FT /note="CysA-type"
FT /evidence="ECO:0000250|UniProtKB:P15436"
FT REGION 1..64
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 1040..1058
FT /note="CysB motif"
FT /evidence="ECO:0000250|UniProtKB:P15436"
FT COMPBIAS 27..61
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 993
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:P15436"
FT BINDING 996
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:P15436"
FT BINDING 1008
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:P15436"
FT BINDING 1011
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:P15436"
FT BINDING 1040
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P15436"
FT BINDING 1043
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P15436"
FT BINDING 1053
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P15436"
FT BINDING 1058
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P15436"
FT CONFLICT 102
FT /note="Q -> E (in Ref. 1; CAA41968)"
FT /evidence="ECO:0000305"
FT CONFLICT 290
FT /note="K -> Q (in Ref. 4; BAA87100)"
FT /evidence="ECO:0000305"
FT CONFLICT 419
FT /note="T -> S (in Ref. 1; CAA41968)"
FT /evidence="ECO:0000305"
FT CONFLICT 545
FT /note="R -> C (in Ref. 1; CAA41968 and 2; AAA35303)"
FT /evidence="ECO:0000305"
FT CONFLICT 777..784
FT /note="KLEFEKVY -> NWSFST (in Ref. 1; CAA41968)"
FT /evidence="ECO:0000305"
FT CONFLICT 866
FT /note="L -> H (in Ref. 1; CAA41968)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1086 AA; 123569 MW; 99F528413220C3CA CRC64;
MTDRSSNEGV VLNKENYPFP RRNGSIHGEI TDVKRRRLSE RNGYGDKKGS SSKEKTSSFE
DELAEYASQL DQDEIKSSKD QQWQRPALPA INPEKDDIYF QQIDSEEFTE GSVPSIRLFG
VTDNGNSILV HVVGFLPYFY VKAPVGFRPE MLERFTQDLD ATCNGGVIDH CIIEMKENLY
GFQGNEKSPF IKIFTTNPRI LSRARNVFER GEFNFEELFP VGVGVTTFES NTQYLLRFMI
DCDVVGMNWI HLPASKYQFR YQNRVSNCQI EAWINYKDLI SLPAEGQWSK MAPLRIMSFD
IECAGRKGVF PDPSIDPVIQ IASIVTQYGD STPFVRNVFC VDTCSQIVGT QVYEFQNQAE
MLSSWSKFVR DVDPDVLIGY NICNFDIPYL LDRAKSLRIH NFPLLGRIHN FFSVAKETTF
SSKAYGTRES KTTSIPGRLQ LDMLQVMQRD FKLRSYSLNA VCSQFLGEQK EDVHYSIITD
LQNGTADSRR RLAIYCLKDA YLPQRLMDKL MCFVNYTEMA RVTGVPFNFL LARGQQIKVI
SQLFRKALQH DLVVPNIRVN GTDEQYEGAT VIEPIKGYYD TPIATLDFSS LYPSIMQAHN
LCYTTLLDSN TAELLKLKQD VDYSVTPNGD YFVKPHVRKG LLPIILADLL NARKKAKADL
KKETDPFKKA VLDGRQLALK VSANSVYGFT GATNGRLPCL AISSSVTSYG RQMIEKTKDV
VEKRYRIENG YSHDAVVIYG DTDSVMVKFG VKTLPEAMKL GEEAANYVSD QFPNPIKLEF
EKVYFPYLLI SKKRYAGLFW TRTDTYDKMD SKGIETVRRD NCPLVSYVID TALRKMLIDQ
DVEGAQLFTK KVISDLLQNK IDMSQLVITK ALSKTDYAAK MAHVELAERM RKRDAGSAPA
IGDRVAYVII KGAQGDQFYM RSEDPIYVLE NNIPIDAKYY LENQLSKPLL RIFEPILGEK
ASSLLHGDHT RTISMAAPSV GGIMKFAVKV ETCLGCKAPI KKGKTALCEN CLNRSAELYQ
RQVAQVNDLE VRFARLWTQC QRCQGSMHQD VICTSRDCPI FYMRIAEHKK LQQSVDLLKR
FDEMSW
