DPB4_SCHPO
ID DPB4_SCHPO Reviewed; 210 AA.
AC P87174;
DT 13-SEP-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1997, sequence version 1.
DT 03-AUG-2022, entry version 133.
DE RecName: Full=DNA polymerase epsilon subunit D {ECO:0000303|PubMed:15388803};
DE AltName: Full=DNA polymerase II subunit D {ECO:0000305};
GN Name=dpb4 {ECO:0000303|PubMed:15388803};
GN ORFNames=SPBC3D6.09 {ECO:0000312|PomBase:SPBC3D6.09};
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 [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 [2]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=15388803; DOI=10.1093/nar/gkh811;
RA Spiga M.-G., D'Urso G.;
RT "Identification and cloning of two putative subunits of DNA polymerase
RT epsilon in fission yeast.";
RL Nucleic Acids Res. 32:4945-4953(2004).
RN [3] {ECO:0007744|PDB:5Y26, ECO:0007744|PDB:5Y27}
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) IN COMPLEX WITH DPB3, DISRUPTION
RP PHENOTYPE, FUNCTION, AND INTERACTION WITH DPB3; CDC20; PCNA; RFC5; MCM3;
RP MCM4; SPT16; POB3; HRP3; SNF22; ARP9; ARP42; SSR1; SSR3; SSR4; H4; H2B;
RP NAP1 AND HIP1; SIR2 AND CLR6.
RX PubMed=29109278; DOI=10.1073/pnas.1712961114;
RA He H., Li Y., Dong Q., Chang A.Y., Gao F., Chi Z., Su M., Zhang F., Ban H.,
RA Martienssen R., Chen Y.H., Li F.;
RT "Coordinated regulation of heterochromatin inheritance by Dpb3-Dpb4
RT complex.";
RL Proc. Natl. Acad. Sci. U.S.A. 114:12524-12529(2017).
RN [4]
RP INTERACTION WITH DRI1, AND DISRUPTION PHENOTYPE.
RX PubMed=33693625; DOI=10.1093/genetics/iyab032;
RA Ban H., Sun W., Chen Y.H., Chen Y., Li F.;
RT "Dri1 mediates heterochromatin assembly via RNAi and histone
RT deacetylation.";
RL Genetics 217:iyab032-iyab032(2021).
CC -!- FUNCTION: As accessory component of the DNA polymerase epsilon (DNA
CC polymerase II) participates in chromosomal DNA replication. It is
CC required during synthesis of the leading and lagging DNA strands at the
CC replication fork and binds at/or near replication origins and moves
CC along DNA with the replication fork. It has 3'-5' proofreading
CC exonuclease activity that correct errors arising during DNA
CC replication. It is also involved in DNA synthesis during DNA repair (By
CC similarity). The dpb3-dpb4 dimer associates with histone deacetylases,
CC chromatin remodelers, and histones and plays a crucial role in the
CC inheritance of histone hypoacetylation and H3K9 methylation in
CC heterochromatin (PubMed:29109278). The dpb3-dpb4 dimer is also required
CC for the recruitment of sir2 to heterochromatin (PubMed:29109278).
CC {ECO:0000250|UniProtKB:Q04603, ECO:0000269|PubMed:29109278}.
CC -!- SUBUNIT: DNA polymerase epsilon is a heterotetramer consisting of
CC cdc20/Pol2, dpb2, dpb3, and dpb4 (By similarity). Heterodimer
CC consisting dpb3 and dpb4 (PubMed:29109278). Interacts with the
CC replication factor dpb3, cdc20, PCNA and rfc5; the replication
CC licensing factors mcm3 and mcm4; the FACT complex subunits spt16 and
CC pob3; the CHD1-type remodeler hrp3; the SWI/SNF chromatin remodeling
CC complex subunits snf22, arp9, arp42, ssr1, ssr3, and ssr4; the histones
CC H4 and H2B; the histone chaperones Nap1 and h; and the histone
CC deacetylases sir2 and clr6 (PubMed:29109278). Interacts with dri1
CC (PubMed:33693625). {ECO:0000250|UniProtKB:Q04603,
CC ECO:0000269|PubMed:29109278, ECO:0000269|PubMed:33693625}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:15388803}.
CC -!- DISRUPTION PHENOTYPE: Decreases H3K9 methylation and impairs
CC heterochromatin silencing; simultaneous disruption of dri1 exacerbates
CC the effect. {ECO:0000269|PubMed:29109278, ECO:0000269|PubMed:33693625}.
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DR EMBL; CU329671; CAB09118.1; -; Genomic_DNA.
DR PIR; T40369; T40369.
DR RefSeq; NP_595521.1; NM_001021430.2.
DR PDB; 5Y26; X-ray; 2.00 A; A=2-210.
DR PDB; 5Y27; X-ray; 1.90 A; A=2-210.
DR PDBsum; 5Y26; -.
DR PDBsum; 5Y27; -.
DR AlphaFoldDB; P87174; -.
DR SMR; P87174; -.
DR BioGRID; 277482; 16.
DR ComplexPortal; CPX-2111; DNA polymerase epsilon complex.
DR IntAct; P87174; 1.
DR STRING; 4896.SPBC3D6.09.1; -.
DR MaxQB; P87174; -.
DR PaxDb; P87174; -.
DR EnsemblFungi; SPBC3D6.09.1; SPBC3D6.09.1:pep; SPBC3D6.09.
DR GeneID; 2540966; -.
DR KEGG; spo:SPBC3D6.09; -.
DR PomBase; SPBC3D6.09; dpb4.
DR VEuPathDB; FungiDB:SPBC3D6.09; -.
DR eggNOG; KOG0870; Eukaryota.
DR HOGENOM; CLU_1278288_0_0_1; -.
DR InParanoid; P87174; -.
DR OMA; ALDHIGH; -.
DR PhylomeDB; P87174; -.
DR Reactome; R-SPO-110314; Recognition of DNA damage by PCNA-containing replication complex.
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-68952; DNA replication initiation.
DR Reactome; R-SPO-68962; Activation of the pre-replicative complex.
DR PRO; PR:P87174; -.
DR Proteomes; UP000002485; Chromosome II.
DR GO; GO:0000785; C:chromatin; IDA:PomBase.
DR GO; GO:0005829; C:cytosol; HDA:PomBase.
DR GO; GO:0008622; C:epsilon DNA polymerase complex; IPI:PomBase.
DR GO; GO:0043596; C:nuclear replication fork; IC:PomBase.
DR GO; GO:0005634; C:nucleus; IDA:PomBase.
DR GO; GO:0031490; F:chromatin DNA binding; IBA:GO_Central.
DR GO; GO:0046982; F:protein heterodimerization activity; IEA:InterPro.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; IBA:GO_Central.
DR GO; GO:0140529; P:CMG complex assembly; IC:PomBase.
DR GO; GO:1902983; P:DNA strand elongation involved in mitotic DNA replication; IC:PomBase.
DR GO; GO:0006261; P:DNA-templated DNA replication; IC:ComplexPortal.
DR GO; GO:0031507; P:heterochromatin assembly; IMP:PomBase.
DR GO; GO:0006272; P:leading strand elongation; IBA:GO_Central.
DR Gene3D; 1.10.20.10; -; 1.
DR InterPro; IPR003958; CBFA_NFYB_domain.
DR InterPro; IPR009072; Histone-fold.
DR Pfam; PF00808; CBFD_NFYB_HMF; 1.
DR SUPFAM; SSF47113; SSF47113; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA replication; Nucleus; Reference proteome.
FT CHAIN 1..210
FT /note="DNA polymerase epsilon subunit D"
FT /id="PRO_0000191752"
FT REGION 121..140
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 147..210
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 147..169
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 171..194
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT HELIX 10..15
FT /evidence="ECO:0007829|PDB:5Y27"
FT HELIX 19..28
FT /evidence="ECO:0007829|PDB:5Y27"
FT HELIX 38..65
FT /evidence="ECO:0007829|PDB:5Y27"
FT STRAND 69..71
FT /evidence="ECO:0007829|PDB:5Y27"
FT HELIX 73..82
FT /evidence="ECO:0007829|PDB:5Y27"
FT HELIX 86..88
FT /evidence="ECO:0007829|PDB:5Y27"
FT HELIX 89..105
FT /evidence="ECO:0007829|PDB:5Y27"
SQ SEQUENCE 210 AA; 23550 MW; F0DE2BF224914EED CRC64;
MNQDKSKETS ELDDLALPRS IIMRLVKGVL PEKSLVQKEA LKAMINSATL FVSFLTSASG
EIATNNNRKI LMPQDVLNAL DEIEYPEFSK TLKKHLEAYE LALKEKRLKL PNVSDVDNRK
KAKIDAHDTT PLDEEKDELE EERIAEDIAQ NEVEQNIDDV EDLEEVNDTL DANAESPQIE
TIHLTDATGN PIEDSSESDS EESLQLNDSS
