DPB4_YEAST
ID DPB4_YEAST Reviewed; 196 AA.
AC Q04603; D6VSA7;
DT 13-SEP-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 171.
DE RecName: Full=DNA polymerase epsilon subunit D;
DE AltName: Full=DNA polymerase II subunit D;
GN Name=DPB4; OrderedLocusNames=YDR121W;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169867;
RA Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA Mewes H.-W., Zollner A., Zaccaria P.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL Nature 387:75-78(1997).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [4]
RP PROTEIN SEQUENCE OF 115-125 AND 157-176, FUNCTION, SUBUNIT, AND SUBCELLULAR
RP LOCATION.
RX PubMed=11024162; DOI=10.1093/nar/28.20.3846;
RA Ohya T., Maki S., Kawasaki Y., Sugino A.;
RT "Structure and function of the fourth subunit (Dpb4p) of DNA polymerase
RT epsilon in Saccharomyces cerevisiae.";
RL Nucleic Acids Res. 28:3846-3852(2000).
RN [5]
RP FUNCTION OF THE ISW2 COMPLEX.
RX PubMed=11081629; DOI=10.1016/s0092-8674(00)00134-3;
RA Goldmark J.P., Fazzio T.G., Estep P.W., Church G.M., Tsukiyama T.;
RT "The Isw2 chromatin remodeling complex represses early meiotic genes upon
RT recruitment by Ume6p.";
RL Cell 103:423-433(2000).
RN [6]
RP FUNCTION OF THE ISW2 COMPLEX.
RX PubMed=11238944; DOI=10.1128/mcb.21.6.2098-2106.2001;
RA Gelbart M.E., Rechsteiner T., Richmond T.J., Tsukiyama T.;
RT "Interactions of Isw2 chromatin remodeling complex with nucleosomal arrays:
RT analyses using recombinant yeast histones and immobilized templates.";
RL Mol. Cell. Biol. 21:2098-2106(2001).
RN [7]
RP FUNCTION OF THE ISW2 COMPLEX.
RX PubMed=11533234; DOI=10.1128/mcb.21.19.6450-6460.2001;
RA Fazzio T.G., Kooperberg C., Goldmark J.P., Neal C., Basom R., Delrow J.,
RA Tsukiyama T.;
RT "Widespread collaboration of Isw2 and Sin3-Rpd3 chromatin remodeling
RT complexes in transcriptional repression.";
RL Mol. Cell. Biol. 21:6450-6460(2001).
RN [8]
RP FUNCTION.
RX PubMed=12124389; DOI=10.1074/jbc.m204476200;
RA Shimizu K., Hashimoto K., Kirchner J.M., Nakai W., Nishikawa H.,
RA Resnick M.A., Sugino A.;
RT "Fidelity of DNA polymerase epsilon holoenzyme from budding yeast
RT Saccharomyces cerevisiae.";
RL J. Biol. Chem. 277:37422-37429(2002).
RN [9]
RP COMPOSITION OF THE DNA POLYMERASE EPSILON COMPLEX.
RX PubMed=12571237; DOI=10.1074/jbc.m211818200;
RA Chilkova O., Jonsson B.-H., Johansson E.;
RT "The quaternary structure of DNA polymerase epsilon from Saccharomyces
RT cerevisiae.";
RL J. Biol. Chem. 278:14082-14086(2003).
RN [10]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [11]
RP IDENTIFICATION IN THE ISW2 COMPLEX, AND FUNCTION OF THE ISW2 COMPLEX.
RX PubMed=14673157; DOI=10.1128/mcb.24.1.217-227.2004;
RA Iida T., Araki H.;
RT "Noncompetitive counteractions of DNA polymerase epsilon and ISW2/yCHRAC
RT for epigenetic inheritance of telomere position effect in Saccharomyces
RT cerevisiae.";
RL Mol. Cell. Biol. 24:217-227(2004).
RN [12]
RP IDENTIFICATION IN THE ISW2 COMPLEX.
RX PubMed=15024052; DOI=10.1128/mcb.24.7.2605-2613.2004;
RA McConnell A.D., Gelbart M.E., Tsukiyama T.;
RT "Histone fold protein Dls1p is required for Isw2-dependent chromatin
RT remodeling in vivo.";
RL Mol. Cell. Biol. 24:2605-2613(2004).
RN [13]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-183, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
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.
CC Also functions as component of the ISW2 complex, which acts in
CC remodeling the chromatin by catalyzing an ATP-dependent alteration in
CC the structure of nucleosomal DNA. The ISW2 complex is involved in
CC coordinating transcriptional repression and in inheritance of telomeric
CC silencing. It is involved in repression of MAT a-specific genes, INO1,
CC and early meiotic genes during mitotic growth dependent upon
CC transcription factor UME6 and in a parallel pathway to the RPD3-SIN3
CC histone deacetylase complex. {ECO:0000269|PubMed:11024162,
CC ECO:0000269|PubMed:11081629, ECO:0000269|PubMed:11238944,
CC ECO:0000269|PubMed:11533234, ECO:0000269|PubMed:12124389,
CC ECO:0000269|PubMed:14673157}.
CC -!- SUBUNIT: DNA polymerase epsilon is a heterotetramer consisting of POL2,
CC DPB2, DPB3 and DPB4. Component of the ISW2 complex, which at least
CC consists of ISW2, ITC1, DLS1 and DPB4. {ECO:0000269|PubMed:11024162,
CC ECO:0000269|PubMed:14673157, ECO:0000269|PubMed:15024052}.
CC -!- INTERACTION:
CC Q04603; P40366: DLS1; NbExp=3; IntAct=EBI-29938, EBI-25910;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:11024162}.
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 -!- MISCELLANEOUS: Present with 2100 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
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DR EMBL; Z48758; CAA88674.1; -; Genomic_DNA.
DR EMBL; AY557673; AAS55999.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA11967.1; -; Genomic_DNA.
DR PIR; S52686; S52686.
DR RefSeq; NP_010406.3; NM_001180429.3.
DR PDB; 6WJV; EM; 3.50 A; 4=1-196.
DR PDBsum; 6WJV; -.
DR AlphaFoldDB; Q04603; -.
DR SMR; Q04603; -.
DR BioGRID; 32177; 157.
DR ComplexPortal; CPX-2110; DNA polymerase epsilon complex.
DR ComplexPortal; CPX-728; ISW2 chromatin remodeling complex.
DR DIP; DIP-4621N; -.
DR IntAct; Q04603; 21.
DR MINT; Q04603; -.
DR STRING; 4932.YDR121W; -.
DR iPTMnet; Q04603; -.
DR MaxQB; Q04603; -.
DR PaxDb; Q04603; -.
DR PRIDE; Q04603; -.
DR EnsemblFungi; YDR121W_mRNA; YDR121W; YDR121W.
DR GeneID; 851699; -.
DR KEGG; sce:YDR121W; -.
DR SGD; S000002528; DPB4.
DR VEuPathDB; FungiDB:YDR121W; -.
DR eggNOG; KOG0870; Eukaryota.
DR HOGENOM; CLU_087036_1_0_1; -.
DR InParanoid; Q04603; -.
DR OMA; ALDHIGH; -.
DR BioCyc; YEAST:G3O-29721-MON; -.
DR Reactome; R-SCE-5656169; Termination of translesion DNA synthesis.
DR Reactome; R-SCE-6782135; Dual incision in TC-NER.
DR Reactome; R-SCE-68952; DNA replication initiation.
DR Reactome; R-SCE-68962; Activation of the pre-replicative complex.
DR PRO; PR:Q04603; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; Q04603; protein.
DR GO; GO:0008623; C:CHRAC; IDA:SGD.
DR GO; GO:0008622; C:epsilon DNA polymerase complex; IDA:SGD.
DR GO; GO:0043596; C:nuclear replication fork; IDA:ComplexPortal.
DR GO; GO:0005634; C:nucleus; IC:ComplexPortal.
DR GO; GO:0031490; F:chromatin DNA binding; IDA:SGD.
DR GO; GO:0031492; F:nucleosomal DNA binding; IDA:SGD.
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:0006338; P:chromatin remodeling; IDA:SGD.
DR GO; GO:0006261; P:DNA-templated DNA replication; IDA:SGD.
DR GO; GO:0042276; P:error-prone translesion synthesis; IDA:SGD.
DR GO; GO:0031507; P:heterochromatin assembly; IBA:GO_Central.
DR GO; GO:0006272; P:leading strand elongation; IMP:SGD.
DR GO; GO:0090305; P:nucleic acid phosphodiester bond hydrolysis; IEA:GOC.
DR GO; GO:0050790; P:regulation of catalytic activity; IEA:GOC.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IC:ComplexPortal.
DR Gene3D; 1.10.20.10; -; 1.
DR InterPro; IPR009072; Histone-fold.
DR SUPFAM; SSF47113; SSF47113; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; DNA replication; Nucleus;
KW Phosphoprotein; Reference proteome; Transcription;
KW Transcription regulation.
FT CHAIN 1..196
FT /note="DNA polymerase epsilon subunit D"
FT /id="PRO_0000191754"
FT REGION 125..196
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 144..163
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 170..187
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 183
FT /note="Phosphoserine; by ATM or ATR"
FT /evidence="ECO:0007744|PubMed:18407956"
FT HELIX 36..40
FT /evidence="ECO:0007829|PDB:6WJV"
FT STRAND 47..49
FT /evidence="ECO:0007829|PDB:6WJV"
FT HELIX 57..82
FT /evidence="ECO:0007829|PDB:6WJV"
FT TURN 83..86
FT /evidence="ECO:0007829|PDB:6WJV"
FT HELIX 92..95
FT /evidence="ECO:0007829|PDB:6WJV"
FT TURN 99..103
FT /evidence="ECO:0007829|PDB:6WJV"
FT HELIX 105..121
FT /evidence="ECO:0007829|PDB:6WJV"
SQ SEQUENCE 196 AA; 21997 MW; 5D061EEA836B8BD3 CRC64;
MPPKGWRKDA QGNYPTTSYI KEQENITIQD LLFPKSTIVN LAREVPQQSG KKLLINKDAS
LALQRGATVF VNHLLLFARE IAKSQDKKSC SVDDVLSALD HIGHSALKGP VRDKLDEYQA
AVEQRKKEKL DSGEVDADGD IDMGEDKENV PVEKVKEHDE IEEQGDALQD VEESSEKKQK
TESQDVETRV QNLEQT
