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Protein

DNA polymerase epsilon subunit D

Gene

DPB4

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

DNA polymerase epsilon (DNA polymerase II) participates in chromosomal DNA replication. It is required during synthesis of the leading and lagging DNA strands at the replication fork and binds at/or near replication origins and moves along DNA with the replication fork. It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. It is also involved in DNA synthesis during DNA repair. Also functions as component of the ISW2 complex, which acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA. THe ISW2 complex is involved in coordinating transcriptional repression and in inheritance of telomeric silencing. It is involved in repression of MAT a-specific genes, INO1, and early meiotic genes during mitotic growth dependent upon transcription factor UME6 and in a parallel pathway to the RPD3-SIN3 histone deacetylase complex.6 Publications

Catalytic activityi

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).

GO - Molecular functioni

  • chromatin DNA binding Source: SGD
  • DNA-directed DNA polymerase activity Source: UniProtKB-KW
  • nucleosomal DNA binding Source: SGD

GO - Biological processi

  • ATP-dependent chromatin remodeling Source: SGD
  • DNA-dependent DNA replication Source: SGD
  • error-prone translesion synthesis Source: SGD
  • heterochromatin organization involved in chromatin silencing Source: SGD
  • leading strand elongation Source: SGD
  • nucleosome mobilization Source: SGD
  • replicative senescence Source: SGD
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

DNA-directed DNA polymerase, Nucleotidyltransferase, Transferase

Keywords - Biological processi

DNA replication, Transcription, Transcription regulation

Enzyme and pathway databases

BioCyciYEAST:G3O-29721-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase epsilon subunit D (EC:2.7.7.7)
Alternative name(s):
DNA polymerase II subunit D
Gene namesi
Name:DPB4
Ordered Locus Names:YDR121W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDR121W.
SGDiS000002528. DPB4.

Subcellular locationi

GO - Cellular componenti

  • CHRAC Source: SGD
  • epsilon DNA polymerase complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 196196DNA polymerase epsilon subunit DPRO_0000191754Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei183 – 1831Phosphoserine; by ATM or ATRCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ04603.

PTM databases

iPTMnetiQ04603.

Interactioni

Subunit structurei

DNA polymerase epsilon is a heterotetramer consisting of POL2, DPB2, DPB3 and DPB4. Component of the ISW2 complex, which at least consists of ISW2, ITC1, DLS1 and DPB4.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
DLS1P403663EBI-29938,EBI-25910
DPB3P273443EBI-29938,EBI-6076

GO - Molecular functioni

  • nucleosomal DNA binding Source: SGD

Protein-protein interaction databases

BioGridi32177. 97 interactions.
DIPiDIP-4621N.
IntActiQ04603. 21 interactions.
MINTiMINT-481682.

Structurei

3D structure databases

ProteinModelPortaliQ04603.
SMRiQ04603. Positions 31-100.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Phylogenomic databases

HOGENOMiHOG000112253.
InParanoidiQ04603.
KOiK02326.
OMAiQGNYPTT.
OrthoDBiEOG7WQ856.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.

Sequencei

Sequence statusi: Complete.

Q04603-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPPKGWRKDA QGNYPTTSYI KEQENITIQD LLFPKSTIVN LAREVPQQSG
60 70 80 90 100
KKLLINKDAS LALQRGATVF VNHLLLFARE IAKSQDKKSC SVDDVLSALD
110 120 130 140 150
HIGHSALKGP VRDKLDEYQA AVEQRKKEKL DSGEVDADGD IDMGEDKENV
160 170 180 190
PVEKVKEHDE IEEQGDALQD VEESSEKKQK TESQDVETRV QNLEQT
Length:196
Mass (Da):21,997
Last modified:November 1, 1996 - v1
Checksum:i5D061EEA836B8BD3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z48758 Genomic DNA. Translation: CAA88674.1.
AY557673 Genomic DNA. Translation: AAS55999.1.
BK006938 Genomic DNA. Translation: DAA11967.1.
PIRiS52686.
RefSeqiNP_010406.3. NM_001180429.3.

Genome annotation databases

EnsemblFungiiYDR121W; YDR121W; YDR121W.
GeneIDi851699.
KEGGisce:YDR121W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z48758 Genomic DNA. Translation: CAA88674.1.
AY557673 Genomic DNA. Translation: AAS55999.1.
BK006938 Genomic DNA. Translation: DAA11967.1.
PIRiS52686.
RefSeqiNP_010406.3. NM_001180429.3.

3D structure databases

ProteinModelPortaliQ04603.
SMRiQ04603. Positions 31-100.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32177. 97 interactions.
DIPiDIP-4621N.
IntActiQ04603. 21 interactions.
MINTiMINT-481682.

PTM databases

iPTMnetiQ04603.

Proteomic databases

MaxQBiQ04603.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDR121W; YDR121W; YDR121W.
GeneIDi851699.
KEGGisce:YDR121W.

Organism-specific databases

EuPathDBiFungiDB:YDR121W.
SGDiS000002528. DPB4.

Phylogenomic databases

HOGENOMiHOG000112253.
InParanoidiQ04603.
KOiK02326.
OMAiQGNYPTT.
OrthoDBiEOG7WQ856.

Enzyme and pathway databases

BioCyciYEAST:G3O-29721-MONOMER.

Miscellaneous databases

PROiQ04603.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
    Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
    , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
    Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. "Structure and function of the fourth subunit (Dpb4p) of DNA polymerase epsilon in Saccharomyces cerevisiae."
    Ohya T., Maki S., Kawasaki Y., Sugino A.
    Nucleic Acids Res. 28:3846-3852(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 115-125 AND 157-176, FUNCTION, SUBUNIT, SUBCELLULAR LOCATION.
  5. "The Isw2 chromatin remodeling complex represses early meiotic genes upon recruitment by Ume6p."
    Goldmark J.P., Fazzio T.G., Estep P.W., Church G.M., Tsukiyama T.
    Cell 103:423-433(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION OF THE ISW2 COMPLEX.
  6. "Interactions of Isw2 chromatin remodeling complex with nucleosomal arrays: analyses using recombinant yeast histones and immobilized templates."
    Gelbart M.E., Rechsteiner T., Richmond T.J., Tsukiyama T.
    Mol. Cell. Biol. 21:2098-2106(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION OF THE ISW2 COMPLEX.
  7. "Widespread collaboration of Isw2 and Sin3-Rpd3 chromatin remodeling complexes in transcriptional repression."
    Fazzio T.G., Kooperberg C., Goldmark J.P., Neal C., Basom R., Delrow J., Tsukiyama T.
    Mol. Cell. Biol. 21:6450-6460(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION OF THE ISW2 COMPLEX.
  8. "Fidelity of DNA polymerase epsilon holoenzyme from budding yeast Saccharomyces cerevisiae."
    Shimizu K., Hashimoto K., Kirchner J.M., Nakai W., Nishikawa H., Resnick M.A., Sugino A.
    J. Biol. Chem. 277:37422-37429(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  9. "The quaternary structure of DNA polymerase epsilon from Saccharomyces cerevisiae."
    Chilkova O., Jonsson B.-H., Johansson E.
    J. Biol. Chem. 278:14082-14086(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: COMPOSITION OF THE DNA POLYMERASE EPSILON COMPLEX.
  10. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  11. "Noncompetitive counteractions of DNA polymerase epsilon and ISW2/yCHRAC for epigenetic inheritance of telomere position effect in Saccharomyces cerevisiae."
    Iida T., Araki H.
    Mol. Cell. Biol. 24:217-227(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE ISW2 COMPLEX, FUNCTION OF THE ISW2 COMPLEX.
  12. "Histone fold protein Dls1p is required for Isw2-dependent chromatin remodeling in vivo."
    McConnell A.D., Gelbart M.E., Tsukiyama T.
    Mol. Cell. Biol. 24:2605-2613(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE ISW2 COMPLEX.
  13. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-183, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiDPB4_YEAST
AccessioniPrimary (citable) accession number: Q04603
Secondary accession number(s): D6VSA7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 13, 2005
Last sequence update: November 1, 1996
Last modified: July 6, 2016
This is version 130 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

In eukaryotes there are five DNA polymerases: alpha, beta, gamma, delta, and epsilon which are responsible for different reactions of DNA synthesis.
Present with 2100 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  2. Yeast chromosome IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.