DNA polymerase epsilon 


Replicative polymerase; synthesizes DNA at the replication fork. May function on the leading strand




Sc Pol2 (catalytic), Dpb2, Dpb3, Dpb4

Sp Cdc20 (catalytic)

Molecular weight

P256; p79; p23;p22 (Sc)???


•200, (80 34/30* 29  *not needed, although removal does give decrease in fidelity (1)



• (80 = 55) (2)

• 260 and 60 (3)


Biochemical properties

• Polymerase – high processivity

• Exonuclease  (for proofreading) isolation of low fidelity mutants (4)

• DNA binding (ss and ds DNA)



• suggested role in leading strand synthesis (5)


•Dpb3 and Dpb4 contain histone folds (6)

• Nls big subunit


Protein interactions


• Dpb11

• Pol sigma increases polymerase activity? (7)

• Mdm2 (8) Activity stimulated

• GINS (9) is accessory factor (10) ****

• Cdc45 (9)

• MRC1 to link replication and S phase checkpoint (11)



• Pcna eg (12) but nb foci overlap early but not late s (adjacent then) (13)

• RNApolII (14)



• Dpb2 phosphorylated late g1 by cdc28 (15)





• solution structure (17)

Cellular location and expression


•If eliminate pol and exo domains viable but short telomeres and rapid senescence (18)

• binds early at origins via dbp11 and needed to load pol alpha. (19)

• role in silencing (20)

• needed for BIR (21)



• association during s rises at start then plateaus (22) - neutralizing antibodies more effective early. 

• Found mainly in ring like structures at electron dense regions of the chromatin. (22)

•2x increase g1/s (23)


Other comments


•Pol2, Dpb2 essential; Dpb3,4 subunits not essential (24) (6)

•Dpb4 found as component of chromatin remodelling complex (25)

• role for c terminus of Pol2 (catalytic subunit) in checkpoint (both replication and damage) (26) (27)

•C-terminus of Pol2 alone (which lacks polymerase and exonuclease motifs is enough for viability (28) (27)

• Dpb2 involved in fidelity (29)



• not required for replication checkpoint (30) .

•N terminus (containing catalytic domain) not required for viability (31)

•Dpb3 subunit essential, Dpb4 subunit not essential (cf Sc where both are nonessential)



• depletion in xenopus extracts gives  replication defects which look like lagging and leading defects. Delta depletes like lagging strand only (32) , neither substitute for each other.



•Proofreads opposite strand from pol delta (33) (34) may be leading strand polymerase.

•Activity stimulated by PCNA (35)

•May function independently of PCNA at least for some stages of S phase (13)

• sometimes see 140kDa form which can be generated by caspase (36) this form doesn’t bind pcna


Revised by


Last edited

13 July 09



1.    Araki,H., Leem,S.H., Phongdara,A. and Sugino,A. (1995) Dpb11, which interacts with DNA polymerase II(epsilon) in Saccharomyces cerevisiae, has a dual role in S-phase progression and at a cell cycle checkpoint. Proc Natl Acad Sci U S A 92, 11791-11795.

2.    Kesti,T. and Syvaoja,J.E. (1991) Identification and tryptic cleavage of the catalytic core of HeLa and calf thymus DNA polymerase epsilon. J Biol Chem 266, 6336-6341.

3.    Waga,S., Masuda,T., Takisawa,H. and Sugino,A. (2001) DNA polymerase epsilon is required for coordinated and efficient chromosomal DNA replication in Xenopus egg extracts. Proc Natl Acad Sci U S A 98, 4978-4983.

4.    Pursell,Z.F., Isoz,I., Lundstrom,E.B., Johansson,E. and Kunkel,T.A. (2007) Regulation of B family DNA polymerase fidelity by a conserved active site residue: characterization of M644W, M644L and M644F mutants of yeast DNA polymerase epsilon. Nucleic Acids Res 35, 3076-3086.

5.    Pursell,Z.F., Isoz,I., Lundstrom,E.B., Johansson,E. and Kunkel,T.A. (2007) Yeast DNA polymerase epsilon participates in leading-strand DNA replication. Science 317, 127-130.

6.    Li,Y., Pursell,Z.F. and Linn,S. (2000) Identification and cloning of two histone fold motif-containing subunits of HeLa DNA polymerase epsilon. J Biol Chem 275, 23247-23252.

7.    Edwards,S., Li,C.M., Levy,D.L., Brown,J., Snow,P.M. and Campbell,J.L. (2003) Saccharomyces cerevisiae DNA polymerase epsilon and polymerase sigma interact physically and functionally, suggesting a role for polymerase epsilon in sister chromatid cohesion. Mol Cell Biol 23, 2733-2748.

8.    Asahara,H., Li,Y., Fuss,J., Haines,D.S., Vlatkovic,N., Boyd,M.T. and Linn,S. (2003) Stimulation of human DNA polymerase epsilon by MDM2. Nucleic Acids Res 31, 2451-2459.

9.    Nedelcheva-Veleva,M.N., Krastev,D.B. and Stoynov,S.S. (2006) Coordination of DNA synthesis and replicative unwinding by the S-phase checkpoint pathways. Nucleic Acids Res 34, 4138-4146.

10.  Seki,T., Akita,M., Kamimura,Y., Muramatsu,S., Araki,H. and Sugino,A. (2006) GINS is a DNA polymerase epsilon accessory factor during chromosomal DNA replication in budding yeast. J Biol Chem 281, 21422-21432.

11.  Lou,H., Komata,M., Katou,Y., Guan,Z., Reis,C.C., Budd,M., Shirahige,K. and Campbell,J.L. (2008) Mrc1 and DNA polymerase epsilon function together in linking DNA replication and the S phase checkpoint. Mol Cell 32, 106-117.

12.  Maga,G. and Hubscher,U. (1995) DNA polymerase epsilon interacts with proliferating cell nuclear antigen in primer recognition and elongation. Biochemistry34, 891-901.

13.  Fuss,J. and Linn,S. (2002) Human DNA polymerase epsilon colocalizes with proliferating cell nuclear antigen and DNA replication late, but not early, in S phase. J Biol Chem 277, 8658-8666.

14.  Rytkonen,A.K., Hillukkala,T., Vaara,M., Sokka,M., Jokela,M., Sormunen,R., Nasheuer,H.P., Nethanel,T., Kaufmann,G., Pospiech,H. and Syvaoja,J.E. (2006) DNA polymerase epsilon associates with the elongating form of RNA polymerase II and nascent transcripts. FEBS J 273, 5535-5549.

15.  Kesti,T., McDonald,W.H., Yates,J.R.r. and Wittenberg,C. (2004) Cell cycle-dependent phosphorylation of the DNA polymerase epsilon subunit, Dpb2, by the Cdc28 cyclin-dependent protein kinase. J Biol Chem 279, 14245-14255.

16.  Asturias,F.J., Cheung,I.K., Sabouri,N., Chilkova,O., Wepplo,D. and Johansson,E. (2006) Structure of Saccharomyces cerevisiae DNA polymerase epsilon by cryo-electron microscopy. Nat Struct Mol Biol 13, 35-43.

17.  Nuutinen,T., Tossavainen,H., Fredriksson,K., Pirila,P., Permi,P., Pospiech,H. and Syvaoja,J.E. (2008) The solution structure of the amino-terminal domain of human DNA polymerase epsilon subunit B is homologous to C-domains of AAA+ proteins. Nucleic Acids Res 36, 5102-5110.

18.  Ohya,T., Kawasaki,Y., Hiraga,S., Kanbara,S., Nakajo,K., Nakashima,N., Suzuki,A. and Sugino,A. (2002) The DNA polymerase domain of pol(epsilon) is required for rapid, efficient, and highly accurate chromosomal DNA replication, telomere length maintenance, and normal cell senescence in Saccharomyces cerevisiae. J Biol Chem 277, 28099-28108.

19.  Masumoto,H., Sugino,A. and Araki,H. (2000) Dpb11 controls the association between DNA polymerases alpha and epsilon and the autonomously replicating sequence region of budding yeast. Mol Cell Biol 20, 2809-2817.

20.  Tsubota,T., Tajima,R., Ode,K., Kubota,H., Fukuhara,N., Kawabata,T., Maki,S. and Maki,H. (2006) Double-stranded DNA binding, an unusual property of DNA polymerase epsilon, promotes epigenetic silencing in Saccharomyces cerevisiae. J Biol Chem 281, 32898-32908.

21.  Lydeard,J.R., Jain,S., Yamaguchi,M. and Haber,J.E. (2007) Break-induced replication and telomerase-independent telomere maintenance require Pol32. Nature448, 820-823.

22.  Rytkonen,A.K., Vaara,M., Nethanel,T., Kaufmann,G., Sormunen,R., Laara,E., Nasheuer,H.P., Rahmeh,A., Lee,M.Y., Syvaoja,J.E. and Pospiech,H. (2006) Distinctive activities of DNA polymerases during human DNA replication. FEBS J 273, 2984-3001.

23.  Tuusa,J., Uitto,L. and Syvaoja,J.E. (1995) Human DNA polymerase epsilon is expressed during cell proliferation in a manner characteristic of replicative DNA polymerases. Nucleic Acids Res 23, 2178-2183.

24.  Ohya,T., Maki,S., Kawasaki,Y. and Sugino,A. (2000) Structure and function of the fourth subunit (Dpb4p) of DNA polymerase epsilon in Saccharomyces cerevisiae. Nucleic Acids Res 28, 3846-3852.

25.  Dang,W., Kagalwala,M.N. and Bartholomew,B. (2007) The Dpb4 subunit of ISW2 is anchored to extranucleosomal DNA. J Biol Chem

26.  Navas,T.A., Zhou,Z. and Elledge,S.J. (1995) DNA polymerase epsilon links the DNA replication machinery to the S phase checkpoint. Cell 80, 29-39.

27.  Dua,R., Levy,D.L. and Campbell,J.L. (1999) Analysis of the essential functions of the C-terminal protein/protein interaction domain of Saccharomyces cerevisiae pol epsilon and its unexpected ability to support growth in the absence of the DNA polymerase domain. J Biol Chem 274, 22283-22288.

28.  Kesti,T., Flick,K., Keranen,S., Syvaoja,J.E. and Wittenberg,C. (1999) DNA polymerase epsilon catalytic domains are dispensable for DNA replication, DNA repair, and cell viability. Mol Cell 3, 679-685.

29.  Jaszczur,M., Flis,K., Rudzka,J., Kraszewska,J., Budd,M.E., Polaczek,P., Campbell,J.L., Jonczyk,P. and Fijalkowska,I.J. (2008) Dpb2p, a noncatalytic subunit of DNA polymerase epsilon, contributes to the fidelity of DNA replication in Saccharomyces cerevisiae. Genetics 178, 633-647.

30.  D'Urso,G. and Nurse,P. (1997) Schizosaccharomyces pombe cdc20+ encodes DNA polymerase epsilon and is required for chromosomal replication but not for the S phase checkpoint. Proc Natl Acad Sci U S A 94, 12491-12496.

31.  Feng,W. and D'Urso,G. (2001) Schizosaccharomyces pombe cells lacking the amino-terminal catalytic domains of DNA polymerase epsilon are viable but require the DNA damage checkpoint control. Mol Cell Biol 21, 4495-4504.

32.  Fukui,T., Yamauchi,K., Muroya,T., Akiyama,M., Maki,H., Sugino,A. and Waga,S. (2004) Distinct roles of DNA polymerases delta and epsilon at the replication fork in Xenopus egg extracts. Genes Cells 9, 179-191.

33.  Shcherbakova,P.V. and Pavlov,Y.I. (1996) 3'-->5' exonucleases of DNA polymerases epsilon and delta correct base analog induced DNA replication errors on opposite DNA strands in Saccharomyces cerevisiae. Genetics 142, 717-726.

34.  Karthikeyan,R., Vonarx,E.J., Straffon,A.F., Simon,M., Faye,G. and Kunz,B.A. (2000) Evidence from mutational specificity studies that yeast DNA polymerases delta and epsilon replicate different DNA strands at an intracellular replication fork. J Mol Biol 299, 405-419.

35.  Hamatake,R.K., Hasegawa,H., Clark,A.B., Bebenek,K., Kunkel,T.A. and Sugino,A. (1990) Purification and characterization of DNA polymerase II from the yeast Saccharomyces cerevisiae. Identification of the catalytic core and a possible holoenzyme form of the enzyme. J Biol Chem 265, 4072-4083.

36.  Liu,W. and Linn,S. (2000) Proteolysis of the human DNA polymerase epsilon catalytic subunit by caspase-3 and calpain specifically during apoptosis. Nucleic Acids Res 28, 4180-4188.