Structure of Saccharomyces cerevisiae DNA polymerase epsilon by cryo-electron microscopy

Nat Struct Mol Biol. 2006 Jan;13(1):35-43. doi: 10.1038/nsmb1040. Epub 2005 Dec 20.


The structure of the multisubunit yeast DNA polymerase epsilon (Pol epsilon) was determined to 20-A resolution using cryo-EM and single-particle image analysis. A globular domain comprising the catalytic Pol2 subunit is flexibly connected to an extended structure formed by subunits Dpb2, Dpb3 and Dpb4. Consistent with the reported involvement of the latter in interaction with nucleic acids, the Dpb portion of the structure directly faces a single cleft in the Pol2 subunit that seems wide enough to accommodate double-stranded DNA. Primer-extension experiments reveal that Pol epsilon processivity requires a minimum length of primer-template duplex that corresponds to the dimensions of the extended Dpb structure. Together, these observations suggest a mechanism for interaction of Pol epsilon with DNA that might explain how the structure of the enzyme contributes to its intrinsic processivity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Catalysis
  • Cryoelectron Microscopy
  • DEAD-box RNA Helicases
  • DNA Polymerase II / chemistry*
  • DNA Polymerase II / metabolism
  • DNA Polymerase II / ultrastructure*
  • DNA, Fungal / chemistry
  • DNA, Fungal / metabolism
  • DNA, Fungal / ultrastructure
  • Models, Molecular
  • Protein Binding
  • Protein Structure, Quaternary
  • Protein Structure, Tertiary
  • Protein Subunits / chemistry
  • Protein Subunits / metabolism
  • RNA Helicases / chemistry
  • RNA Helicases / metabolism
  • RNA Helicases / ultrastructure
  • Saccharomyces cerevisiae / enzymology*
  • Saccharomyces cerevisiae Proteins / chemistry
  • Saccharomyces cerevisiae Proteins / metabolism
  • Saccharomyces cerevisiae Proteins / ultrastructure


  • DNA, Fungal
  • Protein Subunits
  • Saccharomyces cerevisiae Proteins
  • DNA Polymerase II
  • Dbp2 protein, S cerevisiae
  • DEAD-box RNA Helicases
  • RNA Helicases