Structural insights into yeast DNA polymerase delta by small angle X-ray scattering

J Mol Biol. 2009 Dec 4;394(3):377-82. doi: 10.1016/j.jmb.2009.09.066. Epub 2009 Oct 8.


DNA polymerase delta (Poldelta) is a multisubunit polymerase that plays an indispensable role in replication from yeast to humans. Poldelta from Saccharomyces cerevisiae is composed of three subunits: Pol3, Pol31, and Pol32. Despite the elucidation of the structures and models of the individual subunits (or portions, thereof), the nature of their assembly remains unclear. We present here a small-angle X-ray scattering analysis of a yeast Poldelta complex (Poldelta(T)) composed of Pol3, Pol31, and Pol32N (amino acids 1-103 of Pol32). From the small angle X-ray scattering global parameters and reconstructed envelopes, we show that Poldelta(T) adopts an elongated conformation with a radius of gyration (R(g)) of approximately 52 A and a maximal dimension of approximately 190 A. We also propose an orientation for the accessory Pol31-Pol32N subunits relative to the Pol3 catalytic core that best agrees with the experimental scattering profile. The analysis also points to significant conformational variability that may allow Poldelta to better coordinate its action with other proteins at the replication fork.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Catalytic Domain
  • DNA Polymerase III / chemistry*
  • DNA-Directed DNA Polymerase / chemistry
  • Models, Molecular
  • Protein Folding
  • Protein Structure, Quaternary
  • Protein Subunits
  • Saccharomyces cerevisiae / enzymology*
  • Saccharomyces cerevisiae Proteins / chemistry*
  • Scattering, Small Angle
  • X-Ray Diffraction


  • POL3 protein, S cerevisiae
  • Pol32 protein, S cerevisiae
  • Protein Subunits
  • Saccharomyces cerevisiae Proteins
  • DNA Polymerase III
  • DNA-Directed DNA Polymerase
  • POL31 protein, S cerevisiae