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

Abstract

The structure of the multisubunit yeast DNA polymerase ε (Pol ε) was determined to 20-Å 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 ε 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 ε with DNA that might explain how the structure of the enzyme contributes to its intrinsic processivity.

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Figure 1: Classification and initial analysis of Pol ε particle images.
Figure 2: Evaluation of unstained Pol ε images from specimens preserved in amorphous ice.
Figure 3: Structure of Pol ε calculated from images of Pol ε particles preserved in amorphous ice.
Figure 4: Structure of the Pol2 catalytic subunit calculated from images of Pol2 particles preserved in stain.
Figure 5: Structure of the Pol2–Dpb2 subunit complex calculated from images of Pol2–Dpb2 particles preserved in stain.
Figure 6: Primer-extension assay to determine the correlation between primer length and Pol ε processivity.
Figure 7: Average termination probability for 3 ≤ N ≤ 13 for the different primer templates.
Figure 8: Analysis of Pol ε structural flexibility on the basis of classification of images of particles preserved in stain.
Figure 9: A model for the interaction of Pol ε with DNA.

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Acknowledgements

F.J.A. is a Scholar of the Leukemia and Lymphoma Society of America. N.S. and O.C. were supported by the Kempe foundation. E.J. is supported by grants from The Swedish Research Council, The Swedish Cancer Society and The Medical Faculty of Umeå University. We thank M. Sedova for help with figures of the final Pol ε model and T.A. Kunkel for comments on the primer-extension assays.

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Correspondence to Francisco J Asturias.

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Supplementary information

Supplementary Fig. 1

Determination of single-hit kinetics conditions (PDF 633 kb)

Supplementary Fig. 2

Relative motion of Pol epsilon domains (PDF 140 kb)

Supplementary Table 1 (PDF 57 kb)

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Asturias, F., Cheung, I., Sabouri, N. et al. Structure of Saccharomyces cerevisiae DNA polymerase epsilon by cryo–electron microscopy. Nat Struct Mol Biol 13, 35–43 (2006). https://doi.org/10.1038/nsmb1040

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