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Structural basis of high-fidelity DNA synthesis by yeast DNA polymerase δ

Abstract

DNA polymerase δ (Pol δ) is a high-fidelity polymerase that has a central role in replication from yeast to humans. We present the crystal structure of the catalytic subunit of yeast Pol δ in ternary complex with a template primer and an incoming nucleotide. The structure, determined at 2.0-Å resolution, catches the enzyme in the act of replication, revealing how the polymerase and exonuclease domains are juxtaposed relative to each other and how a correct nucleotide is selected and incorporated. The structure also reveals the 'sensing' interactions near the primer terminus, which signal a switch from the polymerizing to the editing mode. Taken together, the structure provides a chemical basis for the bulk of DNA synthesis in eukaryotic cells and a framework for understanding the effects of cancer-causing mutations in Pol δ.

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Figure 1: Structure of the Pol3–DNA–dCTP ternary complex.
Figure 2: Comparison between the Pol3 and RB69 Pol ternary complexes.
Figure 3: Close-up view of the polymerase active site region.
Figure 4: Pol3–DNA base interactions.
Figure 5: β-hairpin–DNA interactions.
Figure 6: Mapping of cancer mutations.

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Acknowledgements

We thank the staff at Brookhaven National Laboratory and the Advanced Photon Source for facilitating X-ray data collection. This work was supported by grant CA138546 from the US National Institutes of Health.

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M.K.S. and R.E.J. performed the experiments; all of the authors contributed to the concepts and to the writing of the paper.

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Correspondence to Aneel K Aggarwal.

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Swan, M., Johnson, R., Prakash, L. et al. Structural basis of high-fidelity DNA synthesis by yeast DNA polymerase δ. Nat Struct Mol Biol 16, 979–986 (2009). https://doi.org/10.1038/nsmb.1663

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