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Replication of a cissyn thymine dimer at atomic resolution

Abstract

Ultraviolet light damages DNA by catalysing covalent bond formation between adjacent pyrimidines, generating cissyn cyclobutane pyrimidine dimers (CPDs) as the most common lesion1. CPDs block DNA replication by high-fidelity DNA polymerases, but they can be efficiently bypassed by the Y-family DNA polymerase pol η2,3. Mutations in POLH encoding pol η are implicated in nearly 20% of xeroderma pigmentosum, a human disease characterized by extreme sensitivity to sunlight and predisposition to skin cancer4,5,6. Here we have determined two crystal structures of Dpo4, an archaeal pol η homologue, complexed with CPD-containing DNA, where the 3′ and 5′ thymine of the CPD separately serves as a templating base. The 3′ thymine of the CPD forms a Watson–Crick base pair with the incoming dideoxyATP, but the 5′ thymine forms a Hoogsteen base pair with the dideoxyATP in syn conformation. Dpo4 retains a similar tertiary structure, but each unusual DNA structure is individually fitted into the active site for catalysis. A model of the pol η–CPD complex built from the crystal structures of Saccharomyces cerevisiae apo-pol η and the Dpo4–CPD complex suggests unique features that allow pol η to efficiently bypass CPDs.

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Figure 1: Replication of a CPD by Dpo4 in solution and crystals.
Figure 2: Structural comparison of the CPD complexed with Dpo4 and protein free.
Figure 3: Modelling of S. cerevisiae pol η complexed with a CPD.

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Acknowledgements

We thank R. Craigie and D. Leahy for critical reading of the manuscript.

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Correspondence to Wei Yang.

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The authors declare that they have no competing financial interests.

Supplementary information

41586_2003_BFnature01919_MOESM1_ESM.gif

Supplementary Animation 1: Structural comparison of TT-1, TT-2 and the Type I Dpo4 and undamaged DNA complex 11. The three structures are shown sequentially after superposition of the palm, finger and thumb domains of Dpo4. The protein domains are colour coded as in Fig. 3a, and the DNA is shown in a blue stick model. The incoming nucleotide is highlighted in yellow, and the thymine dimer in orange. The metal ions are shown as grey spheres. There is only one metal ion in the type I structure because the incoming ddATP was hydrolyzed to ddADP. (GIF 177 kb)

41586_2003_BFnature01919_MOESM2_ESM.gif

Supplementary Animation 2: Modeling of Pol eta complexed with a CPD. The crystal structure of Pol eta apo-protein presented in a multi-colour ribbon diagram and the TT-1 structure in grey-blue are shown together after superimposing the palm domains of Pol eta and Dpo4. For Pol eta to interact with the DNA substrate as the domains of Dpo4 do in TT-1, the finger, thumb and little finger domains of Pol eta have to rotate 16°, 16° and 45°, respectively, toward the DNA as shown in the next frame. (GIF 115 kb)

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Ling, H., Boudsocq, F., Plosky, B. et al. Replication of a cissyn thymine dimer at atomic resolution. Nature 424, 1083–1087 (2003). https://doi.org/10.1038/nature01919

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