Electron Fate and Mutational Robustness in the Mechanism of (6-4)Photolyase-Mediated DNA Repair

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Abstract

UV radiation triggers the formation of an adjacent pyrimidine lesion in DNA, pyrimidine(6-4)pyrimidone photoproduct ((6-4)PP). These lesions are cytotoxic and interfere with cell replication and transcription, eventually inducing apoptosis, but they are readily repaired by (6-4)photolyase. However, the details of the repair mechanism have been debated. Here, we describe the mechanism of the photorepair cycle, the roles of the active site His365 and His369 residues, and the robustness against mutation of these residues. Using molecular dynamics simulations, quantum mechanical/molecular mechanical (QM/MM) calculations, large-QM/MM which includes 982 atoms in the QM layer, Marcus theory, and Fourier transform infrared (FTIR) spectroscopic measurements, we found that an electron is first transferred to the 5′-base of (6-4)PP to form a radical; subsequently a proton transfer from His365 to (6-4)PP causes water formation, which induces further OH transfer upon water activation and ultimately DNA repair. A H365A mutant repairs (6-4)PP similarly, with His369 compensating for His365 through a 3′-base radical. Our findings also provide an explanation of the observed low quantum yield in the wild-type and mutant proteins.

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Dokainish, H. M., Yamada, D., Iwata, T., Kandori, H., & Kitao, A. (2017). Electron Fate and Mutational Robustness in the Mechanism of (6-4)Photolyase-Mediated DNA Repair. ACS Catalysis, 7(7), 4835–4845. https://doi.org/10.1021/acscatal.7b00751

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