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Discrimination of Class I Cyclobutane Pyrimidine Dimer Photolyase from Blue Light Photoreceptors by Single Methionine Residue

Yuji Miyazawa ^*, Hirotaka Nishioka , Kei Yura   and Takahisa Yamato ^* ¶

^* Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan; Graduate School of Environmental and Human Science, Meijo University, Nagoya 468-8502, Japan; Quantum Bioinformatics Team, Center for Computational Science and Engineering, Japan Atomic Energy Agency, Kyoto 619-0215, Japan; Research Unit for Quantum Beam Life Science Initiative, Quantum Beam Science Directorate, Japan Atomic Energy Agency, Kyoto 619-0215, Japan; and ^¶ CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan

Correspondence: Address reprint requests to Takahisa Yamato, E-mail: yamato{at}phys.nagoya-u.ac.jp.

DNA photolyase recognizes ultraviolet-damaged DNA and breaks improperly formed covalent bonds within the cyclobutane pyrimidine dimer by a light-activated electron transfer reaction between the flavin adenine dinucleotide, the electron donor, and cyclobutane pyrimidine dimer, the electron acceptor. Theoretical analysis of the electron-tunneling pathways of the DNA photolyase derived from Anacystis nidulans can reveal the active role of the protein environment in the electron transfer reaction. Here, we report the unexpectedly important role of the single methionine residue, Met-353, where busy trafficking of electron-tunneling currents is observed. The amino acid conservation pattern of Met-353 in the homologous sequences perfectly correlates with experimentally verified annotation as photolyases. The bioinformatics sequence analysis also suggests that the residue plays a pivotal role in biological function. Consistent findings from different disciplines of computational biology strongly suggest the pivotal role of Met-353 in the biological function of DNA photolyase.