Visualizing the DNA repair process by a photolyase at atomic resolution
Manuel Maestre‐Reyna, Po‐Hsun Wang, Eriko Nango, Yuhei Hosokawa, Martin Saft, Antonia Furrer, Cheng‐Han Yang, Eka Putra Gusti Ngurah Putu, Wen‐Jin Wu, Hans‐Joachim Emmerich, Nicolas Caramello, Sophie Franz-Badur, Chao Yang, Sylvain Engilberge, Maximilian Wranik, Hannah Glover, Tobias Weinert, Hsiang-Yi Wu, Cheng‐Chung Lee, Wei‐Cheng Huang, Kai-Fa Huang, Yao-Kai Chang, Jiahn‐Haur Liao, Jui‐Hung Weng, Wael Gad, Chiung‐Wen Chang, Allan H. Pang, Kai‐Chun Yang, Wei-Ting Lin, Y.S. Chang, Dardan Gashi, Emma V. Beale, D. Ozerov, Karol Nass, Gregor Knopp, Philip J. M. Johnson, Claudio Cirelli, Christopher J. Milne, Camila Bacellar, Michihiro Sugahara, Shigeki Owada, Yasumasa Joti, A. Yamashita, Rie Tanaka, Tomoyuki Tanaka, Fangjia Luo, Kensuke Tono, Wiktoria Zarzycka, Pavel Müller, Maisa Alkheder Alahmad, Filipp Bezold, Valerie Fuchs, Petra Gnau, Stephan Kiontke, Lukas Korf, Viktoria Reithofer, Christian Rosner, Elisa Marie Seiler, Mohamed Watad, Laura Werel, Roberta Spadaccini, Junpei Yamamoto, So Iwata, Dongping Zhong, Jörg Standfuss, Antoine Royant, Yoshitaka Bessho, Lars‐Oliver Essen, Ming‐Daw Tsai
Abstract
Photolyases, a ubiquitous class of flavoproteins, use blue light to repair DNA photolesions. In this work, we determined the structural mechanism of the photolyase-catalyzed repair of a cyclobutane pyrimidine dimer (CPD) lesion using time-resolved serial femtosecond crystallography (TR-SFX). We obtained 18 snapshots that show time-dependent changes in four reaction loci. We used these results to create a movie that depicts the repair of CPD lesions in the picosecond-to-nanosecond range, followed by the recovery of the enzymatic moieties involved in catalysis, completing the formation of the fully reduced enzyme-product complex at 500 nanoseconds. Finally, back-flip intermediates of the thymine bases to reanneal the DNA were captured at 25 to 200 microseconds. Our data cover the complete molecular mechanism of a photolyase and, importantly, its chemistry and enzymatic catalysis at work across a wide timescale and at atomic resolution.