Visualizing the DNA repair process by a photolyase at atomic resolution

• 成果类型: Article
• 署名作者: Maestre-Reyna, Manuel; Wang, Po-Hsun; Nango, Eriko; Hosokawa, Yuhei; Saft, Martin; Furrer, Antonia; Yang, Cheng-Han; Putu, Eka Putra Gusti Ngurah; Wu, Wen-Jin; Emmerich, Hans-Joachim; Caramello, Nicolas; Franz-Badur, Sophie; Yang, Chao; Engilberge, Sylvain; Wranik, Maximilian; Glover, Hannah Louise; Weinert, Tobias; Wu, Hsiang-Yi; Lee, Cheng-Chung; Huang, Wei-Cheng; Huang, Kai-Fa; Chang, Yao-Kai; Liao, Jiahn-Haur; Weng, Jui-Hung; Gad, Wael; Chang, Chiung-Wen; Pang, Allan H.; Yang, Kai-Chun; Lin, Wei-Ting; Chang, Yu-Chen; Gashi, Dardan; Beale, Emma; Ozerov, Dmitry; Nass, Karol; Knopp, Gregor; Johnson, Philip J. M.; Cirelli, Claudio; Milne, Chris; Bacellar, Camila; Sugahara, Michihiro; Owada, Shigeki; Joti, Yasumasa; Yamashita, Ayumi; Tanaka, Rie; Tanaka, Tomoyuki; Luo, Fangjia; Tono, Kensuke; Zarzycka, Wiktoria; Mueller, Pavel; Alahmad, Maisa Alkheder; Bezold, Filipp; Fuchs, Valerie; Gnau, Petra; Kiontke, Stephan; Korf, Lukas; Reithofer, Viktoria; Rosner, Christian Joshua; Seiler, Elisa Marie; Watad, Mohamed; Werel, Laura; Spadaccini, Roberta; Yamamoto, Junpei; Iwata, So; Zhong, Dongping; Standfuss, Joerg; Royant, Antoine; Bessho, Yoshitaka; Essen, Lars-Oliver; Tsai, Ming-Daw
• 署名单位: Academia Sinica - Taiwan; National Taiwan University; RIKEN; Tohoku University; University of Osaka; Philipps University Marburg; Swiss Federal Institutes of Technology Domain; Paul Scherrer Institute; European Synchrotron Radiation Facility (ESRF); University of Hamburg; University System of Ohio; Ohio State University; Centre National de la Recherche Scientifique (CNRS); Communaute Universite Grenoble Alpes; Universite Grenoble Alpes (UGA); CEA; Japan Synchrotron Radiation Research Institute; Kyoto University; Universite Paris Saclay; Centre National de la Recherche Scientifique (CNRS); CEA; University of Sannio; University System of Ohio; Ohio State University; Shanghai Jiao Tong University; National Taiwan University; University of California System; University of California San Diego
• 刊物名称: SCIENCE
• ISSN/ISSBN: 0036-12491
• DOI: 10.1126/science.add7795
• 发表日期: 2023-12-01
• 关键词: serial femtosecond crystallography; singular-value decomposition; electron-transfer pathways; ultrafast dynamics; crystal-structure; dimer repair; mechanisms; substrate; refinement; complex

摘要

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.