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Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Müller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD. Visualizing the DNA repair process by a photolyase at atomic resolution. Science 2023; 382:eadd7795. [PMID: 38033054 DOI: 10.1126/science.add7795] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/05/2023] [Indexed: 12/02/2023]
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.
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Affiliation(s)
- Manuel Maestre-Reyna
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| | - Po-Hsun Wang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Yuhei Hosokawa
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Martin Saft
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Antonia Furrer
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Cheng-Han Yang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | | | - Wen-Jin Wu
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Hans-Joachim Emmerich
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Nicolas Caramello
- European Synchrotron Radiation Facility, 38043 Grenoble, France
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany
| | - Sophie Franz-Badur
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Chao Yang
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Sylvain Engilberge
- European Synchrotron Radiation Facility, 38043 Grenoble, France
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38044 Grenoble, France
| | - Maximilian Wranik
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | | | - Tobias Weinert
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Hsiang-Yi Wu
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Cheng-Chung Lee
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Wei-Cheng Huang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Yao-Kai Chang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Jiahn-Haur Liao
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Jui-Hung Weng
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Wael Gad
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Chiung-Wen Chang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Allan H Pang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Kai-Chun Yang
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| | - Wei-Ting Lin
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| | - Yu-Chen Chang
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| | - Dardan Gashi
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Emma Beale
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Dmitry Ozerov
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Karol Nass
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Gregor Knopp
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Philip J M Johnson
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Claudio Cirelli
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Chris Milne
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Camila Bacellar
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | | | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Yasumasa Joti
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Ayumi Yamashita
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Fangjia Luo
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Wiktoria Zarzycka
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Pavel Müller
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Maisa Alkheder Alahmad
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Filipp Bezold
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Valerie Fuchs
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Petra Gnau
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Stephan Kiontke
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Lukas Korf
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Viktoria Reithofer
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Christian Joshua Rosner
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Elisa Marie Seiler
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Mohamed Watad
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Laura Werel
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Roberta Spadaccini
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
- Dipartimento di Scienze e tecnologie, Universita degli studi del Sannio, Benevento, Italy
| | - Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Dongping Zhong
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Center for Ultrafast Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jörg Standfuss
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Antoine Royant
- European Synchrotron Radiation Facility, 38043 Grenoble, France
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38044 Grenoble, France
| | - Yoshitaka Bessho
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Lars-Oliver Essen
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
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Zhuang X, Zhang A, Qiu S, Tang C, Zhao S, Li H, Zhang Y, Wang Y, Wang B, Fang B, Hong W. Coenzyme Coupling Boosts Charge Transport through Single Bioactive Enzyme Junctions. iScience 2020; 23:101001. [PMID: 32259671 PMCID: PMC7136626 DOI: 10.1016/j.isci.2020.101001] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/09/2020] [Accepted: 03/18/2020] [Indexed: 12/15/2022] Open
Abstract
Oxidation of formate to CO2 is catalyzed via the donation of electrons from formate dehydrogenase (FDH) to nicotinamide adenine dinucleotide (NAD+), and thus the charge transport characteristics of FDH become essential but remain unexplored. Here, we investigated the charge transport through single-enzyme junctions of FDH using the scanning tunneling microscope break junction technique (STM-BJ). We found that the coupling of NAD+ with FDH boosts the charge transport by ∼2,100%, and the single-enzyme conductance highly correlates with the enzyme activity. The combined flicker noise analysis demonstrated the switching of the coenzyme-mediated charge transport pathway and supported by the significantly reduced HOMO-LUMO gap from calculations. Site-specific mutagenesis analysis demonstrated that FDH-NAD+ stably combined own higher bioactivity and boosts charge transport, and the coupling has been optimized via the natural selection. Our work provides evidence of hydrogen bond coupling in bioactivity but also bridges the charge transport through single-enzyme junctions and enzyme activities. Binding of NAD+ with FDH boosts the charge transport by more than 2,100% Single-enzyme conductance highly correlates with the enzyme activity Hydrogen bond bridges the charge transport and enzyme activities Experiments combined with calculations probe switching of charge transport pathway
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Affiliation(s)
- Xiaoyan Zhuang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; The Key Laboratory for Chemical Biology of Fujian Province, Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China
| | - Aihui Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; The Key Laboratory for Chemical Biology of Fujian Province, Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China
| | - Siyao Qiu
- Science & Technology Innovation Institute, Dongguan University of Technology, Dongguan 523018, China
| | - Chun Tang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Shiqiang Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Hongchun Li
- Research Center for Computer-Aided Drug Discovery, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yonghui Zhang
- College of Food and Biology Engineering, Jimei University, Xiamen 361005, China
| | - Yali Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; The Key Laboratory for Chemical Biology of Fujian Province, Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Baishan Fang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; The Key Laboratory for Chemical Biology of Fujian Province, Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China.
| | - Wenjing Hong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
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