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Hiromoto T, Nishikawa K, Inoue S, Ogata H, Hori Y, Kusaka K, Hirano Y, Kurihara K, Shigeta Y, Tamada T, Higuchi Y. New insights into the oxidation process from neutron and X-ray crystal structures of an O 2-sensitive [NiFe]-hydrogenase. Chem Sci 2023; 14:9306-9315. [PMID: 37712026 PMCID: PMC10498676 DOI: 10.1039/d3sc02156d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/11/2023] [Indexed: 09/16/2023] Open
Abstract
[NiFe]-hydrogenase from Desulfovibrio vulgaris Miyazaki F is an O2-sensitive enzyme that is inactivated in the presence of O2 but the oxidized enzyme can recover its catalytic activity by reacting with H2 under anaerobic conditions. Here, we report the first neutron structure of [NiFe]-hydrogenase in its oxidized state, determined at a resolution of 2.20 Å. This resolution allowed us to reinvestigate the structure of the oxidized active site and to observe the positions of protons in several short hydrogen bonds. X-ray anomalous scattering data revealed that a part of the Ni ion is dissociated from the active site Ni-Fe complex and forms a new square-planar Ni complex, accompanied by rearrangement of the coordinated thiolate ligands. One of the thiolate Sγ atoms is oxidized to a sulfenate anion but remains attached to the Ni ion, which was evaluated by quantum chemical calculations. These results suggest that the square-planar complex can be generated by the attack of reactive oxygen species derived from O2, as distinct from one-electron oxidation leading to a conventional oxidized form of the Ni-Fe complex. Another major finding of this neutron structure analysis is that the Cys17S thiolate Sγ atom coordinating to the proximal Fe-S cluster forms an unusual hydrogen bond with the main-chain amide N atom of Gly19S with a distance of 3.25 Å, where the amide proton appears to be delocalized between the donor and acceptor atoms. This observation provides insight into the contribution of the coordinated thiolate ligands to the redox reaction of the Fe-S cluster.
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Affiliation(s)
- Takeshi Hiromoto
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology 4-9-1 Anagawa, Inage Chiba 263-8555 Japan
- Graduate School of Science, University of Hyogo 3-2-1 Koto, Kamigori Hyogo 678-1297 Japan
| | - Koji Nishikawa
- Graduate School of Science, University of Hyogo 3-2-1 Koto, Kamigori Hyogo 678-1297 Japan
| | - Seiya Inoue
- Graduate School of Science, University of Hyogo 3-2-1 Koto, Kamigori Hyogo 678-1297 Japan
| | - Hideaki Ogata
- Graduate School of Science, University of Hyogo 3-2-1 Koto, Kamigori Hyogo 678-1297 Japan
| | - Yuta Hori
- Center for Computational Sciences, University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8577 Japan
| | - Katsuhiro Kusaka
- Neutron Industrial Application Promotion Center, Comprehensive Research Organization for Science and Society 162-1 Shirakata, Tokai Ibaraki 319-1106 Japan
| | - Yu Hirano
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology 4-9-1 Anagawa, Inage Chiba 263-8555 Japan
- Department of Quantum Life Science, Graduate School of Science, Chiba University 1-33 Yayoi, Inage Chiba 263-8522 Japan
| | - Kazuo Kurihara
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology 4-9-1 Anagawa, Inage Chiba 263-8555 Japan
| | - Yasuteru Shigeta
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology 4-9-1 Anagawa, Inage Chiba 263-8555 Japan
- Center for Computational Sciences, University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8577 Japan
| | - Taro Tamada
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology 4-9-1 Anagawa, Inage Chiba 263-8555 Japan
- Department of Quantum Life Science, Graduate School of Science, Chiba University 1-33 Yayoi, Inage Chiba 263-8522 Japan
| | - Yoshiki Higuchi
- Graduate School of Science, University of Hyogo 3-2-1 Koto, Kamigori Hyogo 678-1297 Japan
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Expression, purification, characterization and direct electrochemistry of two HiPIPs from Acidithiobacillus caldus SM-1. Anal Biochem 2022; 650:114724. [DOI: 10.1016/j.ab.2022.114724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/15/2022] [Accepted: 05/05/2022] [Indexed: 11/18/2022]
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Zhao F, Zhang B, Yan E, Sun B, Wang Z, He J, Yin D. A guide to sample delivery systems for serial crystallography. FEBS J 2019; 286:4402-4417. [PMID: 31618529 DOI: 10.1111/febs.15099] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 09/26/2019] [Accepted: 10/15/2019] [Indexed: 01/07/2023]
Affiliation(s)
- Feng‐Zhu Zhao
- School of Life Sciences Northwestern Polytechnical University Xi'an China
| | - Bin Zhang
- School of Life Sciences Northwestern Polytechnical University Xi'an China
| | - Er‐Kai Yan
- School of Life Sciences Northwestern Polytechnical University Xi'an China
| | - Bo Sun
- Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai China
| | - Zhi‐Jun Wang
- Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai China
| | - Jian‐Hua He
- Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai China
| | - Da‐Chuan Yin
- School of Life Sciences Northwestern Polytechnical University Xi'an China
- Shenzhen Research Institute Northwestern Polytechnical University Shenzhen China
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Cachau RE, Zhu J, Nicklaus MC. The upcoming subatomic resolution revolution. Curr Opin Struct Biol 2019; 58:53-58. [PMID: 31233975 DOI: 10.1016/j.sbi.2019.05.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/12/2019] [Accepted: 05/13/2019] [Indexed: 10/26/2022]
Abstract
Subatomic resolution macromolecular crystallography has been revealing the most fascinating details of macromolecular structures for many years. This most extreme form of macromolecular crystallography is going through rapid changes. A new generation of superbrilliant X-ray sources and detectors is facilitating the rapid acquisition of high-quality datasets. Equally important, a new breed of methods and highly integrated advanced computational tools for structure refinement and analysis is poised to change the way we use subatomic resolution data and reposition high-resolution macromolecular crystallography in medicinal chemistry studies. Subatomic resolution macromolecular crystallography may soon be a routine source of detailed molecular information besides precise geometries, including binding energies and other chemical descriptors, opening new possibilities of application.
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Affiliation(s)
- Raul E Cachau
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Inc., Frederick, MD 21702, USA.
| | - Jianghai Zhu
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Inc., Frederick, MD 21702, USA
| | - Marc C Nicklaus
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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Wachnowsky C, Cowan JA. In Vitro Studies of Cellular Iron–Sulfur Cluster Biosynthesis, Trafficking, and Transport. Methods Enzymol 2017; 595:55-82. [DOI: 10.1016/bs.mie.2017.06.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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