Year: 2025
Type: preprint
Abstract: Summary Our work reveals the structure of the active state of Methyl-Coenzyme M Reductase (MCR), the key and rate-limiting enzyme in biological methane formation. We find large differences between the active Ni(I) and inactive Ni(II) proteins and provide insight into how nature makes and breaks the C-H bond of methane. The Ni(II)-F430 center in inactive MCR contains four planar nitrogen ligands, a lower axial glutamine oxo, and an upper axial thiolate. The Ni(I)-enzyme replaces the axial ligands with a single water. The one-electron redox change results in movement of the Ni ion and upward swing of the β-lactam ring in the tetrapyrrole coupled to a domino-like protein quake through second sphere residues, inter-subunit interactions, a substrate tunnel, affecting even the dimensions of the unit cell. These structural changes lead Ni(I)-MCR to release a charge clamp that, in the Ni(II) state, locks down substrate Coenzyme B. Determining the Ni(I)-MCR structure required development of rigorous anaerobic crystallographic techniques. Validation of the MCR redox state was accomplished by in-line and parallel spectroscopic and unit cell analyses. This structure has large implications for developing technologies to limit methane emissions and efficiently produce biofuels. Methodology described here will enhance structural biology for other oxygen-sensitive enzymes.
Authors: Christopher J. Ohmer, Macon J. Abernathy, Darya Marchany-Rivera, David G. Villareal, Philipp S. Simon, Artem Lyubimov, Asmit Bhowmick, Kuntal Chatterjee, Hiroki Makita, Vandana Tiwari, Medhanjali Dasgupta, Stephen Keable, David Mittan-Moreau, Daniel W. Paley, Nigel W. Moriarty, Humberto Sanchez, Daniel J. Rosenberg, Leland B. Gee, Roberto Alonso-Mori, Nicholas K. Sauter, Aaron S. Brewster, Uwe Bergmann, Vittal K. Yachandra, Aina E. Cohen, Junko Yano, Jan F. Kern, Ritimukta Sarangi, Stephen W. Ragsdale
Institutions: University of Michigan, SLAC National Accelerator Laboratory, Michigan Medicine, Stanford Synchrotron Radiation Lightsource, Lawrence Berkeley National Laboratory, Linac Coherent Light Source, University of Nebraska Medical Center, Oak Ridge National Laboratory, University of Wisconsin–Madison
Language: English
Subfield: Biochemistry
Domain: Life Sciences
Open Access status: green
Funders: U.S. Department of Energy, National Institutes of Health, Office of Science, Oak Ridge Institute for Science and Education, National Institute of General Medical Sciences, Basic Energy Sciences, Workforce Development for Teachers and Scientists, Chemical Sciences, Geosciences, and Biosciences Division, SLAC National Accelerator Laboratory
Awards: G1124288891, G1229526393, G1286236842, G1286251239, G1311044274, G1451874870, ENZYMOLOGY OF METHANOGENESIS, G1538770391, G17040919, G2037563265, G222768804, DIALS / CCTBX: Serial crystallography computational methods aimed at biomolecular function, G2371548206, G262532246, G2917895714, G303061748, G30714459, G3083819904, G3653110791, G382641700, G419881185, G4235786860, G42916606, G4501827968, G473123490, G473396326, G4775691204, G495301720, G498139845, G5070048936, G5570207115, G5648016710, G601061201, G6017181652, G650090426, G6550344761, G7283024673, G7331630580, High-end X-ray Detector System for Femtosecond Crystallography, G7619220232, G8382000481, G8570346810, G8715997042, G8925327636, DIALS: supporting structural biology through open source diffraction processing software, A Synchrotron Radiation Structural Biology Resource, Biological Spectroscopy and Crystallography Using an X-ray Free Electron Laser, Cctbx.xfel: Serial crystallography computational methods aimed at biomolecular function, Structural Dynamics at LCLS, High throughput sample delivery method for time resolved studies of enzyme reactions with X-ray and complementary techniques, Taking Snapshots of Enzymatic Reactions Using X-ray Crystallography and Spectroscopy, G911061179, G969889393
OpenAlex ID: W4409900972