Abstract
Methyl-Coenzyme M Reductase (MCR) catalyzes the biosynthesis of methane in methanogenic archaea, using a catalytic Ni-centered Cofactor F430 in its active site. It also catalyzes the reverse reaction, that is, the anaerobic activation and oxidation, including the cleavage of the C–H bond in methane. Because methanogenesis is the major source of methane on earth, understanding the reaction mechanism of this enzyme can have massive implications in global energy balances. While recent publications have proposed a radical-based catalytic mechanism as well as novel sulfonate-based binding modes of MCR for its native substrates, the structure of the active state of MCR, as well as a complete characterization of the reaction, remain elusive. Previous attempts to structurally characterize the active MCR-Ni(I) state have been unsuccessful due to oxidation of the redox- sensitive catalytic Ni center. Further, while many cryo structures of the inactive Ni(II)-enzyme in various substrates-bound forms have been published, no room temperature structures have been reported, and the structure and mechanism of MCR under physiologically relevant conditions is not known. In this study, we report the first room temperature structure of the MCRred1-silent Ni(II) form using an X-ray Free-Electron Laser (XFEL), with simultaneous X-ray Emission Spectroscopy (XES) and X-ray Diffraction (XRD) data collection. In celebration of the seminal contributions of inorganic chemist Dick Holm to our understanding of nickel-based catalysis, we are honored to announce our findings in this special issue dedicated to this remarkable pioneer of bioinorganic chemistry.
| Original language | English |
|---|---|
| Article number | 111768 |
| Journal | Journal of Inorganic Biochemistry |
| Volume | 230 |
| DOIs | |
| State | Published - May 2022 |
| Externally published | Yes |
Funding
We thank staff from LCLS and ALS (BL 5.0.2, 8.2.1 and 8.3.1) for their support. P.Y.-, T.C. and C.L.D. thank Dr. Corie Ralston and Dr. Steven E. Cohen for helping with Xe-pressurized cryo- crystallography. C.L.D. is a Howard Hughes Medical Institute investigator and a Fellow of the Bio- inspired Solar Energy Program, Canadian Institute for Advanced Research. This work was supported by the Director, Office of Science, Office of Basic Energy Sciences (OBES), Division of Chemical Sciences, Geosciences, and Biosciences of the Department of Energy (DOE) (J.Y. V.K.Y. J.F.K.) for X-ray methodology and instrumentation and spectroscopy and crystallography data collection and analysis, by National Institutes of Health, National Institute of General Medical Sciences (NIH NIGMS) grants 1P41GM139687 (R.A.-M.), GM55302 (V.K.Y.), GM110501 (J.Y.), GM126289 (J.F.K.), GM117126 (N.K.S.), R35 GM126982 (C.L.D.), PO1GM063210 (N.W.M). Vetenskapsrådet 2017-00356 (T.F.), and the Air Force Office of Scientific Research grant FA8655-20-1-7010 (T.F.) are acknowledged for support. This work also was supported by the Physical Biosciences Program within the OBES at DOE by contract DE-FG02-08ER15931 (S.W.R.). Beamlines 5.0.2, 8.2.1, 8.2.2 and 8.3.1 of the Advanced Light Source, a DOE Office of Science User Facility under Contract No. DE-AC02-05CH11231, are supported in part by the ALS-ENABLE Program funded by the NIH NIGMS, grant P30 GM124169-01. Use of the LCLS, SLAC National Accelerator Laboratory, is supported by the US DOE, Office of Science, OBES under contract DE-AC02-76SF00515. The Rayonix detector used at LCLS was supported by the NIH NIGMS grant S10 OD023453. This research used resources of the National Energy Research Scientific Computing Center, a User Facility supported by the Office of Science, DOE, under contract DE-AC02-05CH11231. We thank staff from LCLS and ALS (BL 5.0.2, 8.2.1 and 8.3.1) for their support. P.Y.-, T.C. and C.L.D. thank Dr. Corie Ralston and Dr. Steven E. Cohen for helping with Xe-pressurized cryo- crystallography. C.L.D. is a Howard Hughes Medical Institute investigator and a Fellow of the Bio- inspired Solar Energy Program, Canadian Institute for Advanced Research. This work was supported by the Director, Office of Science, Office of Basic Energy Sciences (OBES), Division of Chemical Sciences, Geosciences, and Biosciences of the Department of Energy (DOE) (J.Y., V.K.Y., J.F.K.) for X-ray methodology and instrumentation and spectroscopy and crystallography data collection and analysis, by National Institutes of Health, National Institute of General Medical Sciences (NIH NIGMS) grants 1P41GM139687 (R.A.-M.), GM55302 (V.K.Y.), GM110501 (J.Y.), GM126289 (J.F.K.), GM117126 (N.K.S.), R35 GM126982 (C.L.D.), PO1GM063210 (N.W.M). Vetenskapsrådet 2017-00356 (T.F.), and the Air Force Office of Scientific Research grant FA8655-20-1-7010 (T.F.) are acknowledged for support. This work also was supported by the Physical Biosciences Program within the OBES at DOE by contract DE-FG02-08ER15931 (S.W.R.). Beamlines 5.0.2, 8.2.1, 8.2.2 and 8.3.1 of the Advanced Light Source, a DOE Office of Science User Facility under Contract No. DE-AC02-05CH11231, are supported in part by the ALS-ENABLE Program funded by the NIH NIGMS , grant P30 GM124169-01 . Use of the LCLS, SLAC National Accelerator Laboratory, is supported by the US DOE, Office of Science, OBES under contract DE-AC02-76SF00515. The Rayonix detector used at LCLS was supported by the NIH NIGMS grant S10 OD023453. This research used resources of the National Energy Research Scientific Computing Center, a User Facility supported by the Office of Science, DOE, under contract DE-AC02-05CH11231.
Keywords
- Methanogens
- Nickel
- Serial femtosecond crystallography (SFX)
- X-ray Diffraction (XRD)
- X-ray Emission Spectroscopy (XES)
- X-ray Free-Electron Laser (XFEL)