How Anaerobic Microbes Make & Break Methane: Structural Biology & Mechanism of Methyl-Coenzyme M Reductase

Abstract:

Methane is an important contributor to the carbon cycle of our planet as well as a key energy source in homes and industry. On the other hand, it is roughly 25 times more potent as a greenhouse gas than carbon dioxide and thus is a major contributor to earth’s warming. Methanogenic microbes are responsible for generating about 1 gigaton of methane per year, constituting the primary producer of methane within the atmosphere.  Methyl-CoM reductase (MCR) is the enzyme responsible for generating methane.  Learning the structure of the active state of this enzyme is crucial for understanding the mechanism of this important process. We have learned that MCR-catalyzed methane synthesis involves a methyl radical as well as other substrate radicals during the catalytic cycle. We also recently determined the structure of the active Ni(I) state of MCR. This work involved the invention of novel anaerobic crystallographic techniques that are widely applicable in structural biology. The Ni(I)-metallocenter redox state is demonstrated by 2 anaerobic crystallography techniques: cryo-X-ray Diffraction (XRD) and room-temperature time resolved X-ray free electron laser (XFEL) crystallography paired with in-line and parallel spectroscopic methods and unit cell analyses. Both structural methods (XRD and XFEL) lead to 1.6 angstrom structures that coincide and show a four-coordinate Ni(I) site for the active enzyme, contrasted to a locked-in inactive six-coordinate Ni(II) state. Our work traces this oxidation state change to a domino effect beginning with conformational alterations of the tetrapyrrole ring and continuing through the entire enzyme structure. These large-scale conformational changes result in a more open substrate channel and a much more dynamic overall structure for the active Ni(I)-enzyme.