Structural dynamics of the methyl-coenzyme M reductase active site are influenced by coenzyme F430modifications

Abstract

AbstractMethyl-coenzyme M reductase (MCR) is a central player in methane biogeochemistry, governing methanogenesis and the anaerobic oxidation of methane (AOM) in methanogens and anaerobic methanotrophs (ANME), respectively. The prosthetic group of MCR is coenzyme F430, a nickel-containing tetrapyrrole derivative. Additionally, a few modified versions of F430have been discovered, including the 172-methylthio-F430(mt-F430) that functions with ANME-1 MCR. This study employs molecular dynamics (MD) simulations to unravel the intricacies of the active-site dynamics of MCR fromMethanosarcina acetivoransand ANME-1 when bound to the canonical F430compared to 172-thioether coenzyme F430variants and substrates for methane formation. Overall, our simulations indicate that each MCR active site is optimized for a given version of F430and support the importance of the Gln to Val substitution in accommodating the 172methylthio modification. Notably, modifications in the 172position disrupt the canonical coordination among cofactors inM. acetivoransMCR, implicating structural perturbations, but evidence of active site reorganization to maintain substrate positions suggest that the modified F430s could be accommodated in a methanogenic MCR. We additionally report the first quantitative estimate of MCR intrinsic electric fields pivotal in driving methane formation. Our results suggest that the electric field aligned along the CH3-S-CoM thioether bond facilitates homolytic bond cleavage, coinciding with the proposed catalytic mechanism. Structural perturbations, however, weaken and misalign these electric fields, emphasizing the significance of the active site structure in maintaining their integrity. In conclusion, our results deepen the understanding of MCR active-site dynamics, the enzyme’s organizational role in intrinsic electric fields for catalysis, and the interplay between active site structure and electrostatics. This work not only advances our comprehension of MCR functionality but also provides a foundation for future investigations employing sophisticated models to capture the complex electronic properties of MCR active sites quantitatively.