Structure of the ATP-driven methyl-coenzyme M reductase activation complex

Methyl-coenzyme M reductase (MCR) is the enzyme responsible for nearly all biologically generated methane¹. Its active site comprises coenzyme F₄₃₀, a porphyrin-based cofactor with a central nickel ion that is active exclusively in the Ni(I) state^2,3. How methanogenic archaea perform the reductive activation of F₄₃₀ represents a major gap in our understanding of one of the most ancient bioenergetic systems in nature. Here we purified and characterized the MCR activation complex from Methanococcus maripaludis. McrC, a small subunit encoded in the mcr operon, co-purifies with the methanogenic marker proteins Mmp7, Mmp17, Mmp3 and the A2 component. We demonstrated that this complex can activate MCR in vitro in a strictly ATP-dependent manner, enabling the formation of methane. In addition, we determined the cryo-electron microscopy structure of the MCR activation complex exhibiting different functional states with local resolutions reaching 1.8-2.1 Å. Our data revealed three complex iron-sulfur clusters that formed an electron transfer pathway towards F₄₃₀. Topology and electron paramagnetic resonance spectroscopy analyses indicate that these clusters are similar to the [8Fe-9S-C] cluster, a maturation intermediate of the catalytic cofactor in nitrogenase. Altogether, our findings offer insights into the activation mechanism of MCR and prospects on the early evolution of nitrogenase.