Structure of the ATP-driven methyl-coenzyme M reductase activation complex
Fidel Ramírez-Amador, Sophia Paul, Anuj Kumar, Christian Lorent, Sébastian Keller, Stefan Bohn, V. P. Thinh Nguyen, Stefano Lometto, Dennis Vlegels, Jörg Kahnt, Darja Deobald, Frank Abendroth, Olalla Vázquez, Georg Hochberg, Silvan Scheller, Sven T. Stripp, Jan M. Schuller
Abstract
Abstract Methyl-coenzyme M reductase (MCR) is the enzyme responsible for nearly all biologically generated methane 1 . Its active site comprises coenzyme F 430 , 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 F 430 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 F 430 . 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.