Atomic resolution structures of the methane-activating enzyme in anaerobic methanotrophy reveal extensive post-translational modifications

Marie-C. Müller, Martijn Wissink, Priyadarshini Mukherjee, Nicole Possel, Rafael Laso-Pérez, Sylvain Engilberge, Philippe Carpentier, Jörg Kahnt, Gunter Wegener, Cornelia U. Welte and Tristan Wagner ()
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Marie-C. Müller: Max-Planck-Institute for Marine Microbiology
Martijn Wissink: Radboud University
Priyadarshini Mukherjee: Max-Planck-Institute for Marine Microbiology
Nicole Possel: Max-Planck-Institute for Marine Microbiology
Rafael Laso-Pérez: Museo Nacional de Ciencias Naturales (MNCN-CSIC)
Sylvain Engilberge: Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale
Philippe Carpentier: European Synchrotron Radiation Facility
Jörg Kahnt: Max Planck Institute for Terrestrial Microbiology
Gunter Wegener: Max-Planck-Institute for Marine Microbiology
Cornelia U. Welte: Radboud University
Tristan Wagner: Max-Planck-Institute for Marine Microbiology

Nature Communications, 2025, vol. 16, issue 1, 1-13

Abstract: Abstract Anaerobic methanotrophic archaea (ANME) are crucial to planetary carbon cycling. They oxidise methane in anoxic niches by transferring electrons to nitrate, metal oxides, or sulfate-reducing bacteria. No ANMEs have been isolated, hampering the biochemical investigation of anaerobic methane oxidation. Here, we obtained the true atomic resolution structure of their methane-capturing system (Methyl-Coenzyme M Reductase, MCR), circumventing the isolation barrier by exploiting microbial enrichments of freshwater nitrate-reducing ANME-2d grown in bioreactors, and marine ANME-2c in syntrophy with bacterial partners. Despite their physiological differences, these ANMEs have extremely conserved MCR structures, similar to homologs from methanogenic Methanosarcinales, rather than the phylogenetically distant MCR of ANME-1 isolated from Black Sea mats. The three studied enzymes have seven post-translational modifications, among them was a novel 3(S)-methylhistidine on the γ-chain of both ANME-2d MCRs. Labelling with gaseous krypton did not reveal any internal channels that would facilitate alkane diffusion to the active site, as observed in the ethane-specialised enzyme. Based on our data, the methanotrophic MCRs should follow the same radical reaction mechanism proposed for the methane-generating homologues. The described pattern of post-translational modifications underscores the importance of native purification as a powerful approach to discovering intrinsic enzymatic features in non-isolated microorganisms existing in nature.

Date: 2025
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DOI: 10.1038/s41467-025-63387-1

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