Journal Article

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

Mukherjee, Priyadarshini, Wissink, Martijn, Welte, Cornelia U., Von Possel, Nicole, Laso-Pérez, Rafael, Carpentier, Philippe, Wagner, Tristan, Müller, Marie-C., Wegener, Gunter, Engilberge, Sylvain, Kahnt, Jörg

2025

Overview

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. Biochemical research on methane oxidation in anaerobic methanotrophic archaea is hampered by the lack of cultured isolates. Here, Müller et al. present atomic-resolution snapshots of the methane-oxidising enzymes purified from enrichment cultures, providing molecular insights into the process and revealing unusual post-translational modifications.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 101/58 / 45 / 631/326/171 / 631/326/26/2523 / 631/45/607 / 631/535/1266 / 631/92/458 / 82/83 / Alkanes / Anaerobic microorganisms / Anaerobiosis / Archaea / Archaea - enzymology / Archaea - metabolism / Archaeal Proteins - chemistry / Archaeal Proteins - genetics / Archaeal Proteins - metabolism / Atomic structure / Bacteria / Biomass / Bioreactors / Carbon cycle / Catalytic Domain / Coenzyme M / Enzymes / Ethane / Greenhouse gases / Humanities and Social Sciences / Krypton / Life Sciences / Metal oxides / Methane / Methane - metabolism / Methanosarcinales - enzymology / Methanosarcinales - metabolism / Microorganisms / Models, Molecular / multidisciplinary / Oxidation / Oxidation-Reduction / Oxidoreductases - chemistry / Oxidoreductases - genetics / Oxidoreductases - metabolism / Phylogeny / Physiology / Post-translation / Protein Processing, Post-Translational / Proteins / Reaction mechanisms / Reductases / Science / Science (multidisciplinary) / Sediments / Sulfate reduction / Sulfate-reducing bacteria / Translation