9QQT

Methyl-coenzyme M reductase of ANME-2d Candidatus Methanoperedens Vercelli Strain 1 from a bioreactor enrichment culture

This is a non-PDB format compatible entry.

Summary for 9QQT

• Entry DOI: 10.2210/pdb9qqt/pdb
• Descriptor: Methyl-coenzyme M reductase subunit alpha, O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE, Methyl-coenzyme M reductase subunit beta, ... (11 entities in total)
• Functional Keywords: methanotrophy, anaerobic methanotrophic archaea, methane oxidation, methyl-coenzyme m reductase, anme, mcr, reverse methanogenesis, nickel-dependent enzyme, coenzyme m, coenzyme b, f430 cofactor, post-translational modification, transferase
• Biological source: Candidatus Methanoperedens sp.; More
• Total number of polymer chains: 6
• Total formula weight: 276060.34

Authors

Mueller, M.-C.,Wagner, T. (deposition date: 2025-04-02, release date: 2025-07-23, Last modification date: 2025-09-17)

Primary citation

Muller, M.C.,Wissink, M.,Mukherjee, P.,Von Possel, N.,Laso-Perez, R.,Engilberge, S.,Carpentier, P.,Kahnt, J.,Wegener, G.,Welte, C.U.,Wagner, T.
Atomic resolution structures of the methane-activating enzyme in anaerobic methanotrophy reveal extensive post-translational modifications.
Nat Commun, 16:8229-8229, 2025

PubMed 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.

PubMed: 40913044
DOI: 10.1038/s41467-025-63387-1

Experimental method

X-RAY DIFFRACTION (0.98 Å)