Structural Insights into the Methane-Generating Enzyme from a Methoxydotrophic Methanogen Reveal a Restrained Gallery of Post-Translational Modifications

Abstract

Methanogenic archaea operate an ancient, if not primordial, metabolic pathway that releases methane as an end-product. This last step is orchestrated by the methyl-coenzyme M reductase (MCR), which uses a nickel-containing F430-cofactor as the catalyst. MCR astounds the scientific world by its unique reaction chemistry, its numerous post-translational modifications, and its importance in biotechnology not only for production but also for capturing the greenhouse gas methane. In this report, we investigated MCR natively isolated from Methermicoccus shengliensis. This methanogen was isolated from a high-temperature oil reservoir and has recently been shown to convert lignin and coal derivatives into methane through a process called methoxydotrophic methanogenesis. A methoxydotrophic culture was obtained by growing M. shengliensis with 3,4,5-trimethoxybenzoate as the main carbon and energy source. Under these conditions, MCR represents more than 12% of the total protein content. The native MCR structure refined at a resolution of 1.6-Å precisely depicts the organization of a dimer of heterotrimers. Despite subtle surface remodeling and complete conservation of its active site with other homologues, MCR from the thermophile M. shengliensis contains the most limited number of post-translational modifications reported so far, questioning their physiological relevance in other relatives.

Differences in the regulation mechanisms of the glutamine synthetase from methanogenic archaea unveiled by structural investigations

“…M. shengliensis ZC-1 (DSM 18856) was also obtained from the DSMZ (Braunschweig, Germany) and was grown anaerobically on methanol as previously described in Kurth and Müller et al 2021 46 .…”

Bioelectrocatalytic CO2 Reduction by Mo‐Dependent Formylmethanofuran Dehydrogenase

“…The authors have cited additional references within the Supporting Information. [18,22,[28][29][30][31][32] Raw data are freely available on Zenodo (DOI: 10.5281/zenodo.8250713).…”

A Structural View of Alkyl-Coenzyme M Reductases, the First Step of Alkane Anaerobic Oxidation Catalyzed by Archaea

“…A minimum set of three modifications was observed in M. shengliensis ; two of them, the 5( S )-methylarginine and thioglycine, are not essential as shown by genetics, even if their absence could have dramatic effects on growth depending on the supplied substrate, culture temperature, and methane production. 99 , 103 − 105 Structural superposition shows that additional modifications have only a small, even negligible, impact on the local environment. Of course, it must be mentioned here that all of these MCR structures used for comparison are crystallographic snapshots, with most of them in the inactive state (Ni II -silent).…”

“…(D) Experimentally demonstrated post-translational modifications in characterized ACRs. Modifications demonstrated by X-ray crystallography, mass spectrometry, or both methods are colored yellow, blue, or black, respectively, with the corresponding reference. ,,− ,, A double dagger indicates the modifications that are supposed to be present even if the peptides were not detected by mass spectrometry …”