9nta | pdb_00009nta
Methanosarcina acetivorans 50S subunit obtained from methanol-grown cells
Structural highlights
FunctionRL2_METAC One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome.[HAMAP-Rule:MF_01320] Publication Abstract from PubMedDespite the overall conservation of ribosomes across all domains of life, differences in their 3D architecture, rRNA sequences, ribosomal protein composition, and translation factor requirements reflect lineage-specific adaptations to environmental niches. In the domain Archaea, structural studies have primarily focused on non-methanogenic thermophiles and halophiles, leaving it unclear whether these represent the broader archaeal domain. Here, we report the cryo-electron microscopy (cryo-EM) structure of the ribosome from Methanosarcina acetivorans, a previously unreported high-resolution structure from a model mesophilic methanogenic archaeon. Compared to ribosomes from extremophiles, the M. acetivorans ribosome has a simplified architecture, lacking paralogous duplications and containing a reduced complement of ribosomal proteins. Structures of the large subunit (50S) from cells grown with either methanol or acetate show conserved rRNA folding and protein composition. High-resolution structures of the 50S subunit from the two growth substrates enabled us to investigate structural properties that may influence in vivo dimethyl sulfate (DMS) reactivity, an orthogonal chemical approach used to probe RNA structure. We observed good agreement between in vivo DMS reactivity and ribosome structure. Finally, we identify a previously uncharacterized ribosome dimerization mode involving only 50S subunits and mediated by a heterotetrameric complex of PurH and aEF2-proteins with alternative metabolic and translational roles. This macromolecular assembly, which we term the Methanogen Ribosome Dimerization Factor (MRDF), likely mediates ribosome hibernation, revealing an alternative regulatory mechanism in translation. Cryo-EM Study and In Vivo Chemical Mapping of the Methanosarcina acetivorans Ribosome and Its Dimerization via a Repurposed Enzyme and Translation Factor.,Fordjour GNR, Ghosh A, Ferry JG, Armache JP, Bevilacqua PC, Murakami KS J Biol Chem. 2025 Sep 4:110686. doi: 10.1016/j.jbc.2025.110686. PMID:40914243[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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