8VYD

A novel synthase generates m4(2)C to stabilize the archaeal ribosome

Summary for 8VYD

• Entry DOI: 10.2210/pdb8vyd/pdb
• Descriptor: SAM-dependent methyltransferase, UPF0020 family, SODIUM ION (3 entities in total)
• Functional Keywords: n4, n4-dimethylcytidine, synthase, rna modifications, hyperthermophile, rna binding protein
• Biological source: Thermococcus kodakarensis
• Total number of polymer chains: 2
• Total formula weight: 66031.99

Authors

Ho, P.S.,Santangelo, T.J.,Fluke, K. (deposition date: 2024-02-08, release date: 2024-11-06, Last modification date: 2025-05-21)

Primary citation

Fluke, K.A.,Dai, N.,Wolf, E.J.,Fuchs, R.T.,Ho, P.S.,Talbott, V.,Elkins, L.,Tsai, Y.L.,Schiltz, J.,Febvre, H.P.,Czarny, R.,Robb, G.B.,Correa Jr., I.R.,Santangelo, T.J.
A novel N 4, N 4-dimethylcytidine in the archaeal ribosome enhances hyperthermophily.
Proc.Natl.Acad.Sci.USA, 121:e2405999121-e2405999121, 2024

PubMed Abstract: Ribosome structure and activity are challenged at high temperatures, often demanding modifications to ribosomal RNAs (rRNAs) to retain translation fidelity. LC-MS/MS, bisulfite-sequencing, and high-resolution cryo-EM structures of the archaeal ribosome identified an RNA modification, 4,4-dimethylcytidine (mC), at the universally conserved C918 in the 16S rRNA helix 31 loop. Here, we characterize and structurally resolve a class of RNA methyltransferase that generates mC whose function is critical for hyperthermophilic growth. mC is synthesized by the activity of a unique family of RNA methyltransferase containing a Rossman-fold that targets only intact ribosomes. The phylogenetic distribution of the newly identified mC synthase family implies that mC is biologically relevant in each domain. Resistance of mC to bisulfite-driven deamination suggests that efforts to capture mC profiles via bisulfite sequencing are also capturing mC.

PubMed: 39471227
DOI: 10.1073/pnas.2405999121

Experimental method

X-RAY DIFFRACTION (1.95 Å)