Structure and mechanism of the methyltransferase ribozyme MTR1

Abstract

RNA-catalysed RNA methylation was recently shown to be part of the catalytic repertoire of ribozymes. The methyltransferase ribozyme MTR1 catalyses the sitespecific synthesis of 1-methyladenosine (m 1 A) in RNA, using O 6 -methylguanine (m 6 G) as methyl group donor. Here we report the crystal structure of MTR1 at a resolution of 2.8 Å, which reveals a guanine binding site reminiscent of natural guanine riboswitches. The structure represents the postcatalytic state of a split ribozyme in complex with the m 1 A-containing RNA product and the demethylated cofactor guanine. The structural data suggest the mechanistic involvement of a protonated cytidine in the methyl transfer reaction. A synergistic effect of two 2'-Omethylated ribose residues in the active site results in accelerated methyl group transfer. Supported by these results, it seems plausible that modified nucleotides may have enhanced early RNA catalysis and that metabolite-binding riboswitches may resemble inactivated ribozymes that have lost their catalytic activity during evolution.

A linear CH+–NO3− base pair motif promoted by AgNO3 mediated proton transfer between guanosine and cytidine

“…25 The protonated C was also recently reported to be involved in the catalytic mechanism of the methyltransferase ribozyme MTR1. 26,27 Unlike the intercalation mode of the i-motif, II arranged into planar tapes instead, due to its net neutral and strong CAHB character (Fig. 3C).…”

Scaling Catalytic Contributions of Small Self‐Cleaving Ribozymes

“…Additionally, our FRET folding assay indicates that the extended conformation of the substrate is already adopted prior attack of the nucleophile at the scissile phosphate. Notably, given the prominent role of substrate positioning in the ribosome and of cofactor positioning in recently found methyltransferase ribozymes,[ 61 , 62 ] the feature of “positioning” accommodates perfectly into this argumentation for the pistol ribozymes.…”

RNA-Guided RNA Modifications: Biogenesis, Functions, and Applications

“…MTR1 can install m 1 A on synthetic RNA structures and natural tRNAs within cells. Structure and mechanism analysis of MTR1 have led to insights for improving the reaction rate by adjusting the reaction pH or substituting specific nucleotides with 2′- O -methylated ones. , Furthermore, various other ribozymes have been chosen for RNA alkylation, m 3 C, and m 7 G modification (Figure G). Additionally, specific ribozymes for RNA labeling have been identified, allowing site-specific RNA labeling with fluorescent ATP or repurposed antiviral nucleotide analogues .…”