Does Glutamine Methylation Affect the Intrinsic Conformation of the Universally Conserved GGQ Motif in Ribosomal Release Factors?

Abstract

The GGQ motif is the only universally conserved feature of ribosomal class 1 release factors. Mutational experiments and structural studies have suggested that the glutamine residue of the GGQ motif (Q185 in human eRF1 numbering) is critical for catalysis of the termination reaction on the ribosome. Furthermore, it has been established that Q185 is Nepsilon methylated in prokaryotes as well as eukaryotes, and that methylation significantly enhances the catalytic activity. It is, however, not known whether this methylation affects the intrinsic structure of the free release factor, which could be important for its interaction with the ribosome. In this work, we report molecular dynamics simulations, starting from 25 different NMR structures of human eRF1, in addressing this problem. The results show that there is no such structural effect on the free release factor caused by the Nepsilon methylation of Q185, suggesting that its role is intimately associated with the ribosome environment.

Mechanism of the Translation Termination Reaction on the Ribosome

“…It should again be pointed out here that the crystal structures do apparently not have the Gln side chain methylated, but it is at present unclear whether this has any significant effect on the conformation of the GGQ loop. Our simulations indicated that the main structural effect of removal of the methyl group was an increased mobility of the side chain , and recent studies of free RFs in solution do not reveal any difference in the intrinsic conformational preferences between the methylated and unmethylated GGQ loop .…”

Mechanism of activation of methyltransferases involved in translation by the Trm112 ‘hub’ protein

“…The Mtq2-Trm112 substrate is the eRF1-eRF3-GTP (or any non-hydrolysable GTP analogue) complex, where eRF3 is the class II release factor of the translational GTPase family, which assists eRF1 in peptide release by inducing a rearrangement of the termination complex upon GTP hydrolysis (22–24). As in prokaryotes, the role of this methylation seems to be associated with the ribosome environment, since methylation should not affect the intrinsic structure of eRF1 (25). Deletion of the MTQ2 gene in S. cerevisiae affects growth (2-fold decrease in growth rate at 30°C) and leads to sensitivity to the antibiotic paromomycin, implying a translation defect related to ribosomal A site function (26) (V.H.H.…”