Journal Article

Accuracy mechanism of eukaryotic ribosome translocation

Demeshkina, Natalia, Yusupova, Gulnara, Djumagulov, Muminjon, Yusupov, Marat, Rozov, Alexey, Jenner, Lasse

2021

Overview

Translation of the genetic code into proteins is realized through repetitions of synchronous translocation of messenger RNA (mRNA) and transfer RNAs (tRNA) through the ribosome. In eukaryotes translocation is ensured by elongation factor 2 (eEF2), which catalyses the process and actively contributes to its accuracy 1 . Although numerous studies point to critical roles for both the conserved eukaryotic posttranslational modification diphthamide in eEF2 and tRNA modifications in supporting the accuracy of translocation, detailed molecular mechanisms describing their specific functions are poorly understood. Here we report a high-resolution X-ray structure of the eukaryotic 80S ribosome in a translocation-intermediate state containing mRNA, naturally modified eEF2 and tRNAs. The crystal structure reveals a network of stabilization of codon–anticodon interactions involving diphthamide 1 and the hypermodified nucleoside wybutosine at position 37 of phenylalanine tRNA, which is also known to enhance translation accuracy 2 . The model demonstrates how the decoding centre releases a codon–anticodon duplex, allowing its movement on the ribosome, and emphasizes the function of eEF2 as a ‘pawl’ defining the directionality of translocation 3 . This model suggests how eukaryote-specific elements of the 80S ribosome, eEF2 and tRNAs undergo large-scale molecular reorganizations to ensure maintenance of the mRNA reading frame during the complex process of translocation. Structural analysis of the Saccharomyces cerevisiae 80S ribosome trapped in an intermediate translocation state shows stabilization of codon–anticodon interactions by eukaryote-specific elements of the 80S ribosome, eEF2 and tRNA and demonstrates a major role for eEF2 in maintaining the directionality of translocation.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/337/574/1789 / 631/535/1266 / Anticodon - genetics / Anticodon - metabolism / Biochemistry, Molecular Biology / Codon - genetics / Crystal structure / Decoding / Elongation / Eukaryota - genetics / Eukaryotes / Genetic aspects / Genetic code / Humanities and Social Sciences / Life Sciences / Molecular modelling / mRNA / multidisciplinary / Peptide Elongation Factor 2 - chemistry / Peptide Elongation Factor 2 - genetics / Peptide Elongation Factor 2 - metabolism / Phenylalanine / Physiological aspects / Protein Biosynthesis / Proteins / Ribosomes / Ribosomes - metabolism / RNA, Messenger - metabolism / RNA, Transfer - metabolism / Science / Science (multidisciplinary) / Severe acute respiratory syndrome coronavirus 2 / Transfer RNA / Translation / Translocation / Translocation (Genetics) / tRNA Phe