A structural understanding of the dynamic ribosome machine

Abstract

The ribosome consists of two ribonucleoprotein subunits. The small subunit mediates the interactions between the anticodons of the tRNAs and the codons in the mRNA that they are translating to determine the order of amino acids in the protein being synthesized. The large subunit contains the peptidyl-transferase centre (PTC), which catalyses the formation of peptide bonds in the growing polypeptide. An incoming tRNA is delivered to the A site in complex with elongation factor (EF)-Tu–GTP. Correct codon–anticodon pairing activates the GTPase centre of the ribosome that causes hydrolysis of GTP and EF-Tu to release the aminoacyl end of the tRNA. Watson–Crick base pairs are formed between the mRNA and the P-site tRNA, which positions the peptidyl-tRNA, but unlike the A site, the rRNA does not make interactions with the codon–anticodon base-paired triplets that 'check' the accuracy of this interaction. Binding of tRNA induces conformational changes in ribosomal (r)RNA that optimally orientates the peptidyl-tRNA and aminoacyl-tRNA for the peptidyl-transferase reaction to occur, which involves the transfer of the peptide chain onto the A-site tRNA. The ribosome must then shift in the 3′ mRNA direction so that it can decode the next mRNA codon. Translocation of the tRNAs and mRNA is facilitated by binding of the GTPase EF-G, which causes the P-site deacylated tRNA to move to the E site and the A-site peptidyl-tRNA to move to the P site on GTP hydrolysis. The ribosome is then ready for the next round of elongation. When a stop codon in the mRNA reaches the A site of the ribosome at the end of the elongation phase of protein synthesis, translocational release factors catalyse the hydrolysis and release of the ester-linked polypeptide on the P-site tRNA.