TRNA binding

Abstract: An integrated mechanism for decoding is proposed, based on six X-ray structures of the 70S ribosome determined at 3.1–3.4 A resolution, modelling cognate or near-cognate states of the decoding centre at the proofreading step. The ribosome has a pivotal role in protein synthesis, translating the genetic code into a sequence of amino acids with remarkable accuracy. The structural basis of this accuracy has long been a puzzle. In one ribosomal proofreading step, conserved residues around the A site, which binds the incoming aminoacylated tRNA, ensure that codon–anticodon pairing is correct before a conformational change in the ribosome occurs. Gulnara Yusupova and colleagues have solved six X-ray crystal structures of 70S ribosomal complexes, with either a cognate or a near-cognate tRNA, as a model of the decoding process. They propose a mechanism for tRNA discrimination in which the ribosomal structure forces the first two nucleotides in the A site to adopt canonical Watson–Crick geometry. Elsewhere, wobble base pairs — non-Watson–Crick base pairs essential to the secondary structure of RNA — induce distortion that causes release of the near-cognate tRNA. During protein synthesis, the ribosome accurately selects transfer RNAs (tRNAs) in accordance with the messenger RNA (mRNA) triplet in the decoding centre. tRNA selection is initiated by elongation factor Tu, which delivers tRNA to the aminoacyl tRNA-binding site (A site) and hydrolyses GTP upon establishing codon–anticodon interactions in the decoding centre1,2,3,4,5,6,7,8,9. At the following proofreading step the ribosome re-examines the tRNA and rejects it if it does not match the A codon2,3,10,11,12,13,14. It was suggested that universally conserved G530, A1492 and A1493 of 16S ribosomal RNA, critical for tRNA binding in the A site15,16,17, actively monitor cognate tRNA18, and that recognition of the correct codon–anticodon duplex induces an overall ribosome conformational change (domain closure)19. Here we propose an integrated mechanism for decoding based on six X-ray structures of the 70S ribosome determined at 3.1–3.4 A resolution, modelling cognate or near-cognate states of the decoding centre at the proofreading step. We show that the 30S subunit undergoes an identical domain closure upon binding of either cognate or near-cognate tRNA. This conformational change of the 30S subunit forms a decoding centre that constrains the mRNA in such a way that the first two nucleotides of the A codon are limited to form Watson–Crick base pairs. When U·G and G·U mismatches, generally considered to form wobble base pairs, are at the first or second codon–anticodon position, the decoding centre forces this pair to adopt the geometry close to that of a canonical C·G pair. This by itself, or with distortions in the codon–anticodon mini-helix and the anticodon loop, causes the near-cognate tRNA to dissociate from the ribosome.