Selection of tRNA by the ribosome requires a transition from an open to a closed form.
A structural and mechanistic explanation for the selection of tRNAs by the ribosome has been elusive. Here, we report crystal structures of the 30S ribosomal subunit with codon and near-cognate tRNA anticodon stem loops bound at the decoding center and compare affinities of equivalent complexes in solution. In ribosomal interactions with near-cognate tRNA, deviation from Watson-Crick geometry results in uncompensated desolvation of hydrogen-bonding partners at the codon-anticodon minor groove. As a result, the transition to a closed form of the 30S induced by cognate tRNA is unfavorable for near-cognate tRNA unless paromomycin induces part of the rearrangement. We conclude that stabilization of a closed 30S conformation is required for tRNA selection, and thereby structurally rationalize much previous data on translational fidelity.
Ogle
James M
JM
MRC Laboratory of Molecular Biology, Hills Road, CB2 2QH, Cambridge, United Kingdom.
Murphy
Frank V
FV
Tarry
Michael J
MJ
Ramakrishnan
V
V
D000900:Anti-Bacterial Agents / Q000378:metabolism / Q000494:pharmacology; D000926:Anticodon / Q000737:chemistry / Q000378:metabolism; D020029:Base Pairing; D001667:Binding, Competitive; D003062:Codon / Q000737:chemistry / Q000378:metabolism; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010303:Paromomycin / Q000378:metabolism / Q000494:pharmacology; D012329:RNA, Bacterial / Q000737:chemistry / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry* / Q000378:metabolism*; D012360:RNA, Transfer, Phe / Q000737:chemistry / Q000378:metabolism; D012270:Ribosomes / Q000737:chemistry / Q000378:metabolism*; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D016963:Thermus thermophilus
D000900:Anti-Bacterial Agents; D000926:Anticodon; D003062:Codon; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012360:RNA, Transfer, Phe; D010303:Paromomycin; D012343:RNA, Transfer