Science · 2012 · 115 citations · 34 references
Life SciencesBiochemistryMolecular BiologyMolecular EvolutionRna ProcessingStructural BiologyRibosome StructureRna StructureRna-binding ProteinsTranslation FactorsTranslation In ProkaryotesTranslation InitiationC-terminal Domain StructureConserved Motif AnalysisCrystal Structure AnalysisMrna Entry ChannelRibosomal Rna Domain ArchitectureRibosome Rescue PathwaysRibosome-associated Rna-binding ProteinsTrna Binding Sites
In bacteria, the hybrid transfer-messenger RNA (tmRNA) rescues ribosomes stalled on defective messenger RNAs (mRNAs). However, certain gram-negative bacteria have evolved proteins that are capable of rescuing stalled ribosomes in a tmRNA-independent manner. Here, we report a 3.2 angstrom-resolution crystal structure of the rescue factor YaeJ bound to the Thermus thermophilus 70S ribosome in complex with the initiator tRNA(i)(fMet) and a short mRNA. The structure reveals that the C-terminal tail of YaeJ functions as a sensor to discriminate between stalled and actively translating ribosomes by binding in the mRNA entry channel downstream of the A site between the head and shoulder of the 30S subunit. This allows the N-terminal globular domain to sample different conformations, so that its conserved GGQ motif is optimally positioned to catalyze the hydrolysis of peptidyl-tRNA. This structure gives insights into the mechanism of YaeJ function and provides a basis for understanding how it rescues stalled ribosomes.
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Clustal W and Clustal X version 2.0
Mark Larkin, Gordon Blackshields, Nigel P. Brown et al. · Bioinformatics · 2007 · 29.1K citations · Full text