Kinetic discrimination of tRNA identity by the conserved motif 2 loop of a class II aminoacyl-tRNA synthetase

The selection of tRNAs by their cognate aminoacyl-tRNA synthetases is critical for ensuring the fidelity of protein synthesis. While nucleotides that comprise tRNA identity sets have been readily identified, their specific role in the elementary steps of aminoacylation is poorly understood. By use of a rapid kinetics analysis employing mutants in tRNA H's and its cognate aminoacyl-tRNA synthetase, the role of tRNA identity in aminoacylation was investigated. While mutations in the tRNA anticodon preferentially affected the thermodynamics of initial complex formation, mutations in the acceptor stem or the conserved motif 2 loop of the tRNA synthetase imposed a specific kinetic block on aminoacyl transfer and decreased tRNA-mediated kinetic control of amino acid activation. The mechanistic basis of tRNA identity is analogous to fidelity control by DNA polymerases and the ribosome, whose reactions also demand high accuracy.