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The aminoacyl-tRNA synthetases (aaRS) catalyze the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific reaction. Editing activities of aminoacyl-tRNA synthetases play important roles in genetic information transfer in translation. The accuracy of protein biosynthesis depends on the correct recognition of amino acids and tRNA by aaRSs. Discrimination between L-isoleucine and L-valine is one of the most difficult recognition to achieve, because they differ by only one methylene group in their aliphatic side chains. Pauling estimated, from a value of 1 kcal mol-1 for the hydrophobic binding energy of a methylene group, the error rate for L-valine replacing L-isoleucine to be about one in five (3). Thus, it is impossible for isoleucyl-tRNA synthetase (IleRS) to achieve strict discrimination [an error rate as low as 1/40000] between L-isoleucine and L-valinethrough ordinary one-step recognition.
A "double-sieve" mechanism for two-step substrate selection has been proposed by Fershit (1, 2) to interpret how IleRS to distinguish L-isoleucine from L-valine. First, amino acids larger than L-isoleucine are excluded by the first, amino acid activation site, serving as the "coarse sieve", and smaller ones, such as L-valine, are strictly eliminated by the “fine sieve” of the second hydrolytic site.
1. Coarse sieve : exclude a.a. larger than Ile
IleRS + a.a. + ATP IleRSa.a.-AMP + PPi
IleRSVal-AMP + tRNAIle IleRS + Val +AMP + tRNAIle