Rules that govern tRNA identity in protein synthesis.

The specificity of tRNA in protein synthesis depends not only on its recognition of the codon in the mRNA, but also on its recognition of the correct aminoacyl-tRNA synthetase enzyme. The specificity of tRNA in aminoacylation (tRNA identity) depends on the tRNAs productive interaction with the correct enzyme and non-productive interaction with all other enzymes. Although extensive regions of the tRNA interact with the enzyme, only a small number of nucleotides comprise the major determinants of tRNA identity. They often lie in the same positions (acceptor end and anticodon, and variable pocket less often) in different tRNAs. Therefore, a determinant in a given tRNA simultaneously ensures both productive and non-productive interactions with the respective enzymes. Specificity for the acceptor end of the tRNA is achieved, in part, by the specific amino acid sequence within protein binding pocket domains that are part of all aminoacyl-tRNA synthetases. These domains also bind the other two substrates of the enzyme, amino acid and ATP. Specificity for the anticodon and variable pocket of the tRNA is more idiosyncratic. Irrespective of their location in the tRNA, the determinants either interact directly with the enzyme or give the tRNA a conformation for a complementary fit with the enzyme.