Aminoacyl thioester chemistry of class II aminoacyl-tRNA synthetases

Lysyl-tRNA synthetase, a class II enzyme, edits homocysteine by converting it into homocysteine thiolactone. In a similar reaction, the enzyme converts homoserine into homoserine lactone. Other class II enzymes, aspartyl-tRNA synthetase and seryl-tRNA synthetase, do not edit any of the amino acids tested. However, all three class II aminoacyl-tRNA synthetases catalyze AMP- and pyrophosphate-independent deacylation of cognate aminoacyl-tRNA in the presence of thiols, mimicking editing of homocysteine. Thiol-dependent deacylations exhibit saturation kinetics with respect to concentration of thiols, suggesting the presence of a thiol binding site on each enzyme. 3-Mercaptopropionate-, N-acetyl-L-cysteine-, and dithiothreitol-dependent deacylations of aminoacyl-tRNA yield corresponding aminoacyl thioesters. Cysteine-dependent enzymatic deacylations of aminoacyl-tRNA by these class II enzymes yield dipeptides, N-(aminoacyl)cysteine. The formation of N-(aminoacyl)cysteine involves thioester intermediates S-(aminoacyl)-L-cysteine, which are not observed because of the facile transacylation of the aminoacyl residue from the sulfur to the alpha-amino group of cysteine to form a stable peptide bond. These data indicate that class II aminoacyl-tRNA synthetases possess unique thiol-binding subsites within their active sites. That the thiol-binding subsite exists also in AspRS and SerRS, which do not need editing function, suggests that these class II enzymes possess vestigial editing functions.