Attachment of amino acids to adapter RNA molecules is a key reaction in protein biosynthesis. The aminoacylation reaction is catalyzed in the cell by aminoacyl-tRNA synthetases. Recently, three classes of catalytic RNAs (ribozymes) that recapitulate this activity by transferring the aminoacyl moiety from a pre-formed adenylate to their own 3'-termini have been obtained through in vitro selection. The first class contains RNAs that accept any aminoacyl moiety, whereas members of the second class are specific for phenylalanine and tyrosine. Ribozymes of the third class also catalyze the formation of dipeptides, a reaction analogous to that catalyzed by a large ribozyme, the ribosome. In this proposal, the three-dimensional structures of self-aminoacylating RNAs of the three classes will be determined by x-ray crystallography. The ribozymes will be analyzed in complex with substrate and product analogs. The structural information obtained in this study will reveal the configuration of the active site of these ribozymes, organization of the amino acid-specific binding pocket and the mechanism of catalysis. It will help clarify the issue of whether the aminoacyl transfer to a peptide or an RNA involves entropic catalysis (i.e., precise positioning of the substrates) or it requires special catalytic groups on the enzyme, such as an acid or base; hence, it will add to our understanding of the reactions catalyzed by the larger biological systems such as the aminoacyl-tRNA synthetases and the ribosome.
