Structural reduction of amino acid activating ribozyme KK13

Protein synthesis requires at least three steps: amino acid activation, amino acid transfer to tRNA, and peptide bond formation. Of these, the energy level of the reaction product in the first step, catalyzed by aminoacyl-tRNA synthetase, is the highest, and this reaction consumes ATP and connects amino acids to AMP via acyl phosphate bonds (formation of aminoacyl-AMP). In this study, we focused on KK13, a ribozyme with a length of 114 nucleotides, which catalyzes the formation of acyl phosphate bonds between the α-phosphate of 5ʹ-terminal triphosphate of the ribozyme and the carboxylate of amino acid with concomitant release of inorganic pyrophosphate. Based on the prediction of the secondary and tertiary structures of KK13, we aimed to reduce the size of the ribozyme, plausible on the primitive Earth, which can activate amino acids. Finally, several mutants were created, and the relationship between their structural and evolutionary features is discussed.