Elongation Cycle Step Ii Transpeptidation Peptide Bond Formation

11.1. Chemistry of the Reaction

After the peptidyl-tRNA has occupied the P site and the aminoacyl-tRNA has been fully bound at the A site, the 3'-ends of the two tRNA residues are found close to each other in the region of the peptidyl transferase center (PTC) of the large ribosomal subunit. This is followed by a nucleophilic attack on the carbonyl group of the ester bond between the peptide residue and the tRNA moiety of the peptidyl-tRNA molecule by the amino group of the aminoacyl-tRNA molecule. As a result, an amide (peptide) bond is formed between the peptide residue and the aminoacyl-tRNA molecule (Fig. 11.1). The peptidyl-tRNA and the aminoacyl-tRNA are the substrates of this reaction. The peptidyl-tRNA is a donor substrate, and the aminoacyl-tRNA plays the part of an acceptor substrate. The products of the reaction are the deacylated tRNA in the P site and the peptidyl-tRNA with the peptide moiety elongated by one aminoacyl residue attached to the tRNA in the A site, as is shown schematically in Fig. 11.2.

It has already been mentioned (Section 9.3) that the 3'-terminal fragments of the aminoacyl-tRNA, the aminoacyl esters of the adenosine, as well as puromycin, can play the part of acceptor (or nucleophilic) substrate in the reaction with the peptidyl-tRNA, instead of the normal aminoacyl-tRNA molecule.

The reaction proceeds only with the NH2-group in the a-position of an aminoacyl residue. The amino acid residue should be of L-configuration. The aminoacyl residue accommodated in a site of PTC must be attached to the 3'-position (not to the 2'-position) of the terminal adenosine of tRNA to serve as an tRNA'cc

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