Modulation of the rate of peptidyl transfer on the ribosome by the nature of substrates

Abstract

The ribosome catalyzes peptide bond formation between peptidyl-tRNA in the P site and aminoacyl-tRNA in the A site. Here, we show that the nature of the C-terminal amino acid residue in the P-site peptidyl-tRNA strongly affects the rate of peptidyl transfer. Depending on the C-terminal amino acid of the peptidyl-tRNA, the rate of reaction with the small A-site substrate puromycin varied between 100 and 0.14 s-1, regardless of the tRNA identity. The reactivity decreased in the order Lys = Arg > Ala > Ser > Phe = Val > Asp ≫ Pro, with Pro being by far the slowest. However, when Phe-tRNAPhe was used as A-site substrate, the rate of peptide bond formation with any peptidyl-tRNA was ∼7 s-1, which corresponds to the rate of binding of Phe-tRNAPhe to the A site (accommodation). Because accommodation is rate-limiting for peptide bond formation, the reaction rate is uniform for all peptidyl-tRNAs, regardless of the variations of the intrinsic chemical reactivities. On the other hand, the 50-fold increase in the reaction rate for peptidyl-tRNA ending with Pro suggests that full-length aminoacyl-tRNA in the A site greatly accelerates peptide bond formation. © 2008 by The American Society for Biochemistry and Molecular Biology, Inc.