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

J Biol Chem. 2008 Nov 21;283(47):32229-35. doi: 10.1074/jbc.M805316200. Epub 2008 Sep 22.

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-tRNA(Phe) was used as A-site substrate, the rate of peptide bond formation with any peptidyl-tRNA was approximately 7 s(-1), which corresponds to the rate of binding of Phe-tRNA(Phe) 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acids / chemistry
  • Catalysis
  • Codon
  • Escherichia coli / metabolism
  • Hydrogen-Ion Concentration
  • Kinetics
  • Nucleic Acid Conformation
  • Peptides / chemistry
  • Proline / chemistry
  • Protein Structure, Tertiary
  • RNA, Catalytic / chemistry
  • RNA, Transfer / chemistry*
  • Ribosomes / chemistry
  • Substrate Specificity
  • Thermodynamics

Substances

  • Amino Acids
  • Codon
  • Peptides
  • RNA, Catalytic
  • RNA, Transfer
  • Proline