Dissecting the ribosomal inhibition mechanisms of edeine and pactamycin: the universally conserved residues G693 and C795 regulate P-site RNA binding

Mol Cell. 2004 Jan 16;13(1):113-24. doi: 10.1016/s1097-2765(04)00002-4.

Abstract

The crystal structures of the universal translation-initiation inhibitors edeine and pactamycin bound to ribosomal 30S subunit have revealed that edeine induces base pairing of G693:C795, residues that constitute the pactamycin binding site. Here, we show that base pair formation by addition of edeine inhibits tRNA binding to the P site by preventing codon-anticodon interaction and that addition of pactamycin, which rebreaks the base pair, can relieve this inhibition. In addition, edeine induces translational misreading in the A site, at levels comparable to those induced by the classic misreading antibiotic streptomycin. Binding of pactamycin between residues G693 and C795 strongly inhibits translocation with a surprising tRNA specificity but has no effect on translation initiation, suggesting that reclassification of this antibiotic is necessary. Collectively, these results suggest that the universally conserved G693:C795 residues regulate tRNA binding at the P site of the ribosome and influence translocation efficiency.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anticodon / metabolism
  • Base Pairing
  • Binding Sites
  • Codon / metabolism
  • Cytosine / metabolism*
  • Edeine / pharmacology*
  • Escherichia coli
  • Green Fluorescent Proteins
  • Guanine / metabolism*
  • Luminescent Proteins / metabolism
  • Models, Biological
  • Models, Molecular
  • Nucleic Acid Synthesis Inhibitors / pharmacology
  • Pactamycin / pharmacology*
  • Protein Biosynthesis
  • Protein Synthesis Inhibitors / pharmacology
  • RNA / metabolism*
  • RNA, Ribosomal / metabolism
  • RNA, Transfer / metabolism
  • Ribosomal Proteins / metabolism
  • Ribosomes / drug effects
  • Ribosomes / metabolism*

Substances

  • Anticodon
  • Codon
  • Luminescent Proteins
  • Nucleic Acid Synthesis Inhibitors
  • Protein Synthesis Inhibitors
  • RNA, Ribosomal
  • Ribosomal Proteins
  • Edeine
  • Green Fluorescent Proteins
  • Pactamycin
  • Guanine
  • RNA
  • Cytosine
  • RNA, Transfer