Resistance mutations in 23 S rRNA identify the site of action of the protein synthesis inhibitor linezolid in the ribosomal peptidyl transferase center

J Mol Biol. 1999 Nov 19;294(1):93-101. doi: 10.1006/jmbi.1999.3247.


Oxazolidinones represent a novel class of antibiotics that inhibit protein synthesis in sensitive bacteria. The mechanism of action and location of the binding site of these drugs is not clear. A new representative of oxazolidinone antibiotics, linezolid, was found to be active against bacteria and against the halophilic archaeon Halobacterium halobium. The use of H. halobium, which possess only one chromosomal copy of rRNA operon, allowed isolation of a number of linezolid-resistance mutations in rRNA. Four types of linezolid-resistant mutants were isolated by direct plating of H. halobium cells on agar medium containing antibiotic. In addition, three more linezolid-resistant mutants were identified among the previously isolated mutants of H. halobium containing mutations in either 16 S or 23 S rRNA genes. All the isolated mutants were found to contain single-point mutations in 23 S rRNA. Seven mutations affecting six different positions in the central loop of domain V of 23 S rRNA were found to confer resistance to linezolid. Domain V of 23 S rRNA is known to be a component of the ribosomal peptidyl transferase center. Clustering of linezolid-resistance mutations within this region strongly suggests that the binding site of the drug is located in the immediate vicinity of the peptidyl transferase center. However, the antibiotic failed to inhibit peptidyl transferase activity of the H. halobium ribosome, supporting the previous conclusion that linezolid inhibits translation at a step different from the catalysis of the peptide bond formation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetamides / pharmacology*
  • Binding Sites
  • Drug Resistance, Microbial / genetics
  • Halobacterium salinarum / genetics
  • Linezolid
  • Mutation
  • Nucleic Acid Conformation
  • Oxazoles / pharmacology*
  • Oxazolidinones*
  • Peptide Chain Initiation, Translational / drug effects*
  • Peptidyl Transferases / metabolism
  • Protein Synthesis Inhibitors / pharmacology*
  • RNA, Ribosomal, 23S / genetics*
  • RNA, Transfer, Met / metabolism
  • Ribosomes / drug effects


  • Acetamides
  • Oxazoles
  • Oxazolidinones
  • Protein Synthesis Inhibitors
  • RNA, Ribosomal, 23S
  • RNA, Transfer, Met
  • fMet-tRNA(fMet)
  • Peptidyl Transferases
  • Linezolid