Structural Analysis of Kasugamycin Inhibition of Translation

Nat Struct Mol Biol. 2006 Oct;13(10):879-86. doi: 10.1038/nsmb1150. Epub 2006 Sep 24.


The prokaryotic ribosome is an important target of antibiotic action. We determined the X-ray structure of the aminoglycoside kasugamycin (Ksg) in complex with the Escherichia coli 70S ribosome at 3.5-A resolution. The structure reveals that the drug binds within the messenger RNA channel of the 30S subunit between the universally conserved G926 and A794 nucleotides in 16S ribosomal RNA, which are sites of Ksg resistance. To our surprise, Ksg resistance mutations do not inhibit binding of the drug to the ribosome. The present structural and biochemical results indicate that inhibition by Ksg and Ksg resistance are closely linked to the structure of the mRNA at the junction of the peptidyl-tRNA and exit-tRNA sites (P and E sites).

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Aminoglycosides / chemistry
  • Aminoglycosides / metabolism
  • Aminoglycosides / pharmacology*
  • Anti-Bacterial Agents / chemistry
  • Anti-Bacterial Agents / pharmacology*
  • Base Sequence
  • Binding Sites
  • Escherichia coli / chemistry*
  • Models, Molecular
  • Molecular Sequence Data
  • Mutation
  • Protein Biosynthesis*
  • Protein Structure, Tertiary
  • RNA, Bacterial / chemistry*
  • RNA, Messenger / chemistry*
  • Ribosomes / genetics
  • Ribosomes / metabolism
  • Structure-Activity Relationship
  • Templates, Genetic


  • Aminoglycosides
  • Anti-Bacterial Agents
  • RNA, Bacterial
  • RNA, Messenger
  • kasugamycin

Associated data

  • PDB/1VS5
  • PDB/1VS6
  • PDB/1VS7
  • PDB/1VS8