Structural origins of aminoglycoside specificity for prokaryotic ribosomes

J Mol Biol. 2001 Mar 9;306(5):1037-58. doi: 10.1006/jmbi.2000.4420.


Aminoglycoside antibiotics, including paromomycin, neomycin and gentamicin, target a region of highly conserved nucleotides in the decoding region aminoacyl-tRNA site (A site) of 16 S rRNA on the 30 S subunit. Change of a single nucleotide, A1408 to G, reduces the affinity of many aminoglycosides for the ribosome; G1408 distinguishes between prokaryotic and eukaryotic ribosomes. The structures of a prokaryotic decoding region A-site oligonucleotide free in solution and bound to the aminoglycosides paromomycin and gentamicin C1a were determined previously. Here, the structure of a eukaryotic decoding region A-site oligonucleotide bound to paromomycin has been determined using NMR spectroscopy and compared to the prokaryotic A-site-paromomycin structure. A conformational change in three adenosine residues of an internal loop, critical for high-affinity antibiotic binding, was observed in the prokaryotic RNA-paromomycin complex in comparison to its free form. This conformational change is not observed in the eukaryotic RNA-paromomycin complex, disrupting the binding pocket for ring I of the antibiotic. The lack of the conformational change supports footprinting and titration calorimetry data that demonstrate approximately 25-50-fold weaker binding of paromomycin to the eukaryotic decoding-site oligonucleotide. Neomycin, which is much less active against Escherichia coli ribosomes with an A1408G mutation, binds non-specifically to the oligonucleotide. These results suggest that eukaryotic ribosomal RNA has a shallow binding pocket for aminoglycosides, which accommodates only certain antibiotics.

Publication types

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

MeSH terms

  • Adenosine / chemistry
  • Anti-Bacterial Agents / chemistry*
  • Anti-Bacterial Agents / metabolism
  • Drug Resistance, Microbial / genetics
  • Guanosine / chemistry
  • Magnetic Resonance Spectroscopy / methods
  • Molecular Structure
  • Neomycin / metabolism
  • Paromomycin / metabolism*
  • RNA, Bacterial / chemistry*
  • RNA, Ribosomal, 16S / chemistry*
  • RNA, Ribosomal, 16S / metabolism
  • RNA, Transfer, Amino Acyl / chemistry*
  • RNA, Transfer, Amino Acyl / metabolism
  • Species Specificity
  • Structure-Activity Relationship
  • Substrate Specificity


  • Anti-Bacterial Agents
  • RNA, Bacterial
  • RNA, Ribosomal, 16S
  • RNA, Transfer, Amino Acyl
  • Guanosine
  • Paromomycin
  • Neomycin
  • Adenosine

Associated data

  • PDB/1FYP