Negamycin interferes with decoding and translocation by simultaneous interaction with rRNA and tRNA

Mol Cell. 2014 Nov 20;56(4):541-50. doi: 10.1016/j.molcel.2014.09.021. Epub 2014 Oct 9.


Negamycin (NEG) is a ribosome-targeting antibiotic that exhibits clinically promising activity. Its binding site and mode of action have remained unknown. We solved the structure of the Thermus thermophilus ribosome bound to mRNA and three tRNAs, in complex with NEG. The drug binds to both small and large ribosomal subunits at nine independent sites. Resistance mutations in the 16S rRNA unequivocally identified the binding site in the vicinity of the conserved helix 34 (h34) in the small subunit as the primary site of antibiotic action in the bacterial and, possibly, eukaryotic ribosome. At this site, NEG contacts 16S rRNA as well as the anticodon loop of the A-site tRNA. Although the NEG site of action overlaps with that of tetracycline (TET), the two antibiotics exhibit different activities: while TET sterically hinders binding of aminoacyl-tRNA to the ribosome, NEG stabilizes its binding, thereby inhibiting translocation and stimulating miscoding.

Publication types

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

MeSH terms

  • Amino Acid Motifs
  • Amino Acids, Diamino / chemistry
  • Anti-Bacterial Agents / chemistry*
  • Base Sequence
  • Binding Sites
  • Crystallography, X-Ray
  • Models, Molecular
  • Protein Biosynthesis
  • Protein Synthesis Inhibitors / chemistry*
  • RNA Stability
  • RNA, Bacterial / chemistry*
  • RNA, Messenger / chemistry
  • RNA, Ribosomal / chemistry*
  • RNA, Transfer / chemistry*
  • Ribosome Subunits, Large, Bacterial / chemistry
  • Ribosome Subunits, Small, Bacterial / chemistry
  • Thermus thermophilus


  • Amino Acids, Diamino
  • Anti-Bacterial Agents
  • Protein Synthesis Inhibitors
  • RNA, Bacterial
  • RNA, Messenger
  • RNA, Ribosomal
  • RNA, Transfer
  • negamycin

Associated data

  • PDB/4RBH
  • PDB/4RBI,
  • PDB/4RBJ
  • PDB/4RBK