A novel site of antibiotic action in the ribosome: Interaction of evernimicin with the large ribosomal subunit

Evernimicin (Evn), an oligosaccharide antibiotic, interacts with the large ribosomal subunit and inhibits bacterial protein synthesis. RNA probing dem onstrated that the drug protects a specific set of nucleotides in the loops of hairpins 89 and 91 of 23S rRNA in bacterial and archaeal ribosomes. Spo ntaneous Evn-resistant mutants of Halobacterium halobium contained mutation s in hairpins 89 and 91 of 23S rRNA, In the ribosome tertiary structure, rR NA residues involved in interaction with the drug form a tight cluster that delineates the drug-binding site. Resistance mutations in the bacterial ri bosomal protein L16, which is shown to be homologous to archaeal protein L1 0e, cluster to the same region as the rRNA mutations. The Evn-binding site overlaps with the binding site of initiation factor 2. Evn inhibits activit y of initiation factor 2 in vitro, suggesting that the drug interferes with formation of the 70S initiation complex. The site of Evn binding and its m ode of action are distinct from other ribosome-targeted antibiotics. This a ntibiotic target site can potentially be used for the development of new an tibacterial drugs.