Tetracenomycin inhibits bacterial translation via binding to a site of the peptide tunnel opposite to that of macrolides

Ribosome is one of the major targets for antibiotics in bacterial cell. Nascent peptide exit tunnel (NPET) serves as a binding site for several classes of antibiotics. Here we report a novel type of ribosome inhibitors, tetracenomycin X (TetrX). Unlike tetracycline, that possesses distant structural similarity, TetrX binds the NPET via stacking over non-canonical 2586U·1782U 23S rRNA basepair, at a place opposite to that of macrolide binding site. Binding of TetrX protects a number of crucial nucleotides of the ribosomal peptidyltransferase center from chemical modification and blocks biosynthesis of a protein after few aminoacids polymerized. On the basis of biochemical and structural results we conclude, that TetrX occludes peptide tunnel and prevent translation via interaction with a new binding site.