Open AccessStructural basis for the context-specific action of the classic peptidyl transferase inhibitor chloramphenicol
Author(s) -
Egor A. Syroegin,
Laurin Flemmich,
Dorota Klepacki,
Nora VázquezLaslop,
Ronald Micura,
Yury S. Polikanov
Publication year - 2022
Publication title -
nature structural and molecular biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.448
H-Index - 270
eISSN - 1545-9993
pISSN - 1545-9985
DOI - 10.1038/s41594-022-00720-y
Subject(s) - peptidyl transferase , ribosome , translation (biology) , a site , context (archaeology) , chemistry , ribosomal rna , biology , computational biology , biochemistry , binding site , rna , messenger rna , gene , paleontology
Ribosome-targeting antibiotics serve as powerful antimicrobials and as tools for studying the ribosome, the catalytic peptidyl transferase center (PTC) of which is targeted by many drugs. The classic PTC-acting antibiotic chloramphenicol (CHL) and the newest clinically significant linezolid (LZD) were considered indiscriminate inhibitors of protein synthesis that cause ribosome stalling at every codon of every gene being translated. However, recent discoveries have shown that CHL and LZD preferentially arrest translation when the ribosome needs to polymerize particular amino acid sequences. The molecular mechanisms that underlie the context-specific action of ribosome inhibitors are unknown. Here we present high-resolution structures of ribosomal complexes, with or without CHL, carrying specific nascent peptides that support or negate the drug action. Our data suggest that the penultimate residue of the nascent peptide directly modulates antibiotic affinity to the ribosome by either establishing specific interactions with the drug or by obstructing its proper placement in the binding site.