Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Other government, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Simons Foundation, Other private, National Science Foundation (NSF, United States)
The antibiotic linezolid, the first clinically approved member of the oxazolidinone class, inhibits translation of bacterial ribosomes by binding to the peptidyl transferase center. Recent work has demonstrated that linezolid does not inhibit peptide bond formation at all sequences but rather acts in a context-specific manner, namely when alanine occupies the penultimate position of the nascent chain ...
The antibiotic linezolid, the first clinically approved member of the oxazolidinone class, inhibits translation of bacterial ribosomes by binding to the peptidyl transferase center. Recent work has demonstrated that linezolid does not inhibit peptide bond formation at all sequences but rather acts in a context-specific manner, namely when alanine occupies the penultimate position of the nascent chain. However, the molecular basis for context-specificity has not been elucidated. Here we show that the second-generation oxazolidinone radezolid also induces stalling with a penultimate alanine, and we determine high-resolution cryo-EM structures of linezolid- and radezolid-stalled ribosome complexes to explain their mechanism of action. These structures reveal that the alanine side chain fits within a small hydrophobic crevice created by oxazolidinone, resulting in improved ribosome binding. Modification of the ribosome by the antibiotic resistance enzyme Cfr disrupts stalling due to repositioning of the modified nucleotide. Together, our findings provide molecular understanding for the context-specificity of oxazolidinones.
ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Croll, T.I. (2018) Acta Crystallogr D Struct Biol 74: 519
Features and development of Coot. Emsley, P., Lohkamp, B., Scott, W.G., Cowtan, K. (2010) Acta Crystallogr D Biol Crystallogr 66: 486
UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Pettersen, E.F., Goddard, T.D., Huang, C.C., Meng, E.C., Couch, G.S., Croll, T.I., Morris, J.H., Ferrin, T.E. (2021) Protein Sci 30: 70
Organizational Affiliation:
Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA. Danica.Fujimori@ucsf.edu.
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