9D0J

Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with BT-33, mRNA, deacylated A-site tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.50A resolution

This is a non-PDB format compatible entry.

Summary for 9D0J

• Entry DOI: 10.2210/pdb9d0j/pdb
• Descriptor: 23S Ribosomal RNA, 50S ribosomal protein L14, 50S ribosomal protein L15, ... (61 entities in total)
• Functional Keywords: bt-33; cresomycin; lincosamides; structure-based drug design; antibiotic; 70s ribosome; x-ray structure; inhibition of translation; peptidyl transferase center; nascent peptide exit tunnel, ribosome
• Biological source: Escherichia coli; More
• Total number of polymer chains: 112
• Total formula weight: 4566036.66

Authors

Aleksandrova, E.V.,Tresco, B.I.C.,Wu, K.J.Y.,Ramkissoon, A.,Purdy, M.,See, D.N.Y.,Liu, R.Y.,Myers, A.G.,Polikanov, Y.S. (deposition date: 2024-08-07, release date: 2024-11-20, Last modification date: 2025-04-09)

Primary citation

Tresco, B.I.C.,Wu, K.J.Y.,Ramkissoon, A.,Aleksandrova, E.V.,Purdy, M.,See, D.N.Y.,Liu, R.Y.,Polikanov, Y.S.,Myers, A.G.
Discovery of a fluorinated macrobicyclic antibiotic through chemical synthesis.
Nat.Chem., 17:582-589, 2025

PubMed Abstract: The emergence of bacterial antimicrobial resistance threatens to undermine the utility of antibiotic therapy in medicine. This threat can be addressed, in part, by reinventing existing antibiotic classes using chemical synthesis. Here we present the discovery of BT-33, a fluorinated macrobicyclic oxepanoprolinamide antibiotic with broad-spectrum activity against multidrug-resistant bacterial pathogens. Structure-activity relationships within the macrobicyclic substructure reveal structural features that are essential to the enhanced potency of BT-33 as well as its increased metabolic stability relative to its predecessors clindamycin, iboxamycin and cresomycin. Using X-ray crystallography, we determine the structure of BT-33 in complex with the bacterial ribosome revealing that its fluorine atom makes an additional van der Waals contact with nucleobase G2505. Through variable-temperature H NMR experiments, density functional theory calculations and vibrational circular dichroism spectroscopy, we compare macrobicyclic homologues of BT-33 and a C7 desmethyl analogue and find that the C7 methyl group of BT-33 rigidifies the macrocyclic ring in a conformation that is highly preorganized for ribosomal binding.

PubMed: 40055575
DOI: 10.1038/s41557-025-01738-7

Experimental method

X-RAY DIFFRACTION (2.5 Å)