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TitleInsights into the improved macrolide inhibitory activity from the high-resolution cryo-EM structure of dirithromycin bound to the 70S ribosome.
Journal, issue, pagesRNA, Vol. 26, Issue 6, Page 715-723, Year 2020
Publish dateMar 6, 2020
AuthorsEvgeny B Pichkur / Alena Paleskava / Andrey G Tereshchenkov / Pavel Kasatsky / Ekaterina S Komarova / Dmitrii I Shiriaev / Alexey A Bogdanov / Olga A Dontsova / Ilya A Osterman / Petr V Sergiev / Yury S Polikanov / Alexander G Myasnikov / Andrey L Konevega /
PubMed AbstractMacrolides are one of the most successful and widely used classes of antibacterials, which kill or stop the growth of pathogenic bacteria by binding near the active site of the ribosome and ...Macrolides are one of the most successful and widely used classes of antibacterials, which kill or stop the growth of pathogenic bacteria by binding near the active site of the ribosome and interfering with protein synthesis. Dirithromycin is a derivative of the prototype macrolide erythromycin with additional hydrophobic side chain. In our recent study, we have discovered that the side chain of dirithromycin forms lone pair-π stacking interaction with the aromatic imidazole ring of the His69 residue in ribosomal protein uL4 of the 70S ribosome. In the current work, we found that neither the presence of the side chain, nor the additional contact with the ribosome, improve the binding affinity of dirithromycin to the ribosome. Nevertheless, we found that dirithromycin is a more potent inhibitor of in vitro protein synthesis in comparison with its parent compound, erythromycin. Using high-resolution cryo-electron microscopy, we determined the structure of the dirithromycin bound to the translating 70S ribosome, which suggests that the better inhibitory properties of the drug could be rationalized by the side chain of dirithromycin pointing into the lumen of the nascent peptide exit tunnel, where it can interfere with the normal passage of the growing polypeptide chain.
External linksRNA / PubMed:32144191 / PubMed Central
MethodsEM (single particle)
Resolution2.1 - 2.66 Å
Structure data

10655

6xz7

EMDB-10655, PDB-6xz7:
E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet).
Method: EM (single particle) / Resolution: 2.1 Å

10656

6xza

EMDB-10656, PDB-6xza:
E. coli 70S ribosome in complex with dirithromycin, and deacylated tRNA(iMet) (focused classification).
Method: EM (single particle) / Resolution: 2.66 Å

10657

6xzb

EMDB-10657, PDB-6xzb:
E. coli 70S ribosome in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet) (focused classification).
Method: EM (single particle) / Resolution: 2.54 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-DI0:
Dirithromycin / antibiotic*YM / Dirithromycin

ChemComp-HOH:
WATER / Water

Source
  • escherichia coli (strain k12) (bacteria)
  • saccharomyces cerevisiae (brewer's yeast)
  • baker's yeast (brewer's yeast)
  • escherichia coli k-12 (bacteria)
KeywordsRIBOSOME / 50S ribosomal subunit / dirithromycin / antibiotics / cryo-EM / 70S ribosome

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