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Structure paper

TitleInsights into the molecular mechanism of translation inhibition by the ribosome-targeting antibiotic thermorubin.
Journal, issue, pagesNucleic Acids Res, Vol. 51, Issue 1, Page 449-462, Year 2023
Publish dateJan 11, 2023
AuthorsMadhura N Paranjpe / Valeria I Marina / Aleksandr A Grachev / Tinashe P Maviza / Olga A Tolicheva / Alena Paleskava / Ilya A Osterman / Petr V Sergiev / Andrey L Konevega / Yury S Polikanov / Matthieu G Gagnon /
PubMed AbstractThermorubin (THR) is an aromatic anthracenopyranone antibiotic active against both Gram-positive and Gram-negative bacteria. It is known to bind to the 70S ribosome at the intersubunit bridge B2a and ...Thermorubin (THR) is an aromatic anthracenopyranone antibiotic active against both Gram-positive and Gram-negative bacteria. It is known to bind to the 70S ribosome at the intersubunit bridge B2a and was thought to inhibit factor-dependent initiation of translation and obstruct the accommodation of tRNAs into the A site. Here, we show that thermorubin causes ribosomes to stall in vivo and in vitro at internal and termination codons, thereby allowing the ribosome to initiate protein synthesis and translate at least a few codons before stalling. Our biochemical data show that THR affects multiple steps of translation elongation with a significant impact on the binding stability of the tRNA in the A site, explaining premature cessation of translation. Our high-resolution crystal and cryo-EM structures of the 70S-THR complex show that THR can co-exist with P- and A-site tRNAs, explaining how ribosomes can elongate in the presence of the drug. Remarkable is the ability of THR to arrest ribosomes at the stop codons. Our data suggest that by causing structural re-arrangements in the decoding center, THR interferes with the accommodation of tRNAs or release factors into the ribosomal A site.
External linksNucleic Acids Res / PubMed:36546783 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.7 Å
Structure data

28197

8ekc

EMDB-28197, PDB-8ekc:
Escherichia coli 70S ribosome bound to thermorubin, deacylated P-site tRNAfMet and aminoacylated A-site Phe-tRNA
Method: EM (single particle) / Resolution: 2.7 Å

PDB-8ekb:
Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, deacylated P-site tRNAmet, and thermorubin at 2.70A resolution
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-K:
Unknown entry

ChemComp-T8B:
Thermorubin

ChemComp-ZN:
Unknown entry

ChemComp-SF4:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

ChemComp-HOH:
WATER / Water

ChemComp-PHE:
PHENYLALANINE / Phenylalanine

Source
  • escherichia coli (E. coli)
  • escherichia phage t4 (virus)
  • thermus thermophilus hb8 (bacteria)
KeywordsRIBOSOME / antibiotic / thermorubin / tRNA / release factor / rapid kinetics / thermodynamics / cryo-EM

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