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TitleThe translation inhibitors kasugamycin, edeine and GE81112 target distinct steps during 30S initiation complex formation.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 2470, Year 2025
Publish dateMar 12, 2025
AuthorsHaaris A Safdari / Martino Morici / Ana Sanchez-Castro / Andrea Dallapè / Helge Paternoga / Anna Maria Giuliodori / Attilio Fabbretti / Pohl Milón / Daniel N Wilson /
PubMed AbstractDuring bacterial translation initiation, the 30S ribosomal subunit, initiation factors, and initiator tRNA define the reading frame of the mRNA. This process is inhibited by kasugamycin, edeine and ...During bacterial translation initiation, the 30S ribosomal subunit, initiation factors, and initiator tRNA define the reading frame of the mRNA. This process is inhibited by kasugamycin, edeine and GE81112, however, their mechanisms of action have not been fully elucidated. Here we present cryo-electron microscopy structures of 30S initiation intermediate complexes formed in the presence of kasugamycin, edeine and GE81112 at resolutions of 2.0-2.9 Å. The structures reveal that all three antibiotics bind within the E-site of the 30S and preclude 30S initiation complex formation. While kasugamycin and edeine affect early steps of 30S pre-initiation complex formation, GE81112 stalls pre-initiation complex formation at a further step by allowing start codon recognition, but impeding IF3 departure. Collectively, our work highlights how chemically distinct compounds binding at a conserved site on the 30S can interfere with translation initiation in a unique manner.
External linksNat Commun / PubMed:40075065 / PubMed Central
MethodsEM (single particle)
Resolution2.0 - 2.9 Å
Structure data

50320

9fco

EMDB-50320, PDB-9fco:
Structure of E. coli 30S-IF1-IF3-mRNA-Kasugamycin complex
Method: EM (single particle) / Resolution: 2.4 Å

50327

9fda

EMDB-50327, PDB-9fda:
Structure of E. coli 30S-IF1-IF3-mRNA-Edeine complex
Method: EM (single particle) / Resolution: 2.0 Å

50476

9fib

EMDB-50476, PDB-9fib:
Structure of 30S-IF1-IF3-mRNA-GE81112A complex
Method: EM (single particle) / Resolution: 2.3 Å

50912

9g06

EMDB-50912, PDB-9g06:
Structure of 30S-IF1-IF3-mRNA-fMet-tRNA-GE81112A complex
Method: EM (single particle) / Resolution: 2.85 Å

EMDB-51214: Structure of Kasugamycin-30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex, open form
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-51217: Structure of Edeine-30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex, open form
Method: EM (single particle) / Resolution: 2.8 Å

Chemicals

ChemComp-KSG:
(1S,2R,3S,4R,5S,6S)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXYL / antibiotic*YM

ChemComp-MG:
Unknown entry

ChemComp-K:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-EDE:
EDEINE B

PDB-1ic4:
CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD32A)-HEN LYSOZYME COMPLEX

Source
  • escherichia coli (E. coli)
KeywordsTRANSLATION / Ribosome / Antibiotic / Ribosomes / 30S subunit / 30S inhibitors / Antibiotics / 30S initiation / Translational inhibitor

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