8RPY

Escherichia coli 50S subunit in complex with the antimicrobial peptide Api137

Summary for 8RPY

• Entry DOI: 10.2210/pdb8rpy/pdb
• EMDB information: 19426
• Descriptor: Large ribosomal subunit protein bL32, Large ribosomal subunit protein uL3, Large ribosomal subunit protein uL4, ... (32 entities in total)
• Functional Keywords: ribosome, antimicrobial peptide, rna, ribosomal protein, pramp, proline-rich peptide, antibiotics, 50s, api137
• Biological source: Escherichia coli; More
• Total number of polymer chains: 33
• Total formula weight: 1349111.71

Authors

Lauer, S.,Nikolay, R.,Spahn, C. (deposition date: 2024-01-17, release date: 2024-05-22, Last modification date: 2024-11-13)

Primary citation

Lauer, S.M.,Reepmeyer, M.,Berendes, O.,Klepacki, D.,Gasse, J.,Gabrielli, S.,Grubmuller, H.,Bock, L.V.,Krizsan, A.,Nikolay, R.,Spahn, C.M.T.,Hoffmann, R.
Multimodal binding and inhibition of bacterial ribosomes by the antimicrobial peptides Api137 and Api88.
Nat Commun, 15:3945-3945, 2024

PubMed Abstract: Proline-rich antimicrobial peptides (PrAMPs) inhibit bacterial protein biosynthesis by binding to the polypeptide exit tunnel (PET) near the peptidyl transferase center. Api137, an optimized derivative of honeybee PrAMP apidaecin, inhibits protein expression by trapping release factors (RFs), which interact with stop codons on ribosomes to terminate translation. This study uses cryo-EM, functional assays and molecular dynamic (MD) simulations to show that Api137 additionally occupies a second binding site near the exit of the PET and can repress translation independently of RF-trapping. Api88, a C-terminally amidated (-CONH) analog of Api137 (-COOH), binds to the same sites, occupies a third binding pocket and interferes with the translation process presumably without RF-trapping. In conclusion, apidaecin-derived PrAMPs inhibit bacterial ribosomes by multimodal mechanisms caused by minor structural changes and thus represent a promising pool for drug development efforts.

PubMed: 38730238
DOI: 10.1038/s41467-024-48027-4

Experimental method

ELECTRON MICROSCOPY (2.64 Å)