EMD-18341

Single-particle
2.3 Å
EMD-18341 Deposition: 30/08/2023
Map released: 20/03/2024
Last modified: 03/04/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-18341

ApdA-SRC with P-tRNA only

EMD-18341

Single-particle
2.3 Å
EMD-18341 Deposition: 30/08/2023
Map released: 20/03/2024
Last modified: 03/04/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Amycolatopsis japonica
Sample: B. subtilis ApdA-stalled ribosomal complex

Deposition Authors: Morici M , Wilson DN
RAPP-containing arrest peptides induce translational stalling by short circuiting the ribosomal peptidyltransferase activity.
Morici M , Gabrielli S , Fujiwara K , Paternoga H , Beckert B , Bock LV , Chiba S , Wilson DN
(2024) Nat Commun , 15 , 2432 - 2432
PUBMED: 38503735
DOI: doi:10.1038/s41467-024-46761-3
ISSN: 2041-1723
Abstract:
Arrest peptides containing RAPP (ArgAlaProPro) motifs have been discovered in both Gram-positive and Gram-negative bacteria, where they are thought to regulate expression of important protein localization machinery components. Here we determine cryo-EM structures of ribosomes stalled on RAPP arrest motifs in both Bacillus subtilis and Escherichia coli. Together with molecular dynamics simulations, our structures reveal that the RAPP motifs allow full accommodation of the A-site tRNA, but prevent the subsequent peptide bond from forming. Our data support a model where the RAP in the P-site interacts and stabilizes a single hydrogen atom on the Pro-tRNA in the A-site, thereby preventing an optimal geometry for the nucleophilic attack required for peptide bond formation to occur. This mechanism to short circuit the ribosomal peptidyltransferase activity is likely to operate for the majority of other RAPP-like arrest peptides found across diverse bacterial phylogenies.