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TitleRAPP-containing arrest peptides induce translational stalling by short circuiting the ribosomal peptidyltransferase activity.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 2432, Year 2024
Publish dateMar 19, 2024
AuthorsMartino Morici / Sara Gabrielli / Keigo Fujiwara / Helge Paternoga / Bertrand Beckert / Lars V Bock / Shinobu Chiba / Daniel N Wilson /
PubMed AbstractArrest 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 ...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.
External linksNat Commun / PubMed:38503735 / PubMed Central
MethodsEM (single particle)
Resolution2.2 - 2.9 Å
Structure data

18320

8qbt

EMDB-18320, PDB-8qbt:
E. coli ApdP-stalled ribosomal complex
Method: EM (single particle) / Resolution: 2.2 Å

18332

8qcq

EMDB-18332, PDB-8qcq:
B. subtilis ApdA-stalled ribosomal complex
Method: EM (single particle) / Resolution: 2.3 Å

EMDB-18340: ApdP-SRC with P-tRNA only
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-18341: ApdA-SRC with P-tRNA only
Method: EM (single particle) / Resolution: 2.3 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-K:
Unknown entry

ChemComp-PRO:
PROLINE / Proline

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER / Water

Source
  • sinorhizobium medicae (bacteria)
  • escherichia coli bw25113 (bacteria)
  • amycolatopsis japonica (bacteria)
  • bacillus subtilis subsp. subtilis str. 168 (bacteria)
KeywordsRIBOSOME / Stalling / nascent chain / translation arrest / regulation / elongation arrest

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