Structural insights into AapA1 toxin

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 1000 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Structural insights into the AapA1 toxin of Helicobacter pylori.

Korkut, D.N.Alves, I.D.Vogel, A.Chabas, S.Sharma, C.M.Martinez, D.Loquet, A.Salgado, G.F.Darfeuille, F.

(2020) Biochim Biophys Acta Gen Subj 1864: 129423-129423

  • DOI: https://doi.org/10.1016/j.bbagen.2019.129423
  • Primary Citation of Related Structures:  
    6GIF, 6GIG

  • PubMed Abstract: 

    We previously reported the identification of the aapA1/IsoA1 locus as part of a new family of toxin-antitoxin (TA) systems in the human pathogen Helicobacter pylori. AapA1 belongs to type I TA bacterial toxins, and both its mechanism of action towards the membrane and toxicity features are still unclear. The biochemical characterization of the AapA1 toxic peptide was carried out using plasmid-borne expression and mutational approaches to follow its toxicity and localization. Biophysical properties of the AapA1 interaction with lipid membranes were studied by solution and solid-state NMR spectroscopy, plasmon waveguide resonance (PWR) and molecular modeling. We show that despite a low hydrophobic index, this toxin has a nanomolar affinity to the prokaryotic membrane. NMR spectroscopy reveals that the AapA1 toxin is structurally organized into three distinct domains: a positively charged disordered N-terminal domain (D), a single α-helix (H), and a basic C-terminal domain (R). The R domain interacts and destabilizes the membrane, while the H domain adopts a transmembrane conformation. These results were confirmed by alanine scanning of the minimal sequence required for toxicity. Our results have shown that specific amino acid residues along the H domain, as well as the R domain, are essential for the toxicity of the AapA1 toxin. Untangling and understanding the mechanism of action of small membrane-targeting toxins are difficult, but nevertheless contributes to a promising search and development of new antimicrobial drugs.

  • Organizational Affiliation

    INSERM, U1212, CNRS UMR 5320, Univ. Bordeaux, Laboratoire ARNA, F-33076 Bordeaux, France; Univ. Bordeaux, IECB, Laboratoire ARNA, F-33600 Pessac, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AapA130Helicobacter pyloriMutation(s): 0 
Membrane Entity: Yes 
Find proteins for P0DUM4 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P0DUM4 
Go to UniProtKB:  P0DUM4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DUM4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 1000 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-12-BSV5-0025

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Database references
  • Version 1.2: 2023-06-14
    Changes: Database references, Other