8PEK

Structure of the dimeric, periplasmic domain of ExbD


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report

Currently 8PEK does not have a validation slider image.


This is version 1.1 of the entry. See complete history


Literature

Ton motor conformational switch and peptidoglycan role in bacterial nutrient uptake.

Zinke, M.Lejeune, M.Mechaly, A.Bardiaux, B.Boneca, I.G.Delepelaire, P.Izadi-Pruneyre, N.

(2024) Nat Commun 15: 331-331

  • DOI: https://doi.org/10.1038/s41467-023-44606-z
  • Primary Citation of Related Structures:  
    8P9R, 8PEK

  • PubMed Abstract: 

    Active nutrient uptake is fundamental for survival and pathogenicity of Gram-negative bacteria, which operate a multi-protein Ton system to transport essential nutrients like metals and vitamins. This system harnesses the proton motive force at the inner membrane to energize the import through the outer membrane, but the mechanism of energy transfer remains enigmatic. Here, we study the periplasmic domain of ExbD, a crucial component of the proton channel of the Ton system. We show that this domain is a dynamic dimer switching between two conformations representing the proton channel's open and closed states. By in vivo phenotypic assays we demonstrate that this conformational switch is essential for the nutrient uptake by bacteria. The open state of ExbD triggers a disorder to order transition of TonB, enabling TonB to supply energy to the nutrient transporter. We also reveal the anchoring role of the peptidoglycan layer in this mechanism. Herein, we propose a mechanistic model for the Ton system, emphasizing ExbD duality and the pivotal catalytic role of peptidoglycan. Sequence analysis suggests that this mechanism is conserved in other systems energizing gliding motility and membrane integrity. Our study fills important gaps in understanding bacterial motor mechanism and proposes novel antibacterial strategies.


  • Organizational Affiliation

    Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015, Paris, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Biopolymer transport protein ExbD
A, B
99Serratia marcescensMutation(s): 0 
Gene Names: 
UniProt
Find proteins for V5YUQ0 (Serratia marcescens)
Explore V5YUQ0 
Go to UniProtKB:  V5YUQ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV5YUQ0
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report

Currently 8PEK does not have a validation slider image.



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-21-CE11-0039
Agence Nationale de la Recherche (ANR)FranceANR-16-CONV-0005

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-06
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Database references