8P9R

Structure of the periplasmic domain of ExbD from E. coli in complex with TonB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.0 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.

(2023) Biorxiv 

  • DOI: https://doi.org/10.1101/2023.08.11.552980
  • 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 ExbDA,
C [auth B]
82Escherichia coliMutation(s): 0 
Gene Names: exbDb3005JW2973
UniProt
Find proteins for P0ABV2 (Escherichia coli (strain K12))
Explore P0ABV2 
Go to UniProtKB:  P0ABV2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABV2
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein TonBB [auth C]23Escherichia coliMutation(s): 0 
UniProt
Find proteins for P02929 (Escherichia coli (strain K12))
Explore P02929 
Go to UniProtKB:  P02929
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02929
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.36α = 90
b = 49.36β = 90
c = 63.94γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report



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