6GEF

X-ray structure of the Yersinia pseudotuberculosis ATPase DotB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.255 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

X-ray crystal structures of the type IVb secretion system DotB ATPases.

Prevost, M.S.Waksman, G.

(2018) Protein Sci. 27: 1464-1475

  • DOI: 10.1002/pro.3439
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human infections by the intracellular bacterial pathogen Legionella pneumophila result in a severe form of pneumonia, the Legionnaire's disease. L. pneumophila utilises a type IVb secretion (T4bS) system termed "dot/icm" to secrete protein effectors ...

    Human infections by the intracellular bacterial pathogen Legionella pneumophila result in a severe form of pneumonia, the Legionnaire's disease. L. pneumophila utilises a type IVb secretion (T4bS) system termed "dot/icm" to secrete protein effectors to the host cytoplasm. The dot/icm system is powered at least in part by a functionally critical AAA+ ATPase, a protein called DotB, thought to belong to the VirB11 family of proteins. Here we present the crystal structure of DotB at 3.19 Å resolution, in its hexameric form. We observe that DotB is in fact a structural intermediate between VirB11 and PilT family proteins, with a PAS-like N-terminal domain coupled to a RecA-like C-terminal domain. It also shares critical structural elements only found in PilT. The structure also reveals two conformers, termed α and β, with an αβαβαβ configuration. The existence of α and β conformers in this class of proteins was confirmed by solving the structure of DotB from another bacterial pathogen, Yersinia, where, intriguingly, we observed an ααβααβ configuration. The two conformers co-exist regardless of the nucleotide-bound states of the proteins. Our investigation therefore reveals that these ATPases can adopt a wider range of conformational states than was known before, shedding new light on the extraordinary spectrum of conformations these ATPases can access to carry out their function. Overall, the structure of DotB provides a template for further rational drug-design to develop more specific antibiotics to tackle Legionnaire's disease. This article is protected by copyright. All rights reserved.


    Organizational Affiliation

    Institute of Structural and Molecular Biology, University College London and Birkbeck, Malet Street, London WC1E 7HX, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Type IV secretion system protein DotB
A, B, C, D, E, F
402Yersinia pseudotuberculosis serotype O:1b (strain IP 31758)Mutation(s): 0 
Find proteins for A0A0U1QTI9 (Yersinia pseudotuberculosis serotype O:1b (strain IP 31758))
Go to UniProtKB:  A0A0U1QTI9
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.255 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 83.040α = 103.90
b = 93.560β = 101.98
c = 109.920γ = 99.94
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilUnited Kingdom321630

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-10-03
    Type: Data collection, Database references