8EZT | pdb_00008ezt

Crystal structure of HipB(Lp) from Legionella pneumophila


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 
    0.343 (Depositor), 0.350 (DCC) 
  • R-Value Work: 
    0.297 (Depositor), 0.300 (DCC) 
  • R-Value Observed: 
    0.300 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Functional diversification despite structural congruence in the HipBST toxin-antitoxin system of Legionella pneumophila.

Lin, J.D.Stogios, P.J.Abe, K.T.Wang, A.MacPherson, J.Skarina, T.Gingras, A.-.C.Savchenko, A.Ensminger, A.W.

(2023) mBio 14: e0151023-e0151023

  • DOI: https://doi.org/10.1128/mbio.01510-23
  • Primary Citation of Related Structures:  
    8EZR, 8EZS, 8EZT

  • PubMed Abstract: 

    Toxin-antitoxin (TA) systems are parasitic genetic elements found in almost all bacterial genomes. They are exchanged horizontally between cells and are typically poorly conserved across closely related strains and species. Here, we report the characterization of a tripartite TA system in the bacterial pathogen Legionella pneumophila that is highly conserved across Legionella species genomes. This system (denoted HipBST Lp ) is a distant homolog of the recently discovered split-HipA system in Escherichia coli (HipBST Ec ). We present bioinformatic, molecular, and structural analyses of the divergence between these two systems and the functionality of this newly described TA system family. Furthermore, we provide evidence to refute previous claims that the toxin in this system (HipT Lp ) possesses bifunctionality as an L. pneumophila virulence protein. Overall, this work expands our understanding of the split-HipA system architecture and illustrates the potential for undiscovered biology in these abundant genetic elements.


  • Organizational Affiliation
    • Department of Molecular Genetics, University of Toronto , Toronto, Ontario, Canada.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HipB(Lp)
A, B, C, D
76Legionella pneumophilaMutation(s): 0 
Gene Names: lpg2368
UniProt
Find proteins for Q5ZSZ8 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZSZ8 
Go to UniProtKB:  Q5ZSZ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZSZ8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free:  0.343 (Depositor), 0.350 (DCC) 
  • R-Value Work:  0.297 (Depositor), 0.300 (DCC) 
  • R-Value Observed: 0.300 (Depositor) 
Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.444α = 90
b = 33.488β = 102.73
c = 74.161γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700060C

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-27
    Type: Initial release
  • Version 1.1: 2026-02-25
    Changes: Database references, Structure summary