9GTX | pdb_00009gtx

Structural and functional analysis of the Helicobacter pylori lipoprotein chaperone LolA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 
    0.251 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and functional analysis of the Helicobacter pylori lipoprotein chaperone LolA.

Jaiman, D.Persson, K.

(2024) Front Microbiol 15: 1512451-1512451

  • DOI: https://doi.org/10.3389/fmicb.2024.1512451
  • Primary Citation of Related Structures:  
    9GTX

  • PubMed Abstract: 

    Lipoproteins are crucial for maintaining the structural integrity of bacterial membranes. In Gram-negative bacteria, the localization of lipoprotein (Lol) system facilitates the transport of these proteins from the inner membrane to the outer membrane. In Helicobacter pylori , an ε-proteobacterium, lipoprotein transport differs significantly from the canonical and well-studied system in Escherichia coli , particularly due to the absence of LolB and the use of a LolF homodimer instead of the LolCE heterodimer. This study presents the crystal structure of the H. pylori lipoprotein chaperone LolA (LolA-HP) and its interaction with lipopeptide antibiotics such as polymyxin B and colistin. Isothermal titration calorimetry revealed that, unlike LolA from Vibrio cholerae and Porphyromonas gingivalis , LolA-HP does not bind to these antibiotics. Structural comparisons showed that LolA-HP has a deeper hydrophobic cleft but lacks the negative electrostatic potential critical for binding polymyxins. These findings offer insights into the structural diversity of LolA across bacterial species and its potential as a target for antibacterial agents.


  • Organizational Affiliation
    • Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer-membrane lipoprotein carrier protein
A, B
166Helicobacter pylori J99Mutation(s): 0 
Gene Names: lolAjhp_0722
UniProt
Find proteins for Q9ZL58 (Helicobacter pylori (strain J99 / ATCC 700824))
Explore Q9ZL58 
Go to UniProtKB:  Q9ZL58
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZL58
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free:  0.251 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.749α = 90
b = 65.461β = 99.237
c = 60.807γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2016-05009
Kempe FoundationSwedenJCSMK23-0215

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-18
    Type: Initial release
  • Version 1.1: 2025-01-15
    Changes: Database references