9GTX | pdb_00009gtx

Structural and functional analysis of the Helicobacter pylori lipoprotein chaperone LolA

• PDB DOI: https://doi.org/10.2210/pdb9GTX/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Helicobacter pylori J99
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-09-18 Released: 2024-12-18 
• Deposition Author(s): Jaiman, D., Persson, K.
• Funding Organization(s): Swedish Research Council, Kempe Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.251 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: in silico

Literature

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

Jaiman, D., Persson, K.

(2024) Front Microbiol 15: 1512451-1512451

• PubMed: 39749131 
• DOI: https://doi.org/10.3389/fmicb.2024.1512451
• Primary Citation 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.

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Organizational Affiliation: 
• Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.
Department of Chemistry, Umeå University, Umeå, Sweden.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 39.18 kDa 
• Atom Count: 2,778 
• Modeled Residue Count: 320 
• Deposited Residue Count: 332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer-membrane lipoprotein carrier protein	A, B	166	Helicobacter pylori J99	Mutation(s): 0  Gene Names: lolA, jhp_0722
UniProt
Find proteins for Q9ZL58 (Helicobacter pylori (strain J99 / ATCC 700824)) Explore Q9ZL58  Go to UniProtKB:  Q9ZL58

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth A], D [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.251 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.749	α = 90
b = 65.461	β = 99.237
c = 60.807	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-18 
Deposition Author(s): Jaiman, D., Persson, K.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2016-05009
Kempe Foundation	Sweden	JCSMK23-0215

Revision History  

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