5LKW | pdb_00005lkw

Crystal structure of the peptidoglycan-associated lipoprotein (Pal) from Burkholderia cepacia in complex with DAP

• PDB DOI: https://doi.org/10.2210/pdb5LKW/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Burkholderia cenocepacia J2315
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-07-25 Released: 2017-08-16 
• Deposition Author(s): Romano, M., Ruggiero, A., Berisio, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.249 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

The Burkholderia cenocepacia peptidoglycan-associated lipoprotein is involved in epithelial cell attachment and elicitation of inflammation.

Dennehy, R., Romano, M., Ruggiero, A., Mohamed, Y.F., Dignam, S.L., Mujica Troncoso, C., Callaghan, M., Valvano, M.A., Berisio, R., McClean, S.

(2017) Cell Microbiol 19

• PubMed: 27886433 
• DOI: https://doi.org/10.1111/cmi.12691
• Primary Citation Related Structures: 
  5LKW


• PubMed Abstract: 
  

  The Burkholderia cepacia complex (Bcc) is a group of Gram-negative opportunistic pathogens causing infections in people with cystic fibrosis (CF). Bcc is highly antibiotic resistant, making conventional antibiotic treatment problematic. The identification of novel targets for anti-virulence therapies should improve therapeutic options for infected CF patients. We previously identified that the peptidoglycan-associated lipoprotein (Pal) was immunogenic in Bcc infected CF patients; however, its role in Bcc pathogenesis is unknown. The virulence of a pal deletion mutant (Δpal) in Galleria mellonella was 88-fold reduced (p < .001) compared to wild type. The lipopolysaccharide profiles of wild type and Δpal were identical, indicating no involvement of Pal in O-antigen transport. However, Δpal was more susceptible to polymyxin B. Structural elucidation by X-ray crystallography and calorimetry demonstrated that Pal binds peptidoglycan fragments. Δpal showed a 1.5-fold reduced stimulation of IL-8 in CF epithelial cells relative to wild type (p < .001), demonstrating that Pal is a significant driver of inflammation. The Δpal mutant had reduced binding to CFBE41o ^- cells, but adhesion of Pal-expressing recombinant E. coli to CFBE41o ^- cells was enhanced compared to wild-type E. coli (p < .0001), confirming that Pal plays a direct role in host cell attachment. Overall, Bcc Pal mediates host cell attachment and stimulation of cytokine secretion, contributing to Bcc pathogenesis.

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Organizational Affiliation: 
• Centre of Microbial Host Interactions, Institute of Technology Tallaght, Dublin, Ireland.
National Research Council, Institute of Biostructures and Bioimaging, Naples, Italy.
Centre for Experimental Medicine, Queen's University, Belfast, Northern Ireland.
Faculty of Pharmacy, Department of Microbiology, Alexandria University, Alexandria, Egypt.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.2 kDa 
• Atom Count: 2,084 
• Modeled Residue Count: 238 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative OmpA family lipoprotein	A, B	130	Burkholderia cenocepacia J2315	Mutation(s): 0  Gene Names: BCAL3204
UniProt
Find proteins for B4EDC1 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4EDC1  Go to UniProtKB:  B4EDC1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
API	C [auth A], D [auth B]	2,6-DIAMINOPIMELIC ACID C7 H14 N2 O4 GMKMEZVLHJARHF-SYDPRGILSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.249 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.706	α = 90
b = 77.706	β = 90
c = 38.606	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-16 
Deposition Author(s): Romano, M., Ruggiero, A., Berisio, R.

Revision History  

• Version 1.0: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2017-12-06
  Changes: Database references
• Version 1.2: 2019-10-16
  Changes: Data collection
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references
• Version 2.1: 2024-01-10
  Changes: Refinement description