4AOC | pdb_00004aoc

crystal structure of BC2L-A Lectin from Burkolderia cenocepacia in complex with methyl-heptoside

• PDB DOI: https://doi.org/10.2210/pdb4AOC/pdb

• Classification: HYDROLASE
• Organism(s): Burkholderia orbicola AU 1054
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-26 Released: 2012-08-15 
• Deposition Author(s): Marchetti, R., Malinovska, L., Lameignere, E., deCastro, C., Cioci, G., Kosma, P., Wimmerova, M., Molinaro, A., Imberty, A., Silipo, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.253 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Burkholderia Cenocepacia Lectin a Binding to Heptoses from the Bacterial Lipopolysaccharide.

Marchetti, R., Malinovska, L., Lameignere, E., Adamova, L., De Castro, C., Cioci, G., Stanetty, C., Kosma, P., Molinaro, A., Wimmerova, M., Imberty, A., Silipo, A.

(2012) Glycobiology 22: 1387

• PubMed: 22763039 
• DOI: https://doi.org/10.1093/glycob/cws105
• Primary Citation Related Structures: 
  4AOC


• PubMed Abstract: 
  

  Bacteria from the Burkholderia cepacia complex (Bcc) cause highly contagious pneumonia among cystic fibrosis (CF) patients. Among them, Burkholderia cenocepacia is one of the most dangerous in the Bcc and is the most frequent cause of morbidity and mortality in CF patients. Indeed, it is responsible of "cepacia syndrome", a deadly exacerbation of infection, that is the main cause of poor outcomes in lung transplantation. Burkholderia cenocepacia produces several soluble lectins with specificity for fucosylated and mannosylated glycoconjugates. These lectins are present on the bacterial cell surface and it has been proposed that they bind to lipopolysaccharide epitopes. In this work, we report on the interaction of one B. cenocepacia lectin, BC2L-A, with heptose and other manno configured sugar residues. Saturation transfer difference NMR spectroscopy studies of BC2L-A with different mono- and disaccharides demonstrated the requirement of manno configuration with the hydroxyl or glycol group at C6 for the binding process. The crystal structure of BC2L-A complexed with the methyl-heptoside confirmed the location of the carbohydrate ring in the binding site and elucidated the orientation of the glycol tail, in agreement with NMR data. Titration calorimetry performed on monosaccharides, heptose disaccharides and bacterial heptose-containing oligosaccharides and polysaccharides confirmed that bacterial cell wall contains carbohydrate epitopes that can bind to BC2L-A. Additionally, the specific binding of fluorescent BC2L-A lectin on B. cenocepacia bacterial surface was demonstrated by microscopy.

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Organizational Affiliation: 
• Dipartimento di Scienze Chimiche, Università di Napoli "Federico II", Italy.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 72.13 kDa 
• Atom Count: 4,828 
• Modeled Residue Count: 596 
• Deposited Residue Count: 645 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BC2L-A LECTIN	A, B, C, D, E	129	Burkholderia orbicola AU 1054	Mutation(s): 0
UniProt
Find proteins for A0A0H2Y045 (Burkholderia orbicola (strain AU 1054)) Explore A0A0H2Y045  Go to UniProtKB:  A0A0H2Y045

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1Q	DA [auth E], H [auth A], M [auth B], Q [auth C], X [auth D]	methyl L-glycero-alpha-D-manno-heptopyranoside C8 H16 O7 GJUAFBSAJCBGRU-IHKZFYOVSA-N
SO4	AA [auth D], EA [auth E], I [auth A], J [auth A], N [auth B], R [auth C], S [auth C], T [auth C], U [auth D], Y [auth D], Z [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	BA [auth E], CA [auth E], F [auth A], G [auth A], K [auth B], L [auth B], O [auth C], P [auth C], V [auth D], W [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.253 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50	α = 90
b = 185.14	β = 90
c = 186.21	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-15 
Deposition Author(s): Marchetti, R., Malinovska, L., Lameignere, E., deCastro, C., Cioci, G., Kosma, P., Wimmerova, M., Molinaro, A., Imberty, A., Silipo, A.

Revision History  

• Version 1.0: 2012-08-15
  Type: Initial release
  
• Version 1.1: 2012-10-03
  Changes: Database references
• Version 1.2: 2014-11-19
  Changes: Data collection
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary