3ZWE

Structure of BambL, a lectin from Burkholderia ambifaria, complexed with blood group B epitope


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Fucose-Binding Lectin from Opportunistic Pathogen Burkholderia Ambifaria Binds to Both Plant and Human Oligosaccharidic Epitopes.

Audfray, A.Claudinon, J.Abounit, S.Ruvoen-Clouet, N.Larson, G.Smith, D.F.Wimmerova, M.Le Pendu, J.Romer, W.Varrot, A.Imberty, A.

(2012) J Biol Chem 287: 4335

  • DOI: 10.1074/jbc.M111.314831
  • Primary Citation of Related Structures:  
    3ZW0, 3ZW2, 3ZWE, 3ZZV

  • PubMed Abstract: 
  • Burkholderia ambifaria is generally associated with the rhizosphere of plants where it has biocontrol effects on other microorganisms. It is also a member of the Burkholderia cepacia complex, a group of closely related bacteria that cause lung infections in immunocompromised patients as well as in patients with granulomatous disease or cystic fibrosis ...

    Burkholderia ambifaria is generally associated with the rhizosphere of plants where it has biocontrol effects on other microorganisms. It is also a member of the Burkholderia cepacia complex, a group of closely related bacteria that cause lung infections in immunocompromised patients as well as in patients with granulomatous disease or cystic fibrosis. Our previous work indicated that fucose on human epithelia is a frequent target for lectins and adhesins of lung pathogens (Sulák, O., Cioci, G., Lameignère, E., Balloy, V., Round, A., Gutsche, I., Malinovská, L., Chignard, M., Kosma, P., Aubert, D. F., Marolda, C. L., Valvano, M. A., Wimmerová, M., and Imberty, A. (2011) PLoS Pathog. 7, e1002238). Analysis of the B. ambifaria genome identified BambL as a putative fucose-binding lectin. The 87-amino acid protein was produced recombinantly and demonstrated to bind to fucosylated oligosaccharides with a preference for αFuc1-2Gal epitopes. Crystal structures revealed that it associates as a trimer with two fucose-binding sites per monomer. The overall fold is a six-bladed β-propeller formed by oligomerization as in the Ralstonia solanacearum lectin and not by sequential domains like the fungal fucose lectin from Aleuria aurantia. The affinity of BambL for small fucosylated glycans is very high as demonstrated by microcalorimetry (K(D) < 1 μM). Plant cell wall oligosaccharides and human histo-blood group oligosaccharides H-type 2 and Lewis Y are bound with equivalent efficiency. Binding to artificial glycosphingolipid-containing vesicles, human saliva, and lung tissues confirmed that BambL could recognize a wide spectrum of fucosylated epitopes, albeit with a lower affinity for biological material from nonsecretor individuals.


    Organizational Affiliation

    Centre de Recherche sur les Macromolécules Végétales (CERMAV)-CNRS, Université Joseph Fourier and Institut de Chimie Moléculaire de Grenoble, 38041 Grenoble, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BAMBL LECTINA, B, C87Burkholderia ambifaria AMMDMutation(s): 0 
Gene Names: rslBamb_5415CH72_5454
UniProt
Find proteins for Q0B4G1 (Burkholderia ambifaria (strain ATCC BAA-244 / AMMD))
Explore Q0B4G1 
Go to UniProtKB:  Q0B4G1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0B4G1
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranoseD 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G00068MO
GlyCosmos:  G00068MO
GlyGen:  G00068MO
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranoseE, F 4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G06873PC
GlyCosmos:  G06873PC
GlyGen:  G06873PC
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

Download Ideal Coordinates CCD File 
G [auth A],
H [auth B],
I [auth C]
alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.98α = 90
b = 49.14β = 90
c = 102.71γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-21
    Type: Initial release
  • Version 1.1: 2012-02-15
    Changes: Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary