5A70

Structure of the LecB lectin from Pseudomonas aeruginosa strain PA14 in complex with lewis x tetrasaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.138 

wwPDB Validation   3D Report Full Report



Literature

Induction of rare conformation of oligosaccharide by binding to calcium-dependent bacterial lectin: X-ray crystallography and modelling study.

Lepsik, M.Sommer, R.Kuhaudomlarp, S.Lelimousin, M.Paci, E.Varrot, A.Titz, A.Imberty, A.

(2019) Eur J Med Chem 177: 212-220

  • DOI: 10.1016/j.ejmech.2019.05.049
  • Primary Citation of Related Structures:  
    5A70, 6R35

  • PubMed Abstract: 
  • Pathogenic micro-organisms utilize protein receptors (lectins) in adhesion to host tissues, a process that in some cases relies on the interaction between lectins and human glycoconjugates. Oligosaccharide epitopes are recognized through their three- ...

    Pathogenic micro-organisms utilize protein receptors (lectins) in adhesion to host tissues, a process that in some cases relies on the interaction between lectins and human glycoconjugates. Oligosaccharide epitopes are recognized through their three-dimensional structure and their flexibility is a key issue in specificity. In this paper, we analysed by X-ray crystallography the structures of the LecB lectin from two strains of Pseudomonas aeruginosa in complex with Lewis x oligosaccharide present on cell surfaces of human tissues. An unusual conformation of the glycan was observed in all binding sites with a non-canonical syn orientation of the N-acetyl group of N-acetyl-glucosamine. A PDB-wide search revealed that such an orientation occurs only in 4% of protein/carbohydrate complexes. Theoretical chemistry calculations showed that the observed conformation is unstable in solution but stabilised by the lectin. A reliable description of LecB/Lewis x complex by force field-based methods had proven especially challenging due to the special feature of the binding site, two closely apposed Ca 2+ ions which induce strong charge delocalisation. By comparing various force-field parametrisations, we propose a general strategy which will be useful in near future for designing carbohydrate-based ligands (glycodrugs) against other calcium-dependent protein receptors.


    Organizational Affiliation

    Université Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France. Electronic address: anne.imberty@cermav.cnrs.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LECBABCD114Pseudomonas aeruginosa UCBPP-PA14Mutation(s): 0 
Gene Names: lecBPA14_20610
Find proteins for A0A0H2ZE85 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Explore A0A0H2ZE85 
Go to UniProtKB:  A0A0H2ZE85
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose
E, F, G, H
4 N/A Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.138 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.898α = 90
b = 63.228β = 91.2
c = 63.889γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2019-08-07
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2020-01-22
    Changes: Data collection, Other, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary