1W8F

PSEUDOMONAS AERUGINOSA LECTIN II (PA-IIL)COMPLEXED WITH LACTO-N-NEO- FUCOPENTAOSE V(LNPFV)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.123 
  • R-Value Work: 0.105 
  • R-Value Observed: 0.106 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural Basis for the Interaction between Human Milk Oligosaccharides and the Bacterial Lectin Pa-Iil of Pseudomonas Aeruginosa.

Perret, S.Sabin, C.Dumon, C.Pokorna, M.Gautier, C.Galanina, O.Ilia, S.Bovin, N.Nicaise, M.Desmadril, M.Gilboa-Garber, N.Wimmerova, M.Mitchell, E.P.Imberty, A.

(2005) Biochem J 389: 325

  • DOI: 10.1042/BJ20050079
  • Primary Citation of Related Structures:  
    1W8H, 1W8F

  • PubMed Abstract: 
  • One of the mechanisms contributing to the protection by breast-feeding of the newborn against enteric diseases is related to the ability of human milk oligosaccharides to prevent the attachment of pathogenic bacteria to the duodenual epithelium. Indeed, a variety of fucosylated oligosaccharides, specific to human milk, form part of the innate immune system ...

    One of the mechanisms contributing to the protection by breast-feeding of the newborn against enteric diseases is related to the ability of human milk oligosaccharides to prevent the attachment of pathogenic bacteria to the duodenual epithelium. Indeed, a variety of fucosylated oligosaccharides, specific to human milk, form part of the innate immune system. In the present study, we demonstrate the specific blocking of PA-IIL, a fucose-binding lectin of the human pathogen Pseudomonas aeruginosa, by milk oligosaccharides. Two fucosylated epitopes, Lewis a and 3-fucosyl-lactose (Lewis x glucose analogue) bind to the lectin with dissociation constants of 2.2x10(-7) M and 3.6x10(-7) M respectively. Thermodynamic studies indicate that these interactions are dominated by enthalpy. The entropy contribution is slightly favourable when binding to fucose and to the highest-affinity ligand, Lewis a. The high-resolution X-ray structures of two complexes of PA-IIL with milk oligosaccharides allow the precise determination of the conformation of a trisaccharide and a pentasaccharide. The different types of interaction between the oligosaccharides and the protein involve not only hydrogen bonding, but also calcium- and water-bridged contacts, allowing a rationalization of the thermodynamic data. This study provides important structural information about compounds that could be of general application in new therapeutic strategies against bacterial infections.


    Related Citations: 
    • Structural Basis for Oligosaccharide-Mediated Adhesion of Pseudomonas Aeruginosa in the Lungs of Cystic Fibrosis Patients.
      Mitchell, E., Houles, C., Sudakevitz, D., Wimmerova, M., Gautier, C., Perez, S., Wu, A., Gilboa-Garber, N., Imberty, A.
      (2002) Nat Struct Biol 12: 918

    Organizational Affiliation

    Centre de Recherches sur les Macromolécules Végétales, CNRS, Université Joseph Fourier, BP53, 38041 Grenoble Cedex 09, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PSEUDOMONAS AERUGINOSA LECTIN IIA, B, C, D115Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for Q9HYN5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HYN5 
Go to UniProtKB:  Q9HYN5
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]beta-D-glucopyranoseE4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G23034ZK
GlyCosmos:  G23034ZK
GlyGen:  G23034ZK
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]beta-D-glucopyranoseF, H5N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G46248BN
GlyCosmos:  G46248BN
GlyGen:  G46248BN
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]beta-D-glucopyranoseG3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G57548NB
GlyCosmos:  G57548NB
GlyGen:  G57548NB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.123 
  • R-Value Work: 0.105 
  • R-Value Observed: 0.106 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.015α = 85.35
b = 48.352β = 80.05
c = 52.472γ = 65.6
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
ACORNphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-31
    Type: Initial release
  • Version 1.1: 2013-01-30
    Changes: Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary