1UZV

High affinity fucose binding of Pseudomonas aeruginosa lectin II: 1.0 A crystal structure of the complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.135 
  • R-Value Observed: 0.115 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

High Affinity Fucose Binding of Pseudomonas Aeruginosa Lectin Pa-Iil: 1.0 A Resolution Crystal Structure of the Complex Combined with Thermodynamics and Computational Chemistry Approaches.

Mitchell, E.P.Sabin, C.Snajdrova, L.Pokorna, M.Perret, S.Gautier, C.Hofr, C.Gilboa-Garber, N.Koca, J.Wimmerova, M.Imberty, A.

(2005) Proteins 58: 735

  • DOI: 10.1002/prot.20330
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • PA-IIL is a fucose-binding lectin from Pseudomonas aeruginosa that is closely related to the virulence factors of the bacterium. Previous structural studies have revealed a new carbohydrate-binding mode with direct involvement of two calcium ions (Mitchell E, Houles C, Sudakevitz D, Wimmerova M, Gautier C, Perez S, Wu AM, Gilboa-Garber N, Imberty A ...

    PA-IIL is a fucose-binding lectin from Pseudomonas aeruginosa that is closely related to the virulence factors of the bacterium. Previous structural studies have revealed a new carbohydrate-binding mode with direct involvement of two calcium ions (Mitchell E, Houles C, Sudakevitz D, Wimmerova M, Gautier C, Perez S, Wu AM, Gilboa-Garber N, Imberty A. Structural basis for selective recognition of oligosaccharides from cystic fibrosis patients by the lectin PA-IIL of Pseudomonas aeruginosa. Nat Struct Biol 2002;9:918-921). A combination of thermodynamic, structural, and computational methods has been used to study the basis of the high affinity for the monosaccharide ligand. A titration microcalorimetry study indicated that the high affinity is enthalpy driven. The crystal structure of the tetrameric PA-IIL in complex with fucose and calcium was refined to 1.0 A resolution and, in combination with modeling, allowed a proposal to be made for the hydrogen-bond network in the binding site. Calculations of partial charges using ab initio computational chemistry methods indicated that extensive delocalization of charges between the calcium ions, the side chains of the protein-binding site and the carbohydrate ligand is responsible for the high enthalpy of binding and therefore for the unusually high affinity observed for this unique mode of carbohydrate recognition.


    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.M., Gilboa-Garber, N., Imberty, A.
      (2002) Nat Struct Biol 9: 918

    Organizational Affiliation

    E.S.R.F. Experiments Division, Grenoble, France.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PSEUDOMONAS AERUGINOSA LECTIN IIA, B, C, D114Pseudomonas aeruginosaMutation(s): 0 
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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

Download CCD File 
A, B, C, D
alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FUCKd:  666.7000122070312   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.135 
  • R-Value Observed: 0.115 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.735α = 90
b = 72.827β = 94.21
c = 54.747γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
ACORNphasing
SHELXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-08
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2019-05-22
    Changes: Data collection, Other, Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary