2ZML

Crystal structure of basic winged bean lectin in complex with Gal-ALPHA 1,4 Gal


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

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Literature

Structure and sugar-specificity of basic winged-bean lectin: structures of new disaccharide complexes and a comparative study with other known disaccharide complexes of the lectin.

Kulkarni, K.A.Katiyar, S.Surolia, A.Vijayan, M.Suguna, K.

(2008) Acta Crystallogr D Biol Crystallogr 64: 730-737

  • DOI: 10.1107/S0907444908011323
  • Primary Citation of Related Structures:  
    2ZMN, 2ZMK, 2ZML

  • PubMed Abstract: 
  • Crystal structures of the complexes of basic winged-bean agglutinin with the disaccharides Galalpha1-4Gal (galabiose), Galalpha1-6Glc (mellibiose) and Galalpha1-4Galbeta-Et have been determined and the complex with Galalpha1-2Gal has been modelled. The i ...

    Crystal structures of the complexes of basic winged-bean agglutinin with the disaccharides Galalpha1-4Gal (galabiose), Galalpha1-6Glc (mellibiose) and Galalpha1-4Galbeta-Et have been determined and the complex with Galalpha1-2Gal has been modelled. The interactions of the nonreducing Gal with the lectin at the primary site are the same as those in the known complexes with disaccharides having the alpha1-->3 linkage. The second residue in Galalpha1-4Gal and Galalpha1-6Glc forms a water bridge to the lectin, while the ethyl group in Galalpha1-4Galbeta-Et makes nonpolar interactions. In complexes involving disaccharides with alpha1-3 linkages, which form part of the A and B blood-group substances, the second sugar residue forms a direct hydrogen bond to the variable loop in the binding site of the lectin. This in part explains the specificity of the lectin for the blood-group substances and also the higher affinity of alpha1-->3-linked disaccharides for the lectin compared with disaccharides involving other linkages. Including those reported here, 14 crystal structures involving the lectin, accounting for 54 crystallographically independent subunits, are available. A comparative study of these structures shows that the region involving the curved beta-sheet which nestles the metal ions is relatively rigid. The carbohydrate-binding region is perched on this region. The flat beta-sheet, which is involved in oligomerization and exhibits considerable variability in legume lectins, is relatively flexible. Indeed, the structures of basic winged-bean lectin have been of critical importance in establishing legume lectins as a family of proteins in which small alterations in essentially the same tertiary structure lead to large variations in quaternary association. They have also provided a structural explanation of the blood-group specificity of the lectin.


    Related Citations: 
    • Generation of blood group specificity: New insights from structural studies on the complexes of A- and B-reactive saccharides with basic winged bean agglutinin.
      Kulkarni, K.A., Katiyar, S., Surolia, A., Vijayan, M., Suguna, K.
      (2007) Proteins 68: 762
    • Carbohydrate specificity and quaternary association in basic winged bean lectin: X-ray analysis of the lectin at 2.5 A resolution
      Prabu, M.M., Sankaranarayanan, R., Puri, K.D., Sharma, V., Surolia, A., Vijayan, M., Suguna, K.
      (1998) J Mol Biol 276: 787

    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Basic agglutinin ABCD241Psophocarpus tetragonolobusMutation(s): 0 
Gene Names: WBAI
Find proteins for O24313 (Psophocarpus tetragonolobus)
Explore O24313 
Go to UniProtKB:  O24313
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.928α = 90
b = 91.524β = 90
c = 73.654γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MAR345dtbdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-02-08
    Changes: Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary