1APN

THE CRYSTALLOGRAPHIC STRUCTURE OF METAL-FREE CONCANAVALIN A AT 2.5 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 

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This is version 1.2 of the entry. See complete history


Literature

Crystallographic structure of metal-free concanavalin A at 2.5 A resolution.

Bouckaert, J.Loris, R.Poortmans, F.Wyns, L.

(1995) Proteins 23: 510-524

  • DOI: 10.1002/prot.340230406
  • Primary Citation of Related Structures:  
    1APN

  • PubMed Abstract: 
  • The three-dimensional structure of demetallized concanavalin A has been determined at 2.5 A resolution and refined to a crystallographic R-factor of 18%. The lectin activity of concanavalin A requires the binding of both a transition metal ion, generally Mn2+, and a Ca2+ ion in two neighboring sites in close proximity to the carbohydrate binding site ...

    The three-dimensional structure of demetallized concanavalin A has been determined at 2.5 A resolution and refined to a crystallographic R-factor of 18%. The lectin activity of concanavalin A requires the binding of both a transition metal ion, generally Mn2+, and a Ca2+ ion in two neighboring sites in close proximity to the carbohydrate binding site. Large structural differences between the native and the metal-free lectin are observed in the metal-binding region and consequently for the residues involved in the specific binding of saccharides. The demetallization invokes a series of conformational changes in the protein backbone, apparently initiated mainly by the loss of the calcium ion. Most of the Mn2+ ligands retain their position, but the Ca2+ binding site is destroyed. The Ala207-Asp208 peptide bond, in the beta-strand neighboring the metal-binding sites, undergoes a cis to trans isomerization. The cis conformation for this bond is a highly conserved feature among the leguminous lectins and is critically maintained by the Ca2+ ion in metal-bound concanavalin A. A further and major change adjacent to the isomerized bond is an expansion of the loop containing the monosaccharide ligand residues Leu99 and Tyr100. The dispersion of the ligand residues for the monosaccharide binding site (Asn14, Agr228, Asp208, Leu99, and Tyr100) in metal-free concanavalin A abolishes the lectin's ability to bind saccharides. Since the quaternary structure of legume lectins is essential to their biological role, the tetramer formation was analyzed. In the crystal (pH 5), the metal-free concanavalin A dimers associate into a tetramer that is similar to the native one, but with a drastically reduced number of inter-dimer interactions. This explains the tetramer dissociation into dimers below pH values of 6.5.


    Related Citations: 
    • Crystal Structure of Demetallized Concanavalin A. The Metal-Binding Region
      Shoham, M., Yonath, A., Sussman, J.L., Moult, J., Traub, W., Gilboa(Kalb), A.J.
      (1979) J Mol Biol 131: 137
    • Changes in the Three-Dimensional Structure of Concanavalin a Upon Demetallization
      Reeke Junior, G.N., Becker, J.W., Edelman, G.M.
      (1978) Proc Natl Acad Sci U S A 75: 2286

    Organizational Affiliation

    Laboratorium voor Ultrastructuur, Vrije Universiteit Brussel, Belgium.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CONCANAVALIN AA, B237Canavalia ensiformisMutation(s): 0 
UniProt
Find proteins for P02866 (Canavalia ensiformis)
Explore P02866 
Go to UniProtKB:  P02866
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.36α = 90
b = 85.46β = 90
c = 91.46γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MADNESSdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-04-03
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance