7WGA

2.2 ANGSTROMS RESOLUTION STRUCTURE ANALYSIS OF TWO REFINED N-ACETYLNEURAMINYLLACTOSE-WHEAT GERM AGGLUTININ ISOLECTIN COMPLEXES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

2.2 A resolution structure analysis of two refined N-acetylneuraminyl-lactose--wheat germ agglutinin isolectin complexes.

Wright, C.S.

(1990) J.Mol.Biol. 215: 635-651

  • DOI: 10.1016/S0022-2836(05)80174-3
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structures of complexes of isolectins 1 and 2 of wheat germ agglutinin (WGA1 and WGA2) with N-acetylneuraminyl-lactose (NeuNAc-alpha(2-3)-Gal-beta(1-4)-Glc) have been refined on the basis of data in the 8 to 2.2 A resolution range to fina ...

    The crystal structures of complexes of isolectins 1 and 2 of wheat germ agglutinin (WGA1 and WGA2) with N-acetylneuraminyl-lactose (NeuNAc-alpha(2-3)-Gal-beta(1-4)-Glc) have been refined on the basis of data in the 8 to 2.2 A resolution range to final crystallographic R-factors of 17.2% and 15.3% (Fo greater than 1 sigma), respectively. Specific binding interactions and water association, as well as changes in conformation and mobility of the structure upon ligand binding, were compared in the two complexes. The temperature factors (B = 16.3 A2 and 18.4 A2) were found to be much lower compared with those of their respective native structures (19 to 22 A2). Residues involved in sugar binding, dimerization and in lattice contacts exhibit the largest decreases in B-value, suggesting that sugar binding reduces the overall mobility of the protein molecules in the crystal lattice. The binding mode of this sialyl-trisaccharide, an important cell receptor analogue, has been compared in the two isolectins. Only one of the two unique binding sites (4 per dimer), located in the subunit/subunit interface, is occupied in the crystals. This site, termed the "primary" binding site, contains one of the five amino acid substitutions that differentiate WGA1 and WGA2. Superposition of the refined models in each of the independent crystallographic environments indicates a close match only of the terminal non-reducing NeuNAc residue (root-mean-square delta r of 0.5 to 0.6 A). The Gal-Glc portion was found to superimpose poorly, lack electron density, and possess high atomic thermal factors. In both complexes NeuNAc is stabilized through contact with six amino acid side-chains (Ser114 and Glu115 of subunit 1 and Ser62, Tyr64, Tyr(His)66 and Tyr73 of subunit 2), involving all NeuNAc ring substituents. Refinement has allowed accurate assessment of the contact distances for four hydrogen bonds, a strong buried non-polar contact with the acetamido CH3 group and a large number of van der Waals' interactions with the three aromatic side-chains. The higher affinity of N-acetylneuraminyl-lactose observed by nuclear magnetic resonance studies for WGA1 can be explained by the more favorable binding interactions that occur when residue 66 is a Tyr. The tyrosyl side-chain provides a larger surface for van der Waals' stacking against the NeuNAc pyranose ring than His66 and a hydrogen bond contact with Gal (C2-OH), not possible in WGA2.(ABSTRACT TRUNCATED AT 400 WORDS)


    Related Citations: 
    • Preliminary X-Ray Diffraction Results on Co-Crystals of Wheat Germ Agglutinin with a Sialoglycopeptide from the Red Cell Receptor Glycophorina
      Wright, C.S.,Kahane, I.
      (1987) J.Mol.Biol. 194: 353
    • Multi-Domain Structure of the Dimeric Lectin Wheat Germ Agglutinin
      Wright, C.S.
      (1980) Biomolecular Structure, Conformation, Function and Evolution --: 9
    • Structural Comparison of the Two Distinct Sugar Binding Sites in Wheat Germ Agglutinin Isolectin II
      Wright, C.S.
      (1984) J.Mol.Biol. 178: 91
    • A Preliminary Crystallographic Study of Wheat Germ Agglutinin
      Wright, C.S.,Keith, C.,Langridge, R.,Nagata, Y.,Burger, M.M.
      (1974) J.Mol.Biol. 87: 843
    • Sequence Variability in Three Wheat Germ Agglutinin Isolectins. Products of Multiple Genes in Polyploid Wheat
      Wright, C.S.,Raikhel, N.
      (1989) J.Mol.Evol. 28: 327
    • Crystallographic Elucidation of the Saccharide Binding Mode in Wheat Germ Agglutinin and its Biological Significance
      Wright, C.S.
      (1980) J.Mol.Biol. 141: 267
    • Comparison of the Refined Crystal Structures of Two Wheat Germ Isolectins
      Wright, C.S.
      (1989) J.Mol.Biol. 209: 475
    • Refinement of the Crystal Structure of Wheat Germ Agglutinin Isolectin 2 at 1.8 Angstroms Resolution
      Wright, C.S.
      (1987) J.Mol.Biol. 194: 501
    • Location of the N-Acetyl-D-Neuraminic Acid Binding Site in Wheat Germ Agglutinin. A Crystallographic Study at 2.8 Angstroms Resolution
      Wright, C.S.
      (1980) J.Mol.Biol. 139: 53
    • Structural Differences in the Two Major Wheat Germ Agglutinin Isolectins
      Wright, C.S.,Olafsdottir, S.
      (1986) J.Biol.Chem. 261: 7191
    • Primary Structure of Wheat Germ Agglutinin Isolectin 2. Peptide Order Deduced from X-Ray Structure
      Wright, C.S.,Gavilanes, F.,Peterson, D.L.
      (1984) Biochemistry 23: 280
    • Erratum. Refinement of the Crystal Structure of Wheat Germ Agglutinin Isolectin 2 at 1.8 Angstroms Resolution
      Wright, C.S.
      (1988) J.Mol.Biol. 199: 239
    • Evolution of the Multidomain Protein Wheat Germ Agglutinin
      Wright, H.T.,Brooks, D.M.,Wright, C.S.
      (1985) J.Mol.Evol. 21: 133
    • The Crystal Structure of Wheat Germ Agglutinin at 2.2 Angstroms Resolution
      Wright, C.S.
      (1977) J.Mol.Biol. 111: 439
    • Histidine Determination in Wheat Germ Agglutinin Isolectin by X-Ray Diffraction Analysis
      Wright, C.S.
      (1981) J.Mol.Biol. 145: 453
    • Non-Crystallographic Symmetry in the Crystal Dimer of Wheat Germ Agglutinin
      Wright, C.S.
      (1974) J.Mol.Biol. 87: 835
    • The Toxin-Agglutinin Fold. A New Group of Small Protein Structures Organized Around a Four-Disulfide Core
      Drenth, J.,Low, B.W.,Richardson, J.S.,Wright, C.S.
      (1980) J.Biol.Chem. 255: 2652


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, MCV/VCU, Richmond 23298-0001.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
WHEAT GERM LECTIN
A, B
171Triticum aestivumMutation(s): 0 
Find proteins for P10968 (Triticum aestivum)
Go to UniProtKB:  P10968
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A, B
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 51.220α = 90.00
b = 73.600β = 98.00
c = 91.420γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1990-04-03 
  • Released Date: 1990-10-15 
  • Deposition Author(s): Wright, C.S.

Revision History 

  • Version 1.0: 1990-10-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model
  • Version 1.4: 2017-11-29
    Type: Derived calculations, Other