Location of the N-acetyl-d-neuraminic acid binding site in wheat germ agglutinin: A crystallographic study at 2.8 Å resolution

The crystal structure of the non-covalent complex between wheat germ agglutinin (isolectin no. 2) and N-acetyl-d-neuraminic acid, a saccharide widely found at the termini of carbohydrate chains in membrane glycoproteins and known to interact with wheat germ agglutinin, has been determined from an electron density difference map at 2.8 Å resolution. This map exhibits two strong binding sites on the wheat germ agglutinin dimer molecule which are located in corresponding crevices at the protomer/protomer interface. Amino acid sidechains from B and C-type domains of opposite protomers contribute to the binding site. The N-acetylneuraminic acid molecule is oriented such that its acetyl group becomes essentially buried upon binding, whereas the charged carboxylate and the glycerol groups point away from the protein surface, but are also able to make contact with surface side-chains. Model building shows that substituents of the pyranoside ring which had been predicted as essential for binding from solution studies, are situated favorably to allow interactions to be made with main and side-chain atoms of the protein molecule.