Refined structure of concanavalin A complexed with methyl α-D-mannopyranoside at 2.0 Å resolution and comparison with the saccharide-free structure

Abstract

The three-dimensional structure of the complex between methyl a-D-mannopyranoside and concanavalin A has been refined at 2.0 A resolution. Diffraction data were recorded from a single crystal (space group P21212~, a = 123.7, b = 128.6, c = 67.2 A) using synchrotron radiation at a wavelength of 1.488 A. The final model has good geometry and an R factor of 19.9% for 58871 reflections (82% complete), within the resolution limits of 8 to 2 A, with F > 1.0tr(F). The asymmetric unit contains four protein subunits arranged as a dimer of dimers with approximate 222 point symmetry. Each monomer binds one saccharide molecule. Each sugar is bound to the protein by hydrogen bonds and van der Waals contacts. Although the four subunits are not crystallographically equivalent, the protein-saccharide interactions are nearly identical in each of the four binding sites. The differences that do occur between the four sites are in the structure of the water network which surrounds each saccharide; these networks are involved in crystal packing. The structure of the complex is compared with a refined saccharide-free concanavalin A structure. The saccharide-free structure is composed of crystallographically identical subunits, again assembled as a f To whom all correspondence should be addressed.(" 1994 International Union or" Crystallography Printed in Great Britain -all rights reserved dimer of dimers, but with exact 222 symmetry. In the saccharide complex the tetramer association is different in that the monomers tend to separate resulting in fewer intersubunit interactions. The average temperature factor of the mannoside complex is considerably higher than that of the saccharide-free protein. The binding site in the saccharide-free structure is occupied by three ordered water molecules and the side chain of Asp71 from a neighbouring molecule in the crystal. These occupy positions similar to those of the four saccharide hydroxyls which are hydrogen bonded to the site. Superposition of the saccharide-binding site from each structure shows that the major changes on binding involve expulsion of these ordered solvents and the reorientation of the side chain of Tyrl00. Overall the surface accessibility of the saccharide decreases from 370 to 100 A 2 when it binds to the protein. This work builds upon the earlier studies of Derewenda et al.

The carbohydrate-binding specificity and molecular modelling of Canavalia maritima and Dioclea grandiflora lectins

“…4). As shown in ConA-sugar complexes (Naismith et al 1994), although the main chain positions of the amino acid residues forming the monosaccharidebinding site of ConA remain very similar in both complexed and native structures of ConA, their side chains are altered in the complexed form. Especially, Leu 99 , Tyr 100 and Arg 228 undergo drastic conformational changes upon binding to sugars.…”

The Crystal Structures of Man(α1–3)Man(α1-O)Me and Man(α1–6)Man(α1-O)Me in Complex with Concanavalin A

“…In this way, they can contribute directly to the properties of the protein by influencing its interaction with the sugar. In this context, Naismith et al (10) observed that the waters that are expelled on binding of MeMan in the monosaccharide-binding site of ConA make similar hydrogen bonds with the protein as the sugar oxygen atoms O-4, O-5, and O-6 of MeMan with Asn-14 N-␦2, Leu-99 N, and Tyr-100 N, respectively. A similar observation was made for the water molecules expelled from the surface of the carbohydrate-binding site of Erythrina corallodendron lectin, a galactose/N-acetylgalactosamine-specific legume lectin (38).…”

“…In the absence of the oligosaccharide, they are replaced by water molecules. The water molecules then compensate for the lack of the polar sugar-protein interaction by sharing the same protein hydrogen-bonding partners as the sugar atoms (10). Not only polar interactions are compensated for.…”

A general method for co-crystallization of concanavalin A with carbohydrates

“…The mannose±conA complex unambiguously identi®ed the binding site and the interactions involved in monosaccharide recognition by the protein. This work has been developed by higher resolution studies of the mannose and glucose complexes (Naismith et al, 1994;Harrop et al, 1996). The lectin itself has now been studied at atomic resolution (Deacon et al, 1997).…”