Molecular recognition of oligosaccharide epitopes by a monoclonal Fab specific for Shigella flexneri Y lipopolysaccharide: X-ray structures and thermodynamics.

The antigenic recognition of Shigella flexneri O-polysaccharide, which consists of a repeating unit ABCD [→2)-α-l-Rhap-(1→2)-α-l-Rhap-(1→3)-α-l-Rhap-(1→3)-β-d-GlcpNAc-(1→], by the monoclonal antibody SYA/J6 (IgG3, κ) has been investigated by crystallographic analysis of the Fab domain and its two complexes with two antigen segments (a pentasaccharide Rha A−Rha B−Rha C−GlcNAc D−Rha A‘ and a modified trisaccharide Rha B−Rha C*−GlcNAc D in which Rha C* is missing a C2−OH group). These complex structures, the first for a Fab specific for a periodic linear heteropolysaccharide, reveal a binding site groove (between the VH and VL domains) that makes polar and nonpolar contacts with all the sugar residues of the pentasaccharide. Both main-chain and side-chain atoms of the Fab are used in ligand binding. The charged side chain of Glu H50 of CDR H2 forms crucial hydrogen bonds to GlcNAc of the oligosaccharides. The modified trisaccharide is more buried and fits more snugly than the pentasaccharide. It also makes a...