1M7D

Crystal structure of a Monoclonal Fab Specific for Shigella flexneri Y Lipopolysaccharide complexed with a trisaccharide

Summary for 1M7D

• Entry DOI: 10.2210/pdb1m7d/pdb
• Related: 1M71 1M7I 1MCP
• Descriptor: light chain of the monoclonal antibody Fab SYA/J6, heavy chain of the monoclonal antibody Fab SYA/J6, alpha-L-rhamnopyranose-(1-3)-alpha-L-Olivopyranose-(1-3)-methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside, ... (4 entities in total)
• Functional Keywords: fab-carbohydrate interactions, shigella o-antigen, anti-carbohydrate antibody, immune system
• Biological source: Mus musculus (house mouse); More
• Total number of polymer chains: 2
• Total formula weight: 47776.23

Authors

Vyas, N.K.,Vyas, M.N.,Chervenak, M.C.,Johnson, M.A.,Pinto, B.M.,Bundle, D.R.,Quiocho, F.A. (deposition date: 2002-07-19, release date: 2003-07-22, Last modification date: 2024-10-16)

Primary citation

Vyas, N.K.,Vyas, M.N.,Chervenak, M.C.,Johnson, M.A.,Pinto, B.M.,Bundle, D.R.,Quiocho, F.A.
Molecular Recognition of Oligosaccharide Epitopes by a Monoclonal Fab Specific for Shigella flexneri Y Lipopolysaccharide: X-ray Structures and Thermodynamics
Biochemistry, 41:13575-13586, 2002

PubMed Abstract: The antigenic recognition of Shigella flexneri O-polysaccharide, which consists of a repeating unit ABCD [-->2)-alpha-L-Rhap-(1-->2)-alpha-L-Rhap-(1-->3)-alpha-L-Rhap-(1-->3)-beta-D-GlcpNAc-(1-->], by the monoclonal antibody SYA/J6 (IgG3, kappa) 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 V(H) and V(L) 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 as many contacts (approximately 75) with the Fab as the pentasaccharide, including the same number of hydrogen bonds (eight, with four being identical). It is further engaged in more hydrophobic interactions than the pentasaccharide. These three features favorable to trisaccharide binding are consistent with the observation of a tighter complex with the trisaccharide than the pentasaccharide. Thermodynamic data demonstrate that the native tri- to pentasaccharides have free energies of binding in the range of 6.8-7.4 kcal mol(-1), and all but one of the hydrogen bonds to individual hydroxyl groups provide no more than approximately 0.7 kcal mol(-1). They further indicate that hydrophobic interactions make significant contributions to binding and, as the native epitope becomes larger across the tri-, tetra-, pentasaccharide series, entropy contributions to the free energy become dominant.

PubMed: 12427018
DOI: 10.1021/bi0261387

Experimental method

X-RAY DIFFRACTION (2.3 Å)