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PDBsum entry 1m7d
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Immune system
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PDB id
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1m7d
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Molecular recognition of oligosaccharide epitopes by a monoclonal FAB specific for shigella flexneri y lipopolysaccharide: x-Ray structures and thermodynamics.
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Authors
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N.K.Vyas,
M.N.Vyas,
M.C.Chervenak,
M.A.Johnson,
B.M.Pinto,
D.R.Bundle,
F.A.Quiocho.
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Ref.
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Biochemistry, 2002,
41,
13575-13586.
[DOI no: ]
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PubMed id
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Abstract
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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.
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Secondary reference #1
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Title
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Preliminary crystallographic analysis of a FAB specific for the o-Antigen of shigella flexneri cell surface lipopolysaccharide with and without bound saccharides.
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Authors
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M.N.Vyas,
N.K.Vyas,
P.J.Meikle,
B.Sinnott,
B.M.Pinto,
D.R.Bundle,
F.A.Quiocho.
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Ref.
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J Mol Biol, 1993,
231,
133-136.
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PubMed id
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