1PZ5

Structural basis of peptide-carbohydrate mimicry in an antibody combining site

Summary for 1PZ5

• Entry DOI: 10.2210/pdb1pz5/pdb
• Related: 1M71 1M7D 1M7I
• Descriptor: Light chain of Fab (SYA/J6), Heavy chain of Fab (SYA/J6), Octapeptide (MDWNMHAA), ... (4 entities in total)
• Functional Keywords: antibody-antigen structure, peptide-carbohydrate mimicry, vaccine design, immune system
• Biological source: Mus musculus (house mouse); More
• Total number of polymer chains: 3
• Total formula weight: 48256.86

Authors

Vyas, N.K.,Vyas, M.N.,Chervenak, M.C.,Bundle, D.R.,Pinto, B.M.,Quiocho, F.A. (deposition date: 2003-07-09, release date: 2003-11-18, Last modification date: 2024-10-30)

Primary citation

Vyas, N.K.,Vyas, M.N.,Chervenak, M.C.,Bundle, D.R.,Pinto, B.M.,Quiocho, F.A.
Structural basis of peptide-carbohydrate mimicry in an antibody combining site.
Proc.Natl.Acad.Sci.USA, 100:15023-15028, 2003

PubMed Abstract: The structure of a complex between the Fab fragment of the antibody (SYA/J6) specific for the cell surface O-antigen polysaccharide of the pathogen Shigella flexneri Y and an octapeptide (Met-Asp-Trp-Asn-Met-His-Ala-Ala), a functional mimic of the O-antigen, has been determined at 1.8-A resolution. Comparison of the structure with that of the complex with the pentasaccharide antigen [-->2)-alpha-L-Rha-(1-->2)-alpha-L-Rha-(1-->3)-alpha-L-Rha-(1-->3)-beta-D-GlcNAc-(1-->2)-alpha-L-Rha-(1-->] reveals the molecular recognition process by which a peptide mimics a carbohydrate in binding to an antibody. The binding modes of the two ligands differ considerably. Octapeptide binding complements the shape of the combining site groove much better than pentasaccharide binding. Moreover, the peptide makes a much greater number of contacts (126), which are mostly van der Waals interactions, with the Fab than the saccharide (74). An unusual feature is also the involvement of 12 water molecules in mediating hydrogen bonds between residues within the peptide or of the peptide and Fab. Despite better shape complementarity and greater number of contacts, the octapeptide binds with an affinity (KA = 2.5 x 10(5) M-1, measured by calorimetry) only approximately 2-fold tighter than the pentasaccharide. The structural results are relevant to the design of peptide mimetics with improved affinity for use as vaccines.

PubMed: 14645714
DOI: 10.1073/pnas.2431286100

Experimental method

X-RAY DIFFRACTION (1.8 Å)