Crystal Structure of the Complex of a Catalytic Antibody Fab Fragment with a Transition State Analog: Structural Similarities in Esterase-Like Catalytic Antibodies

• Published in: Proceedings of the National Academy of Sciences - PNAS 1995-12, Vol.92 (25), p.11721-11725
• Main Authors: Charbonnier, Jean-Baptiste, Carpenter, Elizabeth, Gigant, Benoit, Golinelli-Pimpaneau, Beatrice, Eshhar, Zelig, Green, Bernard S., Knossow, Marcel
• Format: Article
• Language: English
• Subjects: Antibodies; Antibodies, Catalytic - chemistry; Antibodies, Catalytic - metabolism; Antibodies, Monoclonal - chemistry; Antibodies, Monoclonal - metabolism; Atoms; Binding Sites; Biochemistry; Biochemistry, Molecular Biology; Catalysis; Catalysts; Catalytic antibodies; Chemical Sciences; Computer Simulation; Crystallography; Esterases - chemistry; Esterases - metabolism; Haptens; Haptens - chemistry; Haptens - metabolism; Hydrogen bonds; Hydrolysis; Immunoglobulin Fab Fragments - chemistry; Immunoglobulin Fab Fragments - metabolism; Kinetics; Life Sciences; Models, Molecular; Molecular biology; Nitrophenols - chemistry; Nitrophenols - immunology; Phenyls; Phosphonic acids; Protein Conformation; Structural Biology; Substrate Specificity; Synchrotrons
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.92.25.11721

The x-ray structure of the complex of a catalytic antibody Fab fragment with a phosphonate transition-state analog has been determined. The antibody (CNJ206) catalyzes the hydrolysis of p-nitrophenyl esters with significant rate enhancement and substrate specificity. Comparison of this structure with that of the uncomplexed Fab fragment suggests hapten-induced conformational changes: the shape of the combining site changes from a shallow groove in the uncomplexed Fab to a deep pocket where the hapten is buried. Three hydrogen-bond donors appear to stabilize the charged phosphonate group of the hapten: two NH groups of the heavy (H) chain complementarity-determining region 3 (H3 CDR) polypeptide chain and the side-chain of histidine-H35 in the H chain (His-H35) in the H1 CDR. The combining site shows striking structural similarities to that of antibody 17E8, which also has esterase activity. Both catalytic antibody ("abzyme") structures suggest that oxyanion stabilization plays a significant role in their rate acceleration. Additional catalytic groups that improve efficiency are not necessarily induced by the eliciting hapten; these groups may occur because of the variability in the combining sites of different monoclonal antibodies that bind to the same hapten.