Structural origins of efficient proton abstraction from carbon by a catalytic antibody

doi:10.1073/pnas.0409207102

Structural origins of efficient proton abstraction from carbon by a catalytic antibody

^*Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037; and ^†Laboratorium für Organische Chemie, Swiss Federal Institute of Technology, ETH Hönggerberg, CH-8093 Zürich, Switzerland

Edited by Harry B. Gray, California Institute of Technology, Pasadena, CA, and approved February 24, 2005 (received for review December 9, 2004)

Abstract

Antibody 34E4 catalyzes the conversion of benzisoxazoles to salicylonitriles with high rates and multiple turnovers. The crystal structure of its complex with the benzimidazolium hapten at 2.5-Å resolution shows that a combination of hydrogen bonding, π stacking, and van der Waals interactions is exploited to position both the base, Glu^H50, and the substrate for efficient proton transfer. Suboptimal placement of the catalytic carboxylate, as observed in the 2.8-Å structure of the Glu^H50Asp variant, results in substantially reduced catalytic efficiency. In addition to imposing high positional order on the transition state, the antibody pocket provides a highly structured microenvironment for the reaction in which the carboxylate base is activated through partial desolvation, and the highly polarizable transition state is stabilized by dispersion interactions with the aromatic residue Trp^L91 and solvation of the leaving group oxygen by external water. The enzyme-like efficiency of general base catalysis in this system directly reflects the original hapten design, in which a charged guanidinium moiety was strategically used to elicit an accurately positioned functional group in an appropriate reaction environment and suggests that even larger catalytic effects may be achievable by extending this approach to the induction of acid-base pairs capable of bifunctional catalysis.

Footnotes

↵ § To whom correspondence may be addressed. E-mail: hilvert{at}org.chem.ethz.ch or wilson{at}scripps.edu.
↵ ‡ Present address: Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany.
This paper was submitted directly (Track II) to the PNAS office.
Abbreviation: CDR, complementarity-determining region.
Data deposition: The atomic coordinates and structure factors have been deposited in the Protein Data Bank, www.pdb.org (PDB ID codes 1Y0L and 1Y18 for the 34E4 and the Glu^H50Asp variant complexes, respectively).