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

Proc Natl Acad Sci U S A. 2005 Apr 5;102(14):4984-9. doi: 10.1073/pnas.0409207102. Epub 2005 Mar 23.


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-angstroms resolution shows that a combination of hydrogen bonding, pi 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-angstroms structure of the Glu(H50)Asp 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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Substitution
  • Animals
  • Antibodies, Catalytic / chemistry*
  • Antibodies, Catalytic / genetics
  • Benzimidazoles / chemistry
  • Binding Sites, Antibody
  • Carbon / chemistry*
  • Crystallography, X-Ray
  • Genetic Variation
  • Haptens / chemistry
  • Humans
  • Immunoglobulin Fab Fragments / chemistry
  • Immunoglobulin Fab Fragments / genetics
  • In Vitro Techniques
  • Mice
  • Models, Molecular
  • Protein Conformation
  • Protons
  • Recombinant Fusion Proteins / chemistry
  • Recombinant Fusion Proteins / genetics
  • Static Electricity


  • Antibodies, Catalytic
  • Benzimidazoles
  • Haptens
  • Immunoglobulin Fab Fragments
  • Protons
  • Recombinant Fusion Proteins
  • Carbon

Associated data

  • PDB/1Y0L
  • PDB/1Y18