The availability of complete genome sequences permits analyses of the strategies by which Nature can redesign existing enzymes to catalyze diverse reactions. Using tools such as sequence analyses, recombinant DNA methods, enzyme kinetics, and physical organic chemistry, we study three groups of enzymes whose members catalyze different reactions that diverged from a common ancestor.

The members of the enolase superfamily share the ubiquitous β/α-barrel fold. High-resolution structures reveal a conserved binding site for an essential divalent metal ion that stabilizes an enolate anion intermediate. The essential functional groups are located at the ends of the eight β-strands in the pseudosymmetric barrel. Using the paradigm that the reactions catalyzed by members of this superfamily are initiated by abstraction of the α-proton of a carboxylate anion, we have predicted the functions of unknown proteins discovered in genome projects. We are using directed evolution to explore the functional restrictions available to members of this superfamily, aiming to obtain novel catalysts for new reactions.

The members of the crotonase superfamily share an α+ β fold that provides a conserved oxyanion hole used to stabilize enolate anion intermediates derived from coenzyme A esters. In contrast to the enolase superfamily, the positions of the essential functional groups in this superfamily cannot be restricted to known positions within the structure. Therefore, we are studying diverse members to delineate the structural basis for catalytic diversity. For example, we are elucidating the mechanisms of the reactions catalyzed by dihydroxynaphthoyl CoA synthase and 2-ketocyclohexanecarboxyl CoA hydrolase that catalyze the formation and cleavage of carbon-carbon bonds, respectively. By studying this pair of homologous enzymes together, we expect to better define the mechanisms of both reactions.

The members of the orotidine 5'-phosphate decarboxylase "suprafamily" also share the β/α-barrel fold. However, in contrast to the enolase superfamily, these enzymes use conserved functional groups to catalyze reactions involving distinct mechanisms. We are studying enzymes that catalyze aldol and β-ketoacid decarboxylation reactions to better understand this mechanistic plasticity. We will use directed evolution to explore the consequences of this functional plasticity on the design of new enzymes.