John A. Gerlt
Professor of Biochemistry
Professor of Chemistry (0%)
Profesoor of Biophysics
Professor of Basic Medical Sciences
Professor John A. Gerlt attended Michigan State University where he received his B.S. in Biochemistry in 1969. He received his Ph.D. in Biochemistry and Molecular Biology from Harvard University in 1974. After postdoctoral studies at the National Institutes of Health in 1974-75, he held faculty positions at both Yale University and the University of Maryland before joining the Illinois faculty in 1994. In 2003, he was the recipient of the Repligen Corporation Award in Chemistry for Biological Processes from the Division of Biological Chemistry of the American Chemical Society His research interests are in mechanistic enzymology.
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.
Evolutionary Potential of (β/α)8-Barrels: Stepwise Evolution of a "New" Reaction in the Enolase Superfamily, J. E. Vick and J. A. GERLT, Biochemistry, 2007 46, in press.
A Protein Structure (or Function ?) Initiative, J. A. GERLT, Structure 2007, 15, 1353-1356.
Product Deuterium Isotope Effect for Orotidine 5'-Monophosphate Decarboxylase: Evidence for the Existence of a Short-Lived Carbanion Intermediate, K. Toth, T.L. Amyes, B. M. Wood, K. Chan, J. A. GERLT, J. P. Richard, J. Amer. Chem. Soc. 2007, 129, 12946-12947.
Evolution of Enzymatic Activities in the Enolase Superfamily: D-Mannonate Dehydratase from Novosphingobium aromaticivorans, J. R. Rakus, A. A. Fedorov, E. V. Fedorov, M. E. Glasner, J. E. Vick, P. C. Babbitt, S. C. Almo, and J. A. GERLT, Biochemistry 2007, 46, 12896-12908.
Evolution of Enzymatic Activities in the Enolase Superfamily: L-Talarate/Galactarate Dehydratase from Salmonella typhimurium LT2, W. S. Yew, A. A. Federov, E. V. Federo, S. C. Almo, and J. A. GERLT, Biochemistry 2007, 46, 9564-9577.
Prediction and Assignment of Function in the Enolase Superfamily: A Divergent N-Succinyl Amino Acid Racemase from Bacillus cereus, L. Song, C. Kalyanaraman, A. A. Fedorov, E. V. Fedorov, M. E. Glasner, S. Brown, P. C. Babbitt, S. C. Almo, M. P. Jacobson, and J. A. Gerlt, Nature Chemical Biology 2007, 8, 486-491.
Mechanistic Diversity in the RuBisCO Superfamily: The "Enolase" in the Methionine Salvage Pathway in Geobacillus kaustophilus, H. J. Imker, A. A. Fedorov, E. V. Fedorov, S. C. Almo, and J. A. GERLT, Biochemistry 2007, 46, 4077-4083.
Mechanisms of Protein Evolution and Their Application to Protein Engineering, M. E. Glasner, J. A. GERLT, and P. C. Babbitt, Adv. Enzymol. Relat. Area Mol. Biol. 2007, 193-239.
Evolution of Enzymatic Activities in the Enolase Superfamily: D-Tartrate Dehydratase from Bradyrhizobium japonicum, W. S. Yew, A. A. Federov, E. V. Federo, B. M Wood, S. C. Almo, and J. A. GERLT, Biochemistry 2006, 45, 14598-14608.
Evolution of Enzymatic Activities in the Enolase Superfamily: L-Fuconate Dehydratase from Xanthomonas campestris, W. S. Yew, A. A. Federov, E. V. Federo, J. F. Rakus, R. W. Pierce, S. C. Almo, and J. A. GERLT, Biochemistry, 2006 45, 14582-14597.
Evolution of Enzyme Superfamilies, M. E. Glasner, J. A. GERLT, and P. C. Babbitt, Curr. Opin. Chem. Biol. 2006, 492-497.
Evolution of Structure and Function in the o-Succinylbenzoate Synthase/N-Acylamino Acid Racemase Family of the Enolase Superfamily, M.E. Glasner, N. Fayazmanesh, R. Chiang, A. Sakai, M. P. Jacobson, J. A. GERLT, and P. C. Babbitt, J. Mol. Biol. 2006, 360, 228-50.
N-Succinylamino Acid Racemase and a New Pathway for the Irreversible Conversion of D- to L-Amino Acids, A. Sakai, D. F. Xiang, Ch. Xu, L. Song, W. S. Yew, F. M. Raushel, and J. A. GERLT, Biochemistry 2006, 45, 4455-4462.
A Gold Standard Set of Mechanistically Diverse Superfamilies, S. D. Brown, J. A. GERLT, J. L. Seffernick, and P. C. Babbitt, Genome Biology 2006, 7, R8.
D-Ribulose 5-Phosphate 3-Epimerase: Functional and Structural Relationships to Members of the Ribulose-Phosphate Binding (β/α)8-Barrel Superfamily, coauthored by J. Akana, A. A. Federov, E. Federov, W. R. P. Novack, P. C. Babbitt, S. C. Almo, and J. A. GERLT, Biochemistry 2006, 45, 2493-2503.
Evolutionary Potential of (β/α)8-Barrels: In Vitro Enhancement of a "New" Reaction in the Enolase Superfamily, J. E. Vick, D. M. Z. Schmidt, and J. A. GERLT, Biochemistry 2005, 44, 11722-11729.
Evolution of Enzymatic Activities in the Orotidine 5'-Monophosphate Decarboxylase Suprafamily: Structural Basis for Catalytic Promiscuity in Wild-Type and Designed Mutants of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase, E. L. Wise, W.S. Yew, J. Akana, J. A. Gerlt, and I. Rayment, Biochemistry 2005, 44, 1816-1823.
Evolution of Enzymatic Activities in the Orotidine 5'-Monophosphate Decarboxylase Suprafamily: Enhancing the Promiscuous D-Arabino-Hex-3-ulose 6-Phosphate Synthase Reaction Catalyzed by 3-Keto-L-Gulonate 6-Phosphate Decarboxylase, W.S. Yew, J. Akana, E. L. Wise, I. Rayment, and J. A. Gerlt, Biochemistry 2005, 44, 1807-1815.
Divergent Evolution in the Enolase Superfamily: The Interplay of Mechanism and Specificity, J. A. GERLT, P. C. Babbitt, and I. Rayment, Arch. Biochem. Biophys. 2005, 433, 59-70.