Studies of microbial biosynthetic and catabolic pathways provide major insights about enzyme mechanism, specificity, structure, regulation, and evolution. Harnessing these insights and the individual enzymes has many practical uses ranging from the synthesis of new drug compounds to bioremediation. This application will address two questions: how the C ring of the antibiotic antitumor agent tomaymycin is made and how polycyclic aromatic hydrocarbons (PAHs) are degraded by one major bacterial pathway. Both questions arose in the course of our studies on 4-oxalocrotonate tautomerase (4-OT) and other tautomerase superfamily members. 4-OT catalyzes a proton transfer reaction in the meta-fission pathway for the degradation of aromatic hydrocarbons. TomN, a newly discovered 4-OT homologue, led us to the tomaymycin pathway because it reportedly catalyzes a proton transfer reaction using a very different substrate. The second question emerged from our extensive use of acetylene compounds as mechanistic probes and inhibitors of 4-OT and other superfamily members. The answer to the first question advances our understanding of the biosynthesis of a large and highly diverse group of natural products, the pyrrolo[1,4]benzodiazepines that are important sources of antimicrobial and anticancer drugs and drug leads. The answer to the second question advances our understanding of PAH degradative pathways, notably ones used for the degradation of higher molecular weight PAHs, which, along with the lower molecular weight PAHs, are highly toxic and persistent environmental contaminants. Using a combination of mechanistic, biochemical, structural, and kinetic techniques, these questions will be addressed in three specific aims.
These aims are to: (1) identify the reactions that convert L-dopa to the C-ring of tomaymycin;(2) identify the key elements of the TomK mechanism;and (3) establish the mechanism and determinants of specificity for the hydratase/aldolases in the naphthalene, phenanthrene, and fluoranthene degradative pathways. The results will also address our long- term goals, which are to obtain a more comprehensive understanding of the relationship between structure and function in enzyme-catalyzed reactions and to delineate the factors that govern protein structure, substrate recognition, and reaction specificity.

Public Health Relevance

The proposed research will determine how Nature makes a crucial part of an anticancer agent known as tomaymycin, and set the stage for generating similar drugs that are more potent, less costly, and less toxic. The research will also determine how bacteria process polycyclic aromatic hydrocarbons, which are persistent and toxic environmental contaminants. The knowledge can assist in the development of bioremediation technologies.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Macromolecular Structure and Function E Study Section (MSFE)
Program Officer
Barski, Oleg
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Texas Austin
Schools of Pharmacy
United States
Zip Code
LeVieux, Jake A; Baas, Bert-Jan; Kaoud, Tamer S et al. (2017) Kinetic and structural characterization of a cis-3-Chloroacrylic acid dehalogenase homologue in Pseudomonas sp. UW4: A potential step between subgroups in the tautomerase superfamily. Arch Biochem Biophys 636:50-56
Johnson Jr, William H; Stack, Tyler M M; Taylor, Stephanie M et al. (2016) Stereochemical Consequences of Vinylpyruvate Hydratase-Catalyzed Reactions. Biochemistry 55:4055-64
Guimarães, Samuel L; Coitinho, Juliana B; Costa, Débora M A et al. (2016) Crystal Structures of Apo and Liganded 4-Oxalocrotonate Decarboxylase Uncover a Structural Basis for the Metal-Assisted Decarboxylation of a Vinylogous ?-Keto Acid. Biochemistry 55:2632-45
Araújo, Simara Semíramis de; Neves, Cíntia Mara Leal; Guimarães, Samuel Leite et al. (2015) Structural and kinetic characterization of recombinant 2-hydroxymuconate semialdehyde dehydrogenase from Pseudomonas putida G7. Arch Biochem Biophys 579:8-17
Huddleston, Jamison P; Burks, Elizabeth A; Whitman, Christian P (2014) Identification and characterization of new family members in the tautomerase superfamily: analysis and implications. Arch Biochem Biophys 564:189-96
Terrell, Cassidy R; Burks, Elizabeth A; Whitman, Christian P et al. (2013) Structural and kinetic characterization of two 4-oxalocrotonate tautomerases in Methylibium petroleiphilum strain PM1. Arch Biochem Biophys 537:113-24
Burks, Elizabeth A; Yan, Wupeng; Johnson Jr, William H et al. (2011) Kinetic, crystallographic, and mechanistic characterization of TomN: elucidation of a function for a 4-oxalocrotonate tautomerase homologue in the tomaymycin biosynthetic pathway. Biochemistry 50:7600-11
Srivastava, Dhiraj; Zhu, Weidong; Johnson Jr, William H et al. (2010) The structure of the proline utilization a proline dehydrogenase domain inactivated by N-propargylglycine provides insight into conformational changes induced by substrate binding and flavin reduction. Biochemistry 49:560-9
Burks, Elizabeth A; Fleming, Christopher D; Mesecar, Andrew D et al. (2010) Kinetic and structural characterization of a heterohexamer 4-oxalocrotonate tautomerase from Chloroflexus aurantiacus J-10-fl: implications for functional and structural diversity in the tautomerase superfamily . Biochemistry 49:5016-27
Almrud, Jeffrey J; Dasgupta, Rakhi; Czerwinski, Robert M et al. (2010) Kinetic and structural characterization of DmpI from Helicobacter pylori and Archaeoglobus fulgidus, two 4-oxalocrotonate tautomerase family members. Bioorg Chem 38:252-9

Showing the most recent 10 out of 13 publications