We study the structural biology of enzymes. We apply this perspective to understand proline metabolism, substrate channeling, the aldehyde dehydrogenase superfamily, inherited metabolic disorders, domains of unknown function (DUFs), and flavoenzymes. We use structural approaches to discover chemical probes for cancer therapy and infectious diseases. Our experimental approaches include X-ray crystallography, small-angle X-ray scattering, electron microscopy, enzyme kinetics, analytical ultracentrifugation, fluorescence thermal shift, and site-directed mutagenesis.
Structure-Based Engineering of Minimal Proline Dehydrogenase Domains for Inhibitor Discovery
A.N. Bogner, J. Ji, & J.J. Tanner
Protein Engineering, Design, and Selection, 2022.
Proline dehydrogenase (PRODH) catalyzes the FAD-dependent oxidation of l-proline to Δ1-pyrroline-5-carboxylate and is a target for inhibitor discovery because of its importance in cancer cell metabolism. Because human PRODH is challenging to purify, the PRODH domains of the bacterial bifunctional enzyme proline utilization A (PutA) have been used for inhibitor development. These systems have limitations due to large polypeptide chain length, conformational flexibility and the presence of domains unrelated to PRODH activity. Herein, we report the engineering of minimal PRODH domains for inhibitor discovery. The best designs contain one-third of the 1233-residue PutA from Sinorhizobium meliloti and include a linker that replaces the PutA α-domain. The minimal PRODHs exhibit near wild-type enzymatic activity and are susceptible to known inhibitors and inactivators. Crystal structures of minimal PRODHs inhibited by S-(-)-tetrahydro-2-furoic acid and 2-(furan-2-yl)acetic acid were determined at 1.23 and 1.72 Å resolution. Minimal PRODHs should be useful in chemical probe discovery.