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Structure of the E. coli PutA proline dehydrogenase domain (residues 86-630) complexed with (2S)-oxetane-2-carboxylic acid
Structural highlights
FunctionPUTA_ECOLI Oxidizes proline to glutamate for use as a carbon and nitrogen source and also function as a transcriptional repressor of the put operon. Publication Abstract from PubMedProline dehydrogenase (PRODH) catalyzes the first step of proline catabolism, the FAD-dependent oxidation of L-proline to Delta(1)-pyrroline-5-carboxylate. PRODH plays a central role in the metabolic rewiring of cancer cells, which has motivated the discovery of inhibitors. Here, we studied the inhibition of PRODH by 18 proline-like compounds to understand the structural and chemical features responsible for the affinity of the best-known inhibitor, S-(-)-tetrahydro-2-furoic acid (1). The compounds were screened, and then six were selected for more thorough kinetic analysis: cyclobutane-1,1-dicarboxylic acid (2), cyclobutanecarboxylic acid (3), cyclopropanecarboxylic acid (4), cyclopentanecarboxylic acid (16), 2-oxobutyric acid (17), and (2S)-oxetane-2-carboxylic acid (18). These compounds are competitive inhibitors with inhibition constants in the range of 1.4-6 mM, compared to 0.3 mM for 1. Crystal structures of PRODH complexed with 2, 3, 4, and 18 were determined. All four inhibitors bind in the proline substrate site, but the orientations of their rings differ from that of 1. The binding of 3 and 18 is accompanied by compression of the active site to enable nonpolar contacts with Leu513. Compound 2 is unique in that the additional carboxylate displaces a structurally conserved water molecule from the active site. Compound 18 also destabilizes the conserved water, but by an unexpected non-steric mechanism. The results are interpreted using a chemical double mutant thermodynamic cycle. This analysis revealed unanticipated synergism between ring size and hydrogen bonding to the conserved water. These structure-affinity relationships provide new information relevant to the development of new inhibitor design strategies targeting PRODH. Structure-affinity relationships of reversible proline analog inhibitors targeting proline dehydrogenase.,Bogner AN, Tanner JJ Org Biomol Chem. 2022 Jan 26;20(4):895-905. doi: 10.1039/d1ob02328d. PMID:35018940[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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