Structures of the Escherichia coli PutA Proline Dehydrogenase Domain in Complex with Competitive Inhibitors

• Published in: Biochemistry (Easton) Vol. 43; no. 39; pp. 12539 - 12548
• Main Authors: Zhang, Min, White, Tommi A, Schuermann, Jonathan P, Baban, Berevan A, Becker, Donald F, Tanner, John J
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 05.10.2004
• Subjects: Bacterial Proteins - antagonists & inhibitors; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Binding, Competitive - genetics; Cloning, Molecular; Crystallography, X-Ray; Enzyme Inhibitors - chemistry; Enzyme Inhibitors - metabolism; Enzyme Stability - genetics; Escherichia coli; Escherichia coli Proteins - antagonists & inhibitors; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; Flavin-Adenine Dinucleotide - chemistry; Flavin-Adenine Dinucleotide - metabolism; Furans - chemistry; Furans - metabolism; Humans; Leucine - genetics; Macromolecular Substances; Membrane Proteins - antagonists & inhibitors; Membrane Proteins - chemistry; Membrane Proteins - genetics; Membrane Proteins - metabolism; Methylenetetrahydrofolate Reductase (NADPH2) - chemistry; Models, Molecular; Mutagenesis, Site-Directed; Peptide Fragments - antagonists & inhibitors; Peptide Fragments - chemistry; Peptide Fragments - genetics; Proline - genetics; Proline Oxidase - antagonists & inhibitors; Proline Oxidase - chemistry; Proline Oxidase - genetics; Proline Oxidase - metabolism; Protein Binding - genetics; Protein Structure, Secondary; Protein Structure, Tertiary - genetics
• DOI: 10.1021/bi048737e
• ISSN: 0006-2960

Proline dehydrogenase (PRODH) catalyzes the first step of proline catabolism, the flavin-dependent oxidation of proline to Δ1-pyrroline-5-carboxylate. Here we present a structure-based study of the PRODH active site of the multifunctional Escherichia coli proline utilization A (PutA) protein using X-ray crystallography, enzyme kinetic measurements, and site-directed mutagenesis. Structures of the PutA PRODH domain complexed with competitive inhibitors acetate (K i = 30 mM), l-lactate (K i = 1 mM), and l-tetrahydro-2-furoic acid (l-THFA, K i = 0.2 mM) have been determined to high-resolution limits of 2.1−2.0 Å. The discovery of acetate as a competitive inhibitor suggests that the carboxyl is the minimum functional group recognized by the active site, and the structures show how the enzyme exploits hydrogen-bonding and nonpolar interactions to optimize affinity for the substrate. The PRODH/l-THFA complex is the first structure of PRODH with a five-membered ring proline analogue bound in the active site and thus provides new insights into substrate recognition and the catalytic mechanism. The ring of l-THFA is nearly parallel to the middle ring of the FAD isoalloxazine, with the inhibitor C5 atom 3.3 Å from the FAD N5. This geometry suggests direct hydride transfer as a plausible mechanism. Mutation of conserved active site residue Leu432 to Pro caused a 5-fold decrease in k cat and a severe loss in thermostability. These changes are consistent with the location of Leu432 in the hydrophobic core near residues that directly contact FAD. Our results suggest that the molecular basis for increased plasma proline levels in schizophrenic subjects carrying the missense mutation L441P is due to decreased stability of human PRODH2.