Abstract SY21-02: Coenzyme Q-dependent metabolism: Lessons from structure-function studies of DHODH
Authors: Losman Julie-Aurore 
Published: April 2024

Ubiquinone or coenzyme Q (CoQ) is perhaps best known as a key component of the mitochondrial electron transport chain and as an endogenous antioxidant. However, CoQ has another critical function in cells, acting as an essential cosubstrate for a number of important metabolic enzymes that are associated with the inner mitochondrial membrane, including dihydroorotate dehydrogenase (DHODH), choline dehydrogenase (CHDH), proline dehydrogenase 1 and 2 (PRODH1, PRODH2), and glycerol-3-phosphate dehydrogenase 2 (GPD2). These FAD-containing mitochondrial enzymes are all hypothesized to utilize a two-step ‘ping-pong’ mechanism of catalysis. In this kinetic model, the baseline conformation of the enzyme has specific affinity for its first cosubstrate (dihydroorotate, choline, proline, glycerol-3-phosphate) but not its second cosubstrate (CoQ). Binding of the first cosubstrate to the enzyme results in oxidation of the cosubstrate and reduction of FAD to FADH2. This reduced ‘intermediate’ form of the enzyme releases the byproduct of the first reaction and then binds CoQ. Upon binding of CoQ, FADH2 is oxidized back to FAD and CoQ is reduced to CoQH2. The oxidized form of the enzyme has a low affinity for CoQH2 and CoQH2 is therefore released, restoring the enzyme to its baseline ‘empty’ conformation. Although there is considerable biochemical evidence to support this ‘double-displacement’ model of CoQ-dependent catalysis, it has been challenging to study the structures of these enzymes in their catalytically-active states due to the profound insolubility of CoQ and due to technical challenges associated with producing highly purified recombinant forms of membrane-associated proteins.

Perhaps the most well-studied CoQ-dependent metabolic enzyme is DHODH. DHODH catalyzes the fourth and rate-limiting step in the de novo pyrimidine biosynthesis pathway, oxidizing dihydroorotate to orotate, which is then converted to the nucleotide precursor UMP. Due to the critical requirement of rapidly dividing cells for pyrimidines, DHODH has been proposed as a therapeutic target in cancer, and a number of highly potent and highly specific DHODH inhibitors have been developed, all of which act as competitive inhibitors of CoQ. By binding and stabilizing the protein, these inhibitors have made it possible to solve the x-ray crystal structure of DHODH. These structural studies have revealed that the inhibitors (and presumably CoQ) bind in a narrow amphipathic tunnel that spans from the membrane-embedded surface of the protein to its FAD-containing catalytic core. These structural studies have also found that DHO or orotate can bind DHODH when the CoQ tunnel is occupied by drug. Given that the ‘ping-pong’ model of catalysis is predicated on the assumption that cosubstrates and byproducts cannot simultaneously bind enzyme, it would appear that either the ping-pong model does not accurately reflect the catalytic mechanism of DHODH or, alternatively, that the structure of DHODH bound to drug is not an accurate representation of the structure of DHODH bound to CoQ.

In order to gain a greater understanding of the structure of the DHODH-CoQ complex, we undertook to solve the x-ray crystal structure of DHODH in complex with decylubiquinone (dUb), a CoQ analog that can act as an electron acceptor for DHODH in vitro. These studies revealed that the x-ray crystal structure of DHODH in its catalytically-active cofactor-bound state deviates in subtle but important ways from the known structure of drug-bound DHODH, providing novel insights into the catalytic mechanism of CoQ-dependent enzymes.

Citation Format: Julie-Aurore Losman. Coenzyme Q-dependent metabolism: Lessons from structure-function studies of DHODH [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr SY21-02.