Not Once, not Twice, but Thrice: Structure and Catalytic Mechanisms of the Dihydroorotate Dehydrogenases

Dihydroorotate dehydrogenases (DHODs) are common to all life and catalyze the oxidation of dihydroorotate (DHO) to orotate the precursor of all pyrimidine nucleotides. The core structure of all DHODs has a TIM-barrel topology (the PyrD subunit or domain) that harbors an FMN cofactor that interacts with DHO. There are two classes of DHOD enzymes. Each has unique structures and oxidant substrates that conserve part of the energy available by coupling the reaction to ATP synthesis. The class 1 enzymes are soluble and divided into classes 1A and 1B. Class 1A has fumarate as the electron acceptor forming succinate and is the simplest form of DHOD, successively binding DHO and fumarate at the same active site locale. Class 1B uses NAD⁺ as the oxidant and this form of DHOD is heterodimeric having, in addition to the PyrD subunit, a subunit (PyrK) whose structure is like those of ferredoxin reductases. PyrK adds a second active site with a bound FAD that interacts with the NAD⁺ substrate and includes an Fe₂S₂ center that resides at the interface of the subunits, forming a conduit for electrons. Class 2 DHODs have ubiquinone (UQ) as the electron acceptor. This form of DHOD is membrane associated via an N-terminal domain that also forms a quinone binding site end-on to the FMN xylene moiety. This arrangement uses the flavin to mediate between the substrates and as a redox partition between water-soluble NAD⁺ and lipid soluble UQ₁₀. In this review, we summarize the structure and mechanism of DHOD enzymes.