Structural insight into the type-II mitochondrial NADH dehydrogenases.

The single-component type-II NADH dehydrogenases (NDH-2s) serve as alternatives to the multisubunit respiratory complex?I (type-I NADH dehydrogenase (NDH-1), also called NADH:ubiquinone oxidoreductase; EC 1.6.5.3) in catalysing electron transfer from NADH to ubiquinone in the mitochondrial respiratory chain. The yeast NDH-2 (Ndi1) oxidizes NADH on the matrix side and reduces ubiquinone to maintain mitochondrial NADH/NAD⁺ homeostasis. Ndi1 is a potential therapeutic agent for human diseases caused by complex?I defects, particularly Parkinson's disease, because its expression restores the mitochondrial activity in animals with complex?I deficiency. NDH-2s in pathogenic microorganisms are viable targets for new antibiotics. Here we solve the crystal structures of Ndi1 in its substrate-free, NADH-, ubiquinone- and NADH-ubiquinone-bound states, to help understand the catalytic mechanism of NDH-2s. We find that Ndi1 homodimerization through its carboxy-terminal domain is critical for its catalytic activity and membrane targeting. The structures reveal two ubiquinone-binding sites (UQ_I and UQ_II) in Ndi1. NADH and UQ_I can bind to Ndi1 simultaneously to form a substrate-protein complex. We propose that UQ_I interacts with FAD to act as an intermediate for electron transfer, and that NADH transfers electrons through this FAD-UQ_I complex to UQ_II. Together our data reveal the regulatory and catalytic mechanisms of Ndi1 and may facilitate the development or targeting of NDH-2s for potential therapeutic applications. [ABSTRACT FROM AUTHOR]