Structural insight into the type-II mitochondrial NADH dehydrogenases

Abstract

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.

Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site

“…The quinone ring binds within 4 Å of the isoalloxazine, which is consistent with direct electron transfer and reminiscent of other flavoenzyme-quinone complexes (22)(23)(24), especially NAD(P)H/ quinone acceptor oxidoreductase (25,26). Although both MB and THFA bind at the si face of the isoalloxazine, the two ligands associate with different conformations of the active site and provoke different protein conformational changes (Fig.…”

Apoptosis-inducing Factor (AIF) and Its Family Member Protein, AMID, Are Rotenone-sensitive NADH:Ubiquinone Oxidoreductases (NDH-2)

“…These results prompted us to consider the possibility that the C-terminal polyhistidine tag might inhibit AIF association to the membrane. To explore this idea, we compared the x-ray crystal structures of mouse AIF (44) with that of Ndi1 from S. cerevisiae (45,46) and NDH-2 from Caldalkalibacillus thermarum (47). In both the Ndi1 and NDH-2 enzymes, the C-terminal regions are essential for membrane anchoring.…”

Ciona intestinalis NADH dehydrogenase NDX confers stress-resistance and extended lifespan on Drosophila

“…Modeling of NDX based on the structure and catalytic mechanism of yeast Ndi1 [42,43] reveals a compact structure with conservation of amino acids important for substrate binding. These include the first FAD-binding Rossmann fold (Fig.…”