title: 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.
authors.affiliation: State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Feng
authors.forename: Wenfei
authors.initials: W
authors.lastname: Li
authors.forename: Jian
authors.initials: J
authors.lastname: Li
authors.forename: Jiawei
authors.initials: J
authors.lastname: Wang
authors.forename: Jingpeng
authors.initials: J
authors.lastname: Ge
authors.forename: Duo
authors.initials: D
authors.lastname: Xu
authors.forename: Yanjing
authors.initials: Y
authors.lastname: Liu
authors.forename: Kaiqi
authors.initials: K
authors.lastname: Wu
authors.forename: Qingyin
authors.initials: Q
authors.lastname: Zeng
authors.forename: Jia-Wei
authors.initials: JW
authors.lastname: Wu
authors.forename: Changlin
authors.initials: C
authors.lastname: Tian
authors.forename: Bing
authors.initials: B
authors.lastname: Zhou
authors.forename: Maojun
authors.initials: M
authors.lastname: Yang
mesh_terms: D018360:Crystallography, X-Ray; D042967:Electron Transport Complex I / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism; D008928:Mitochondria / Q000201:enzymology*; D008958:Models, Molecular; D009243:NAD / Q000737:chemistry; D011485:Protein Binding; D055503:Protein Multimerization; D017434:Protein Structure, Tertiary; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000201:enzymology; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism; D014451:Ubiquinone / Q000737:chemistry
chemical_list: C493237:Ndi1 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D009243:NAD; D014451:Ubiquinone; D042967:Electron Transport Complex I