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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 chain1. 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 defects2,3,4,5,6,7,8,9, 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 antibiotics10,11. 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 (UQI and UQII) in Ndi1. NADH and UQI can bind to Ndi1 simultaneously to form a substrate–protein complex. We propose that UQI interacts with FAD to act as an intermediate for electron transfer, and that NADH transfers electrons through this FAD–UQI complex to UQII. 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.

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Figure 1: Ndi1 has a unique CTD.
Figure 2: The CTD mediates Ndi1 homodimerization and membrane attachment.
Figure 3: Electron transfer of Ndi1 involves two ubiquinone molecules.

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Primary accessions

Protein Data Bank

Data deposits

The atomic coordinates and structure factors of the apo-, NADH-, ubiquinone- and NADH–ubiquinone-bound forms of Ndi1 have been deposited in the Protein Data Bank under accession codes 4G6G, 4G6H, 4G74 and 4G73, respectively.

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Acknowledgements

We would like to thank the staff at beamline BL17U of the Shanghai Synchrotron Radiation Facility for their assistance with data collection. We thank W. Tong for maintenance and support of the EPR facility at the High Magnetic Field Laboratory, Chinese Academy of Sciences. This work was supported by the Ministry of Science and Technology of China (2011CB910502, 2011CB910900 and 2012CB911101), the National Natural Science Foundation of China (31030020 and 31170679) and Chinese Key Research Plan-Protein Sciences (2011CB911104).

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Authors

Contributions

M.Y. designed and directed the project. Y.F., W.L., J. W., J.G., D.X. and J.-W.W. purified the proteins, grew the crystals, collected data, solved the crystal structures and performed the in vitro activity analyses. Y.L. and Q.Z. performed the genome analysis of the NDHs. B.Z. and J.L. performed the in vivo biological analyses. Y.F., K.W. and C.T. performed the EPR analyses. M.Y. analysed the data and wrote the paper with the help of all the authors.

Corresponding author

Correspondence to Maojun Yang.

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Feng, Y., Li, W., Li, J. et al. Structural insight into the type-II mitochondrial NADH dehydrogenases. Nature 491, 478–482 (2012). https://doi.org/10.1038/nature11541

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