Cryo-EM structure of trimeric Mycobacterium smegmatis succinate dehydrogenase with a membrane-anchor SdhF

Hongri Gong (), Yan Gao, Xiaoting Zhou, Yu Xiao, Weiwei Wang, Yanting Tang, Shan Zhou, Yuying Zhang, Wenxin Ji, Lu Yu, Changlin Tian, Sin Man Lam, Guanghou Shui, Luke W. Guddat, Luet-Lok Wong, Quan Wang () and Zihe Rao ()
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Hongri Gong: Nankai University
Yan Gao: Tsinghua University
Xiaoting Zhou: ShanghaiTech University
Yu Xiao: ShanghaiTech University
Weiwei Wang: ShanghaiTech University
Yanting Tang: Nankai University
Shan Zhou: Nankai University
Yuying Zhang: Nankai University
Wenxin Ji: Institute of Biophysics, CAS
Lu Yu: Chinese Academy of Sciences
Changlin Tian: Chinese Academy of Sciences
Sin Man Lam: Institute of Genetics and Developmental Biology, CAS
Guanghou Shui: Institute of Genetics and Developmental Biology, CAS
Luke W. Guddat: The University of Queensland
Luet-Lok Wong: University of Oxford
Quan Wang: ShanghaiTech University
Zihe Rao: Nankai University

Nature Communications, 2020, vol. 11, issue 1, 1-8

Abstract: Abstract Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are widespread in Gram-positive bacteria but little is known about the catalytic mechanisms they employ for succinate oxidation by menaquinone. Here, we present the 2.8 Å cryo-electron microscopy structure of a Mycobacterium smegmatis Sdh, which forms a trimer. We identified the membrane-anchored SdhF as a subunit of the complex. The 3 kDa SdhF forms a single transmembrane helix and this helix plays a role in blocking the canonically proximal quinone-binding site. We also identified two distal quinone-binding sites with bound quinones. One distal binding site is formed by neighboring subunits of the complex. Our structure further reveals the electron/proton transfer pathway for succinate oxidation by menaquinone. Moreover, this study provides further structural insights into the physiological significance of a trimeric respiratory complex II. The structure of the menaquinone binding site could provide a framework for the development of Sdh-selective anti-mycobacterial drugs.

Date: 2020
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DOI: 10.1038/s41467-020-18011-9

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