6LUM

Structure of Mycobacterium smegmatis succinate dehydrogenase 2

Summary for 6LUM

• Entry DOI: 10.2210/pdb6lum/pdb
• EMDB information: 0981
• Descriptor: Succinate dehydrogenase subunit C, 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE, 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL, ... (15 entities in total)
• Functional Keywords: electron transfer chain, trimer, oxidoreductase
• Biological source: Mycolicibacterium smegmatis MC2 51; More
• Total number of polymer chains: 15
• Total formula weight: 423468.74

Authors

Gao, Y.,Gong, H.,Zhou, X.,Xiao, Y.,Wang, W.,Ji, W.,Wang, Q.,Rao, Z. (deposition date: 2020-01-29, release date: 2020-05-27, Last modification date: 2024-05-29)

Primary citation

Gong, H.,Gao, Y.,Zhou, X.,Xiao, Y.,Wang, W.,Tang, Y.,Zhou, S.,Zhang, Y.,Ji, W.,Yu, L.,Tian, C.,Lam, S.M.,Shui, G.,Guddat, L.W.,Wong, L.L.,Wang, Q.,Rao, Z.
Cryo-EM structure of trimeric Mycobacterium smegmatis succinate dehydrogenase with a membrane-anchor SdhF.
Nat Commun, 11:4245-4245, 2020

PubMed 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.

PubMed: 32843629
DOI: 10.1038/s41467-020-18011-9

Experimental method

ELECTRON MICROSCOPY (2.84 Å)