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TitleCryo-EM structure of trimeric Mycobacterium smegmatis succinate dehydrogenase with a membrane-anchor SdhF.
Journal, issue, pagesNat Commun, Vol. 11, Issue 1, Page 4245, Year 2020
Publish dateAug 25, 2020
AuthorsHongri 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 / Zihe Rao /
PubMed AbstractDiheme-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 ...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.
External linksNat Commun / PubMed:32843629 / PubMed Central
MethodsEM (single particle)
Resolution2.84 Å
Structure data

0981

6lum

EMDB-0981, PDB-6lum:
Structure of Mycobacterium smegmatis succinate dehydrogenase 2
Method: EM (single particle) / Resolution: 2.84 Å

Chemicals

ChemComp-PEV:
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / POPE, phospholipid*YM

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

ChemComp-MQ9:
MENAQUINONE-9

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

ChemComp-LPP:
2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / phospholipid*YM

ChemComp-PIE:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

ChemComp-SF4:
IRON/SULFUR CLUSTER

ChemComp-F3S:
FE3-S4 CLUSTER

Source
  • mycolicibacterium smegmatis mc2 51 (bacteria)
KeywordsOXIDOREDUCTASE / electron transfer chain / trimer

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