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

Abstract

Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are widespread in Grampositive 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.

Identification and assessment of cardiolipin interactions with E. coli inner membrane proteins

“…We then carried out a broader analysis, identifying a further 18 CDL sites across five additional proteins [from (17)(18)(19)(20)(21); see Methods for details]. We compared these to our CDL site rules, observing excellent agreement (Fig.…”

Identification and assessment of cardiolipin interactions withE. coliinner membrane proteins

“…We then carried out a broader analysis, identifying a further 17 CDL sites across 5 additional proteins (from (Fyfe et al, 2000) (Gong et al, 2020) (Wiseman et al, 2018) (Zhang et al, 2020) (Yu et al, 2018); see Methods for details). We compared these to our CDL site rules, observing excellent agreement ( Figure 6 and Supplementary Table 4).…”

Architecture of the mycobacterial succinate dehydrogenase with a membrane-embedded Rieske FeS cluster

“…EPR spectra were acquired as previously described ( 1 , 9 ) using a Bruker X-band (9.4 GHz) EMX plus 10/12 spectrometer with ESR-910 flowing helium cryostat, at a temperature of 10K, and a 5-Gauss modulation amplitude at 100 kHz under nonsaturating microwave power conditions (100 μW). To reveal the iron-sulfur clusters in the complex, samples were in the “air-oxidized” state (as isolated) or in the “reduced” state (by addition of 200 μM succinate or 1 mM dithionite) ( 35 – 37 ).…”

“…Thus, the complex II superfamily has been further divided into five subfamilies (types A through E) depending on their biophysical properties ( 8 ). Several structures of complex II superfamily enzymes have been determined: type A (exemplified by the Mycobacterium smegmatis ( Msm ) Sdh2) ( 9 ), type B (exemplified by the Wolinella succinogenes QFR) ( 6 ), type C [exemplified by the Escherichia coli ( 10 ) and porcine ( 5 ) SQRs], and type D (exemplified by the E. coli QFR) ( 11 ). However, Sdh1 has only recently been identified in mycobacteria and is suggested to represent a new class of respiratory complex II referred to as type F ( 12 ).…”