Structure of mycobacterial respiratory Complex I

Abstract

Oxidative phosphorylation, the combined activity of the electron transport chain (ETC) and adenosine triphosphate synthase, has emerged as a valuable target for the treatment of infection by Mycobacterium tuberculosis and other mycobacteria. The mycobacterial ETC is highly branched with multiple dehydrogenases transferring electrons to a membrane-bound pool of menaquinone and multiple oxidases transferring electrons from the pool. The proton-pumping type I nicotinamide adenine dinucleotide (NADH) dehydrogenase (Complex I) is found at low abundance in the plasma membranes of mycobacteria in typical in vitro culture conditions and is often considered dispensable. We found that growth of Mycobacterium smegmatis in carbon-limited conditions greatly increased the abundance of Complex I and allowed isolation of a rotenone-sensitive preparation of the enzyme. Determination of the structure of the complex by cryoEM revealed the "orphan" two-component response regulator protein MSMEG_2064 as a subunit of the assembly. MSMEG_2064 in the complex occupies a site similar to the proposed redox sensing subunit NDUFA9 in eukaryotic Complex I. An apparent purine nucleoside triphosphate within the NuoG subunit resembles the GTP-derived molybdenum cofactor in homologous formate dehydrogenase enzymes. The membrane region of the complex binds acyl phosphatidylinositol dimannoside, a characteristic three-tailed lipid from the mycobacterial membrane. The structure also shows menaquinone, which is preferentially used over ubiquinone by gram-positive bacteria, in two different positions along the quinone channel and suggests that menaquinone interacts more extensively than ubiquinone with a key catalytic histidine residue in the enzyme.

Structural basis of a regulatory switch in mammalian complex I

“…In our model, ubiquinone-10 binding is essential for refolding disordered loops and reforming the site during reactivation, whereas substrate exchange for catalysis occurs within closed-only states. Our model is consistent with observations of quinone bound partly or fully inserted into the closed channel in mycobacterial complex I 18 , and with molecular dynamics simulations that have illustrated its transit through the closed channel on physiologically relevant timescales 46,47 . We thus conclude it is not necessary to form open2-like states during catalysis, to open the ubiquinone-binding site to the matrix to allow waters to flow in and out to accommodate or replace the substrate, as was proposed previously to justify their assignment to the catalytic cycle 6,12 .…”

Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor

“…This is unlike eukaryotic Complex I, which has lost hydrogenase activity for quinone reduction. Despite the prediction of large lipophilic cavities (similar to experimentally verified structures) between NuoBDH, analyses of structural models indicate that quinone is unable to enter the complex 64,[72][73][74] . Therefore, we predict that Heimdallarchaeia Complex I-like structures reduce protons to H2 instead of quinone, mechanistically similar to MBH respiratory complexes, but architecturally resembling Complex I.…”

Synthetic lethality ofMycobacterium tuberculosisNADH dehydrogenases is due to impaired NADH oxidation

“…However, one could make a case for such an endeavor given the successful identification of inhibitors to Mtb enzymes that have homologues in humans, like bedaquiline (2) (ATP synthase) and Q203 (cytochrome bc1 complex) (19). Moreover, the structure of the mycobacterial Ndh-1 enzyme complex was recently solved (28), which could help in of the design of Ndh-1 inhibitors.…”