A systematic assessment of mycobacterial F₁-ATPase subunit ε’s role in latent ATPase hydrolysis

In contrast to most bacteria, the mycobacterial F₁F_O-ATP synthase (α₃:β₃:γ:δ:ε:a:b:b’:c₉) does not perform ATP hydrolysis-driven proton translocation. Although subunits α, γ and ε of the catalytic F₁-ATPase component α₃:β₃:γ:ε have all been implicated in the suppression of the enzyme’s ATPase activity, the mechanism remains poorly defined. Here, we brought the central stalk subunit ε into focus by generating the recombinant Mycobacterium smegmatis F₁-ATPase (MsF₁-ATPase), whose 3D low-resolution structure is presented, and its ε-free form MsF₁αβγ, which showed an eightfold ATP hydrolysis increase and provided a defined system to systematically study the segments of mycobacterial ε’s suppression of ATPase activity. Deletion of four amino acids at ε’s N terminus, mutant MsF₁αβγε_Δ2-5, revealed similar ATP hydrolysis as MsF₁αβγ. Together with biochemical and NMR solution studies of a single, double, triple and quadruple N-terminal ε-mutants, the importance of the first N-terminal residues of mycobacterial ε in structure stability and latency is described. Engineering ε’s C-terminal mutant MsF₁αβγε_Δ121 and MsF₁αβγε_Δ103-121 with deletion of the C-terminal residue D121 and the two C-terminal ɑ-helices, respectively, revealed the requirement of the very C terminus for communication with the catalytic α₃β₃-headpiece and its function in ATP hydrolysis inhibition. Finally, we applied the tools developed during the study for an in silico screen to identify a novel subunit ε-targeting F-ATP synthase inhibitor.