Structure of a thermophilic F₁-ATPase inhibited by an ε-subunit: Deeper insight into the ε-inhibition mechanism

F₁-ATPase (F₁) is the catalytic sector in F_oF₁-ATP synthase that is responsible for ATP production in living cells. In catalysis, its three catalytic β-subunits undergo nucleotide occupancy-dependent and concerted open-close conformational changes that are accompanied by rotation of the γ-subunit. Bacterial and chloroplast F₁ are inhibited by their own ε-subunit. In the ε-inhibited Escherichia coli F₁ structure, the ε-subunit stabilizes the overall conformation (half-closed, closed, open) of the β-subunits by inserting its C-terminal helix into the α₃β₃ cavity. The structure of ε-inhibited thermophilic F₁ is similar to that of E. coli F₁, showing a similar conformation of the ε-subunit, but the thermophilic ε-subunit stabilizes another unique overall conformation (open, closed, open) of the β-subunits. The ε-C-terminal helix 2 and hook are conserved between the two structures in interactions with target residues and in their positions. Rest of the ε-C-terminal domains are in quite different conformations and positions, and have different modes of interaction with targets. This region is thought to serve ε-inhibition differently. For inhibition, the ε-subunit contacts the second catches of some of the β- and α-subunits, the N- and C-terminal helices, and some of the Rossmann fold segments. Those contacts, as a whole, lead to positioning of those β- and α- second catches in ε-inhibition-specific positions, and prevent rotation of the γ-subunit. Some of the structural features are observed even in IF₁ inhibition in mitochondrial F₁. Database Structural data are available in the Worldwide Protein Data Bank database under the accession number 4XD7 Bacterial F₁-ATPases including thermophilicF₁ (TF₁) are inhibited by its ε-subunit. The ε-inhibited TF₁ structure is solved and compared with ε-inhibited E. coli F₁ (EF₁). TF₁ε-subunit stabilizes one catalytic subunit's conformation in different form from EF₁'s. The ε-structures are different except their core regions, thus different inhibition properties. Bacterial ε-inhibition mechanism is now better understood in terms of structure.