The ζ subunit of the F1FO-ATP synthase of α-proteobacteria controls rotation of the nanomotor with a different structure

The subunit is a novel natural inhibitor of the -proteobacterial F1FO-ATPase described originally in Paracoccus denitrificans. To characterize the mechanism by which this subunit inhibits the F1FO nanomotor, the subunit of Paracoccus denitrificans (Pd-) was analyzed by the combination of kinetic, biochemical, bioinformatic, proteomic, and structural approaches. The subunit causes full inhibition of the sulfite-activated PdF1-ATPase with an apparent IC50 of 270 nM by a mechanism independent of the epsilon subunit. The inhibitory region of the subunit resides in the first 14 N-terminal residues of the protein, which protrude from the 4--helix bundle structure of the isolated subunit, as resolved by NMR. Cross-linking experiments show that the subunit interacts with rotor () and stator (, ) subunits of the F-1-ATPase, indicating that the subunit hinders rotation of the central stalk. In addition, a putatively regulatory nucleotide-binding site was found in the subunit by isothermal titration calorimetry. Together, the data show that the subunit controls the rotation of F1FO-ATPase by a mechanism reminiscent of, but different from, those described for mitochondrial IF1 and bacterial epsilon subunits where the 4--helix bundle of seems to work as an anchoring domain that orients the N-terminal inhibitory domain to hinder rotation of the central stalk.Zarco-Zavala, M., Morales-Rios, E., Mendoza-Hernandez, G., Ramirez-Silva, L., Perez-Hernandez, G., Garcia-Trejo, J. J. The subunit of the F1FO-ATP synthase of -proteobacteria controls rotation of the nanomotor with a different structure.