title: The Inhibitory Mechanism of the ζ Subunit of the F1FO-ATPase Nanomotor of Paracoccus denitrificans and Related α-Proteobacteria.
abstract: The ζ subunit is a novel inhibitor of the F1FO-ATPase of Paracoccus denitrificans and related α-proteobacteria. It is different from the bacterial (ϵ) and mitochondrial (IF1) inhibitors. The N terminus of ζ blocks rotation of the γ subunit of the F1-ATPase of P. denitrificans (Zarco-Zavala, M., Morales-Ríos, E., Mendoza-Hernández, G., Ramírez-Silva, L., Pérez-Hernández, G., and García-Trejo, J. J. (2014) FASEB J. 24, 599-608) by a hitherto unknown quaternary structure that was first modeled here by structural homology and protein docking. The F1-ATPase and F1-ζ models of P. denitrificans were supported by cross-linking, limited proteolysis, mass spectrometry, and functional data. The final models show that ζ enters into F1-ATPase at the open catalytic αE/βE interface, and two partial γ rotations lock the N terminus of ζ in an "inhibition-general core region," blocking further γ rotation, while the ζ globular domain anchors it to the closed αDP/βDP interface. Heterologous inhibition of the F1-ATPase of P. denitrificans by the mitochondrial IF1 supported both the modeled ζ binding site at the αDP/βDP/γ interface and the endosymbiotic α-proteobacterial origin of mitochondria. In summary, the ζ subunit blocks the intrinsic rotation of the nanomotor by inserting its N-terminal inhibitory domain at the same rotor/stator interface where the mitochondrial IF1 or the bacterial ϵ binds. The proposed pawl mechanism is coupled to the rotation of the central γ subunit working as a ratchet but with structural differences that make it a unique control mechanism of the nanomotor to favor the ATP synthase activity over the ATPase turnover in the α-proteobacteria.
authors.affiliation: From the Departamento de Biología, Facultad de Química, and jjgartre@unam.mx.
authors.forename: José J
authors.initials: JJ
authors.lastname: García-Trejo
authors.affiliation: From the Departamento de Biología, Facultad de Química, and.
authors.forename: Mariel
authors.initials: M
authors.lastname: Zarco-Zavala
authors.affiliation: From the Departamento de Biología, Facultad de Química, and.
authors.forename: Francisco
authors.initials: F
authors.lastname: Mendoza-Hoffmann
authors.affiliation: From the Departamento de Biología, Facultad de Química, and.
authors.forename: Eduardo
authors.initials: E
authors.lastname: Hernández-Luna
authors.affiliation: From the Departamento de Biología, Facultad de Química, and.
authors.forename: Raquel
authors.initials: R
authors.lastname: Ortega
authors.affiliation: the Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, Delegación Coyoacán, D.F., CP 04510, México.
authors.forename: Guillermo
authors.initials: G
authors.lastname: Mendoza-Hernández
mesh_terms: D020561:Alphaproteobacteria / Q000201:enzymology*; D018360:Crystallography, X-Ray; D008928:Mitochondria / Q000187:drug effects / Q000378:metabolism; D008958:Models, Molecular; D010231:Paracoccus denitrificans / Q000201:enzymology*; D021122:Protein Subunits / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism; D011506:Proteins / Q000378:metabolism; D006180:Proton-Translocating ATPases / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism; D040681:Structural Homology, Protein; D014357:Trypsin / Q000378:metabolism; D000097795:ATPase Inhibitory Protein
chemical_list: D021122:Protein Subunits; D011506:Proteins; D006180:Proton-Translocating ATPases; D014357:Trypsin; D000097795:ATPase Inhibitory Protein
keywords: ATP synthase; F1FO-ATPase; Paracoccus denitrificans; enzyme inhibitor; homology modeling; inhibition mechanism; nanomotor; rotation; α-proteobacteria; ζ subunit