8YXZ

Vo domain of V/A-ATPase from Thermus thermophilus state1

Summary for 8YXZ

• Entry DOI: 10.2210/pdb8yxz/pdb
• EMDB information: 39661
• Descriptor: V-type ATP synthase subunit C, V-type ATP synthase subunit I, V-type ATP synthase, subunit K (3 entities in total)
• Functional Keywords: v/a-atpase, atp synthase, motor protein
• Biological source: Thermus thermophilus HB8; More
• Total number of polymer chains: 14
• Total formula weight: 231246.71

Authors

Kishikawa, J.,Nishida, Y.,Nakano, A.,Yokoyama, K. (deposition date: 2024-04-03, release date: 2024-12-04)

Primary citation

Kishikawa, J.I.,Nishida, Y.,Nakano, A.,Kato, T.,Mitsuoka, K.,Okazaki, K.I.,Yokoyama, K.
Rotary mechanism of the prokaryotic V o motor driven by proton motive force.
Nat Commun, 15:9883-9883, 2024

PubMed Abstract: ATP synthases play a crucial role in energy production by utilizing the proton motive force (pmf) across the membrane to rotate their membrane-embedded rotor c-ring, and thus driving ATP synthesis in the hydrophilic catalytic hexamer. However, the mechanism of how pmf converts into c-ring rotation remains unclear. This study presents a 2.8 Å cryo-EM structure of the V domain of V/A-ATPase from Thermus thermophilus, revealing precise orientations of glutamate (Glu) residues in the c-ring. Three Glu residues face a water channel, with one forming a salt bridge with the Arginine in the stator (a/Arg). Molecular dynamics (MD) simulations show that protonation of specific Glu residues triggers unidirectional Brownian motion of the c-ring towards ATP synthesis. When the key Glu remains unprotonated, the salt bridge persists, blocking rotation. These findings suggest that asymmetry in the protonation of c/Glu residues biases c-ring movement, facilitating rotation and ATP synthesis.

PubMed: 39567487
DOI: 10.1038/s41467-024-53504-x

Experimental method

ELECTRON MICROSCOPY (3 Å)