8YH8

F1 domain of Non-catalytic site depleted and epsilon C-terminal domain deleted FoF1-ATPase from Bacillus PS3,under ATP saturated condition

Summary for 8YH8

• Entry DOI: 10.2210/pdb8yh8/pdb
• EMDB information: 39284
• Descriptor: ATP synthase subunit alpha, ATP synthase subunit beta, ATP synthase gamma chain, ... (7 entities in total)
• Functional Keywords: complex, motor protein
• Biological source: Bacillus sp. PS3; More
• Total number of polymer chains: 8
• Total formula weight: 352339.85

Authors

Kobayashi, R.,Nakano, A.,Mitsuoka, K.,Yokoyama, K. (deposition date: 2024-02-27, release date: 2025-05-14)

Primary citation

Kobayashi, R.,Nakano, A.,Mitsuoka, K.,Yokoyama, K.
ADP-inhibited structure of non-catalytic site-depleted F o F 1 -ATPase from thermophilic Bacillus sp. PS-3.
Biochim Biophys Acta Bioenerg, 1866:149536-149536, 2025

PubMed Abstract: The F domain of FF-ATP synthases/ATPases (FF) possesses three catalytic sites on the three αβ interfaces, termed αβ, αβ, and αβ, located mainly on the β subunits. The enzyme also has three non-catalytic ATP-binding sites on the three αβ interfaces, located mainly on the α subunits. When ATP does not bind to the non-catalytic site, FF becomes significantly prone to ADP inhibition, ultimately resulting in the loss of ATPase activity. However, the underlying mechanism of ADP inhibition remains unclear. Here, we report the cryo-EM structure of the non-catalytic site-depleted (ΔNC) FF from thermophilic Bacillus sp. PS-3, which completely lacks the ability to bind ATP (and ADP) upon transitioning to the ADP-inhibited form. The structure closely resembled the 81° rotated structure of the wild-type FF, except for minor movements in the C-terminal region of the α subunit. In this structure, unlike the wild-type enzyme, the catalytic site at αβ, responsible for ATP hydrolysis, was occupied by ADP-Mg, with the absence of Pi. Furthermore, the catalytic site at αβ, where ATP enters the F domain during steady-state catalysis, is occupied by ADP, seemingly impeding further ATP binding to the enzyme. The structure suggests that the ADP-inhibited form of the F domain is more likely due to differences in the nucleotide-binding states at the catalytic sites rather than structural differences.

PubMed: 39788275
DOI: 10.1016/j.bbabio.2025.149536

Experimental method

ELECTRON MICROSCOPY (2.7 Å)