On the ATP binding site of the ε subunit from bacterial F-type ATP synthases

Biochimica Et Biophysica Acta
Alexander Krah, Shoji Takada

Abstract

F-type ATP synthases are reversible machinery that not only synthesize adenosine triphosphate (ATP) using an electrochemical gradient across the membrane, but also can hydrolyze ATP to pump ions under certain conditions. To prevent wasteful ATP hydrolysis, subunit ε in bacterial ATP synthases changes its conformation from the non-inhibitory down- to the inhibitory up-state at a low cellular ATP concentration. Recently, a crystal structure of the ε subunit in complex with ATP was solved in a non-biologically relevant dimeric form. Here, to derive the functional ATP binding site motif, we carried out molecular dynamics simulations and free energy calculations. Our results suggest that the ATP binding site markedly differs from the experimental resolved one; we observe a reorientation of several residues, which bind to ATP in the crystal structure. In addition we find that an Mg(2+) ion is coordinated by ATP, replacing interactions of the second chain in the crystal structure. Thus we demonstrate more generally the influence of crystallization effects on ligand binding sites and their respective binding modes. Furthermore, we propose a role for two highly conserved residues to control the ATP binding/unbinding event, which have no...Continue Reading

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Citations

Nov 9, 2016·Journal of Drug Targeting·Nzungize LambertJianping Xie
Mar 5, 2020·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Alexander KrahPeter J Bond
Jul 2, 2020·Chembiochem : a European Journal of Chemical Biology·Alexander KrahPeter J Bond
Oct 19, 2020·Biochimica Et Biophysica Acta. General Subjects·Alexander KrahDuncan G G McMillan

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