bi201595v_si_002.mpg (3.83 MB)
Mitochondrial ATP Synthase Catalytic Mechanism: A Novel Visual Comparative Structural Approach Emphasizes Pivotal Roles for Mg2+ and P-Loop Residues in Making ATP
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posted on 2016-02-22, 05:19 authored by David
J. Blum, Young H. Ko, Peter L. PedersenThe mitochondrial ATP synthase (FoF1) is
one of the most abundant, important, and complex enzymes found in
animals and humans. In earlier studies, we used the photosensitive
phosphate analogue vanadate (Vi) to study the enzyme’s
mechanism in the transition state. Significantly, these studies showed
that Mg2+ plays an important role in transition state formation
during ATP synthesis. Additionally, in both MgADP·Vi-F1 and MgVi-F1 complexes, photoactivation
of orthovanadate (Vi) induced cleavage at the third residue
within the P-loop (GGAGVGKT), i.e., βA158,
suggesting its proximity to the γ-phosphate during transition
state formation. However, despite our recent release of the F1-ATPase structure containing Vi, the structural
details regarding the role of Mg2+ have remained elusive.
Therefore, in this study, we sought to improve our understanding of
the essential role of Mg2+ during transition state formation.
We utilized Protein Data Bank structural data representing different
conformational intermediates of key steps in ATP synthesis to assemble
a database of positional relationships between landmark residues of
the catalytic site and the bound ligand. Applying novel bioinformatics
methods, we combined the resulting interatomic spatial data with an
animated model of the catalytic site to visualize the exact nature
of the changes in these positional relationships during ATP synthesis.
The results of these studies reported here show that the absence of
Mg2+ results in migration of inorganic phosphate (Pi) from βA158 to a more medial position in the P-loop
binding pocket, thereby disrupting essential placement and orientation
of the Pi needed to form the transition state structure
and therefore MgATP.
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transition state structuretransition state formationMitochondrial ATP Synthase Catalytic Mechanismenzymenovel bioinformatics methodsATPThe mitochondrial ATP synthaseresidueMgGGAGVGKTphosphate analogue vanadaterelationshipsiteroleATP synthesisComparative Structural Approach Emphasizes Pivotal RolesdataViProtein Data Bank
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