Abstract
The structure of the proton-pumping vacuolar ATPase (V-ATPase) from bovine brain clathrin coated vesicles was analyzed by electron microscopy and single molecule image analysis. A three-dimensional structural model of the complex was calculated by the angular reconstitution method at a resolution of 27 A. Overall, the appearance of the V(0) and V(1) domains in the three-dimensional model of the intact bovine V-ATPase resembles the models of the isolated bovine V(0) and yeast V(1) domains determined previously. To determine the binding position of subunit H in the V-ATPase, electron microscopy and cysteine-mediated photochemical cross-linking were used. Difference maps calculated from projection images of intact bovine V-ATPase and a V-ATPase preparation in which the two H subunit isoforms were removed by treatment with cystine revealed less protein density at the bottom of the V(1) in the subunit H-depleted enzyme, suggesting that subunit H isoforms bind at the interface of the V(1) and V(0) domains. A comparison of three-dimensional models calculated for intact and subunit H-depleted enzyme indicated that at least one of the subunit H isoforms, although poorly resolved in the three-dimensional electron density, binds near the putative N-terminal domain of the a subunit of the V(0). For photochemical cross-linking, unique cysteine residues were introduced into the yeast V-ATPase B subunit at sites that were localized based on molecular modeling using the crystal structure of the mitochondrial F(1) domain. Cross-linking was performed using the photoactivatable sulfhydryl reagent 4-(N-maleimido)benzophenone. Cross-linking to subunit H was observed from two sites on subunit B (E494 and T501) predicted to be located on the outer surface of the subunit closest to the membrane. Results from both electron microscopy and cross-linking analysis thus place subunit H near the interface of the V(1) and V(0) domains and suggest a close structural similarity between the V-ATPases of yeast and mammals.
Highlights
The structure of the proton-pumping vacuolar ATPase (V-ATPase) from bovine brain clathrin coated vesicles was analyzed by electron microscopy and single molecule image analysis
Difference maps calculated from projection images of intact bovine V-ATPase and a V-ATPase preparation in which the two H subunit isoforms were removed by treatment with cystine revealed less protein density at the bottom of the V1 in the subunit H-depleted enzyme, suggesting that subunit H isoforms bind at the interface of the V1 and V0 domains
We have chosen the enzyme purified from bovine brain clathrin-coated vesicles because of its superior stability and structural integrity which might be because brain clathrin-coated vesicles serve an endocytic function and are likely to be free of the proteases that may result in the lower stability of V-ATPases from digestive organelles, such as lysosomes
Summary
V1V0, proton-pumping vacuolar ATPase; V1, water soluble domain of the vacuolar proton pumping found in both the endomembrane system of subcellular organelles and the plasma membrane of certain specialized cells. Unlike in the F-ATPase, the in vivo proton pumping activity of the eukaryotic V-ATPase is regulated by a dissociation into V1 and V0 [17, 18] The mechanism of this regulation is well studied in the yeast and insect enzyme, and it has been shown that the dissociation is reversible and substrate-dependent and that the regulation is employed by the organism to preserve ATP in periods of limited nutrient availability. It has been proposed that subunit C and the cytoplasmic domain of subunit a are involved in the mechanism of ATPase; V0, membrane bound domain of the proton pumping vacuolar ATPase; 3-D, three dimensional; MBP, 4-(N-maleimido)benzophenone. The data indicate that subunit H is binding at the bottom periphery of the V1, in the interface between the V1 and V0 domains, near the cytoplasmic domain of the V0 a subunit
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