Three-dimensional structure of the vacuolar ATPase. Localization of subunit H by difference imaging and chemical cross-linking.
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.
Wilkens
Stephan
S
Department of Biochemistry, University of California, Riverside, Riverside, California 92521, USA. stephan.wilkens@ucr.edu
Inoue
Takao
T
Forgac
Michael
M
D000818:Animals; D001665:Binding Sites; D002417:Cattle; D022163:Clathrin-Coated Vesicles / Q000201:enzymology; D003432:Cross-Linking Reagents; D005656:Fungal Proteins / Q000737:chemistry; D007091:Image Processing, Computer-Assisted; D008854:Microscopy, Electron / Q000379:methods*; D011487:Protein Conformation; D020836:Protein Structure, Quaternary; D021122:Protein Subunits / Q000737:chemistry; D025262:Vacuolar Proton-Translocating ATPases / Q000737:chemistry*
D003432:Cross-Linking Reagents; D005656:Fungal Proteins; D021122:Protein Subunits; D025262:Vacuolar Proton-Translocating ATPases