Ca-ATPase structure in the E1 and E2 conformations: mechanism, helix-helix and helix-lipid interactions

The determination of the crystal structure of the Ca²⁺-ATPase of sarcoplasmic reticulum (SR) in its Ca²⁺-bound [Nature 405 (2000) 647] and Ca²⁺-free forms [Nature 418 (2002) 605] gives the opportunity for an analysis of conformational changes on the Ca²⁺-ATPase and of helix-helix and helix-lipid interactions in the transmembrane (TM) region of the ATPase. The locations of the ends of the TM α-helices on the cytoplasmic side of the membrane are reasonably well defined by the location of Trp residues and by the location of Lys-262 that snorkels up to the surface. The locations of the lumenal ends of the helices are less clear. The position of Lys-972 on the lumenal side of helix M9 suggests that the hydrophobic thickness of the protein is only about 21 Å, rather than the normal 30 Å. The experimentally determined TM α-helices do not agree well with those predicted theoretically. Charged headgroups are required for strong interaction of lipids with the ATPase, consistent with the large number of charged residues located close to the lipid-water interface. Helix packing appears to be rather irregular. Packing of helices M8 and M10 is of the 3-4 ridges-into-grooves or knobs-into-holes types. Packing of helices M5 and M7 involves two Gly residues in M7 and one Gly residue in M5. Packing of the other helices generally involves just one or two residues on each helix at the crossing point. The irregular packing of the TM α-helices in the Ca²⁺-ATPase, combined with the diffuse structure of the ATPase on the lumenal side of the membrane, is suggested to lead to a relative low activation energy for changing the packing of the TM α-helices, with changes in TM α-helical packing being important in the process of transfer of Ca²⁺ ions across the membrane. The inhibitor thapsigargin binds in a cleft between TM α-helices M3, M5 and M7. It is suggested that this and other similar clefts provide binding sites for a variety of hydrophobic molecules affecting the activity of the Ca²⁺-ATPase.