The activity of P-type plasma membrane H+-ATPases is modulated by H+ and cations, with K+ and Ca2+ being of physiological relevance. Using X-ray crystallography, we have located the binding site for Rb+ as a K+ congener, and for Tb3+ and Ho3+ as Ca2+ congeners. Rb+ is found coordinated by a conserved aspartate residue in the phosphorylation domain. A single Tb3+ ion is identified positioned in the nucleotide-binding domain in close vicinity to the bound nucleotide. Ho3+ ions are coordinated at two distinct sites within the H+-ATPase: One site is at the interface of the nucleotide-binding and phosphorylation domains, and the other is in the transmembrane domain toward the extracellular side. The identified binding sites are suggested to represent binding pockets for regulatory cations and a H+ binding site for protons leaving the pump molecule. This implicates Ho3+ as a novel chemical tool for identification of proton binding sites.
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