Cation-pumping ATPases characterized by a phosphorylated intermediate have been proposed to contain kinase, phosphatase and transduction domains. Evidence is provided for this model by mutagenesis of critical residues in the proposed domains. The Glu233-Gln mutation blocks the turnover of the intermediate and serves to define the phosphatase domain. Mutations in aspartate residues 534, 560 and 638 alter the nucleotide specificity of the enzyme. These amino acids are therefore part of the ATP binding site. Lys474 seems to be essential for activity in this kinase domain. Finally, mutations in Asp378, the amino acid forming the phosphorylated intermediate, indicate that the formation of a phosphorylated intermediate is not an obligatory step in ATP hydrolysis but is required for coupling this process with proton pumping.