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We have detected phosphohistidine and phospholysine phosphatase activities in rat tissue extracts using partially phosphorylated, high-molecular-mass (> 10 kDa) polymers of histidine and lysine as substrates. Multiple phosphohistidine- and phospholysine-specific phosphatases were present in these extracts based on observed differences in heat stability, sensitivity to bivalent metal ions and thiol modifying reagents, and/or elution from DE-52 cellulose. The properties of these phosphohistidine and phospholysine phosphatases were distinct from those of the phosphomonoester-specific protein phosphatases or the N-P phosphohydrolases that act on the free phosphoamino acids phosphoarginine, 3-phosphohistidine or phospholysine