Origin of the pKa shift of the catalytic lysine in acetoacetate decarboxylase

The pKa value of Lys115, the catalytic residue in acetoacetate decarboxylate, was calculated using atomic coordinates of the X-ray crystal structure with consideration of the protonation states of all titratable sites in the protein. The calculated pKa value of Lys115 (pKa(Lys115)) was unusually low (≈6) in agreement with the experimentally measured value. Although charged residues impact pKa(Lys115) considerably in the native protein, the significant pKa(Lys115) downshift in the protein with respect to aqueous solution was mainly due to loss of the solvation energy in the catalytic active site relative to bulk water.