Stabilization of Charges and Protonation States in the Active Site of the Protein Tyrosine Phosphatases: A Computational Study

Abstract

The initial step of the dephosphorylation of phosphotyrosine by the protein tyrosine phosphatases (PTPases) requires an active-site cysteine residue to be in its deprotonated (thiolate) form so as to make a nucleophilic attack on the phosphate to form a phosphoenzyme intermediate. At the same time, an active-site aspartic acid residue must be in its protonated form to serve as a general acid donating a proton to the leaving tyrosyl moiety. The protein must therefore provide an unusual electrostatic environment in the active site to maintain these protonation states in the free enzyme and in the Michaelis complex with the substrate, whose phosphate group is in the −2 charged form. We present electrostatic calculations for the pKa of the ionizable side chains of four different PTPases. The study includes Michaelis complexes with the substrate, as well as free enzymes. The calculations consistently predict that in the neutral to mildly acidic pH range, the active-site cysteine residue is deprotonated and the...