Reciprocally Coupled Residues Crucial for Protein Kinase Pak2 Activity Calculated by Statistical Coupling Analysis

Regulation of Pak2 activity involves at least two mechanisms: (i) phosphorylation of the conserved Thr(402) in the activation loop and (ii) interaction of the autoinhibitory domain (AID) with the catalytic domain. We collected 482 human protein kinase sequences from the kinome database and globally mapped the evolutionary interactions of the residues in the catalytic domain with Thr(402) by sequence-based statistical coupling analysis (SCA). Perturbation of Thr(402) (34.6%) suggests a communication pathway between Thr(402) in the activation loop, and Phe(387) (ΔΔE(387F,402T) = 2.80) in the magnesium positioning loop, Trp(427) (ΔΔE(427W,402T) = 3.12) in the F-helix, and Val(404) (ΔΔE(404V,402T) = 4.43) and Gly(405) (ΔΔE(405G,402T) = 2.95) in the peptide positioning loop. When compared to the cAMP-dependent protein kinase (PKA) and Src, the perturbation pattern of threonine phosphorylation in the activation loop of Pak2 is similar to that of PKA, and different from the tyrosine phosphorylation pattern of Src. Reciprocal coupling analysis by SCA showed the residues perturbed by Thr(402) and the reciprocal coupling pairs formed a network centered at Trp(427) in the F-helix. Nine pairs of reciprocal coupling residues crucial for enzymatic activity and structural stabilization were identified. Pak2, PKA and Src share four pairs. Reciprocal coupling residues exposed to the solvent line up as an activation groove. This is the inhibitor (PKI) binding region in PKA and the activation groove for Pak2. This indicates these evolutionary conserved residues are crucial for the catalytic activity of PKA and Pak2.