Comparison of conservation within and between the Ser/Thr and Tyr protein kinase family: proposed model for the catalytic domain of the epidermal growth factor receptor

Abstract

The protein kinase family can be subdivided into two main groups based on their ability to phosphorylate Ser/Thr or Tyr substrates. In order to understand the basis of this functional difference, we have carried out a comparative analysis of sequence conservation within and between the Ser/Thr and Tyr protein kinases. A multiple sequence alignment of 86 protein kinase sequences was generated. For each position in the alignment we have computed the conservation of residue type in the Ser/Thr, in the Tyr and in both of the kinase subfamilies. To understand the structural and/or functional basis for the conservation, we have mapped these conservation properties onto the backbone of the recently determined structure of the cAMP-dependent Ser/Thr kinase. The results show that the kinase structure can be roughly segregated, based upon conservation, into three zones. The inner zone contains residues highly conserved in all the kinase family and describes the hydrophobic core of the enzyme together with residues essential for substrate and ATP binding and catalysis. The outer zone contains residues highly variable in all kinases and represents the solvent-exposed surface of the protein. The third zone is comprised of residues conserved in either the Ser/Thr or Tyr kinases or in both, but which are not conserved between them. These are sandwiched between the hydrophobic core and the solvent-exposed surface. In addition to analyzing overall conservation in the kinase family, we have also looked at conservation of its substrate and ATP binding sites. The ATP site is highly conserved throughout the kinases, whereas the substrate binding site is more variable. The active site contains several positions which differ between the Ser/Thr and Tyr kinases and may be responsible for discriminating between hydroxyl bearing side chains. Using this information we propose a model for Tyr substrate binding to the catalytic domain of the epidermal growth factor receptor (EGFR).