The Protein Binding Domains of Protein Kinases

Protein kinases are, first and foremost, catalysts that promote the transfer of a phosphoryl group from ATP to the acceptor hydroxyl moiety of serine, threonine, and/or tyrosine. The serine, threonine, and tyrosine residues must be embedded within the proper amino acid sequence in order to be recognized by a given protein kinase, a fact exemplified by the large number of synthetic peptide-based substrates that have been devised for scores of protein kinases. Of all the protein-binding domains contained within protein kinases, the active site region displays the greatest diversity in terms of sequence recognition. However, since all members of the protein kinase family utilize the same phosphoryl donor (ATP) and acceptors (serine, threonine, tyrosine), it is perhaps not too surprising that the conformation of the active site region is remarkably well-conserved (Johnson et al. 1998; Huse and Kuriyan 2002). The "protein kinase fold" is composed of two separate lobes, commonly designated as the N- and C-terminal lobes. The former is the smaller of the two and is composed of five antiparallel b-strands and a single a-helix. The larger C-terminal lobe is primarily a-helical in structure. ATP resides in a cleft that lies at the interface between the N- and C-terminal lobes. By contrast, the peptide/protein phosphoryl acceptor is primarily associated with the C-terminal lobe. The catalytic domain of protein kinases can assume active and inactive conformational states. The lobes in the former migrate toward one another, thereby closing the active site and promoting catalysis.

Protein kinases are commonly differentiated on the basis of their preferred phosphoryl acceptor group on the protein substrate: either the aliphatic hydroxyl moieties of serine and threonine ("serine/threonine protein kinases") or the aromatic phenol of the tyrosine residue ("tyrosine protein kinases"). A few protein kinases display the property of "dual specificity" in terms of their ability to recognize and phosphorylate both aliphatic and aromatic alcohols on peptides or proteins in vitro (fewer still display this property in living cells) (Dhanasekaran and Premkumar Reddy 1998; Marin et al. 1999). However, in a very strict sense, the segregation of protein kinases into these separate camps most likely has less to do with the protein kinases themselves and more to do with the fact that the genetic code is limited to only 20 different amino acids. For example, PKA, a well-known serine/threo-nine-specific protein kinase, phosphorylates appropriately designed aromatic alcohols (e.g., 1-3) (Lee et al. 1994).

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