Homing in: Mechanisms of Substrate Targeting by Protein Kinases

Protein phosphorylation is the most common reversible post-translational modification in eukaryotes. Humans have over 500 protein kinases, of which more than a dozen are established targets for anticancer drugs. All kinases share a structurally similar catalytic domain, yet each one is uniquely positioned within signaling networks controlling essentially all aspects of cell behavior. Kinases are distinguished from one another based on their modes of regulation and their substrate repertoires. Coupling specific inputs to the proper signaling outputs requires that kinases phosphorylate a limited number of sites to the exclusion of hundreds of thousands of off-target phosphorylation sites. Here, we review recent progress in understanding mechanisms of kinase substrate specificity and how they function to shape cellular signaling networks. Knowledge of kinase phosphorylation site motifs has expanded to include noncanonical binding modes and the targeting of folded, structural motifs. Additional kinase–substrate interactions outside the catalytic cleft, such as MAPK docking sites and GPCR kinase recruitment sites, have recently been elaborated. Understanding differences in substrate quality provides insights into the drug sensitivity and timing of phosphorylation events. Basic principles underlying the evolution of phosphorylation networks shed light on understanding how mutations in kinases and their substrates perturb signaling networks to promote disease.