Hierarchical organization endows the kinase domain with regulatory plasticity

The functional diversity of kinases enables specificity in cellular signal transduction. Yet general rules for how the kinase domain allows the more than 500 members of the human kinome to receive specific regulatory inputs and convey information to appropriate substrates - all while using the common signaling currency of phosphorylation - remain enigmatic. Here, using co-evolution analysis and quantitative live-cell assays, we reveal a deep hierarchical organization of the kinase domain that facilitates the orthogonal evolution of regulatory inputs and substrate outputs while maintaining catalytic function. Three quasi-independent functional units in the kinase domain (known as protein sectors) encode for catalysis, substrate specificity and regulation, and these distinct subdomains are differentially exploited by somatic cancer mutations and harnessed by allosteric inhibitors. We propose that this functional architecture endows the kinase domain with inherent regulatory plasticity.