Hierarchical Organization Endows the Kinase Domain with Regulatory Plasticity

Abstract

The functional diversity of kinases enables specificity in cellular signal transduction. Yet how more than 500 members of the human kinome specifically receive regulatory inputs and convey information to appropriate substrates-all while using the common signaling output of phosphorylation-remains enigmatic. Here, we perform statistical co-evolution analysis, mutational scanning, and quantitative live-cell assays to reveal a hierarchical organization of the kinase domain that facilitates the orthogonal evolution of regulatory inputs and substrate outputs while maintaining catalytic function. We find that three quasi-independent "sectors"-groups of evolutionarily coupled residues-represent functional units in the kinase domain that encode for catalytic activity, substrate specificity, and regulation. Sector positions impact both disease and pharmacology: the catalytic sector is significantly enriched for somatic cancer mutations, and residues in the regulatory sector interact with allosteric kinase inhibitors. We propose that this functional architecture endows the kinase domain with inherent regulatory plasticity.

Multi-kinase control of environmental stress responsive transcription

“…The kinase domain evolved a highly plastic structure that enables it to maintain its core catalytic function (transferring a phosphate group from ATP onto a substrate protein) while radiating into a family that includes > 500 members encoded in human cells, each receiving a specific set of inputs and relaying information to a distinct set of substrates [43]. Like wires in electronic devices, kinases transmit information using a common currency-phosphorylationthat enables them form serial and parallel relays.…”

Comprehensive profiling of the STE20 kinase family defines features essential for selective substrate targeting and signaling output

“…Molecular dynamics simulations, for example, revealed a key specificity-determining residue in nonreceptor tyrosine kinases that was not evident from cocrystal structures with peptides [59]. Furthermore, computational analyses have suggested that residues not directly contacting the substrate can contribute to specificity [60, 61]. Because our mutants often had substantially decreased catalytic activity, these other residues may function to maintain activity in the presence of particular residues in the catalytic cleft.…”

Mass Spectrometry-Based Discovery of <i>in vitro</i> Kinome Substrates

“…In addition to phosphoacceptor preference, certain amino acids in the kinase domain are highly correlated with substrate speci city 67,68) and regulatory functions. 69) A computational tool was developed to predict which residues within the kinase domain contribute to substrate speci city based on a position-speci c scoring matrix obtained by a position scanning peptide library. 68)…”