The pathogenic T42A mutation in SHP2 rewires interaction specificity and enhances signaling.

Mutations in the tyrosine phosphatase SHP2 are associated with various human diseases. Most of these mutations increase the basal catalytic activity of SHP2 by disrupting auto-inhibitory interactions between its phosphatase domain and N-terminal SH2 (phosphotyrosine recognition) domain. By contrast, several other disease-associated mutations located in the ligand-binding pockets of the N- or C-terminal SH2 domains do not increase basal activity and likely exert their pathogenicity through alternative mechanisms. We lack a molecular understanding of how these SH2 mutations impact SHP2 structure, activity, and signaling. Here, we characterize five SHP2 SH2 domain ligand-binding pocket mutants through a combination of high-throughput biochemical screens, biophysical and biochemical measurements, molecular dynamics simulations, and cellular assays. We show that, while several of these mutants alter binding affinity to phosphorylation sites, the T42A mutation in the N-SH2 domain is unique in that it also alters ligand-binding specificity. The functional consequence of this altered specificity is that the T42A mutant has biased sensitivity toward a subset of activating ligands. Our study highlights an example of a nuanced mechanism of action for a disease-associated mutation, characterized by a change in protein-protein interaction specificity that alters enzyme activation.