Biochemical and Structural characterization of Noonan syndrome-causing mutations affecting SHP-2’s phoshotyrosyl-binding pockets.

Missense mutations in PTPN11 cause Noonan syndrome (NS), a genetically heterogeneous developmental disorder with a pleiomorphic phenotype. PTPN11 encodes SHP-2, an SH2 domain-containing protein tyrosine phosphatase that relays signals from activated cell-surface receptors to RAS. NS-causing mutations promote SHP-2’s gain of function by either destabilizing its catalytically inactive conformation or increasing the affinity and/or specificity of the SH2 domains for phosphotyrosyl ligands. While the identity of substitution does not seem to be critical in some cases, suggesting a crucial role in SHP-2’s function for the residue being replaced, an invariant amino acid change is frequently observed, indicating a specific role for the introduced residue. Here, we characterized functionally and structurally two invariant NS-causing mutations, T42A and E139D, affecting residues placed in the N- and C-SH2 pockets which mediate SHP-2 binding to phosphotyrosyl-containing signaling partners. By analyzing in vitro biochemical behavior (basal and ligand-stimulated phosphatase activity, and ligand-binding properties assayed by surface plasmon resonance) of all possible substitutions arising from a single base change affecting codons 42 and 139, we show that T42A and E139D SHP-2 proteins are the only mutants exhibiting a significant increase in ligand-induced phosphatase activity and enhanced phophopeptide binding affinity. Molecular dynamics simulations performed on selected mutants provide structural insights of the effects generated by individual mutations on protein function. In conclusion, this study provides functional explanation for the invariant occurrence of the T42A and E139D mutaions in NS as well as the molecular mechanism of their pathogenicity.