Structural insights into the tyrosine phosphorylation–mediated inhibition of SH3 domain–ligand interactions

• Published in: The Journal of biological chemistry Vol. 294; no. 12; pp. 4608 - 4620
• Main Authors: Merő, Balázs, Radnai, László, Gógl, Gergő, Tőke, Orsolya, Leveles, Ibolya, Koprivanacz, Kitti, Szeder, Bálint, Dülk, Metta, Kudlik, Gyöngyi, Vas, Virág, Cserkaszky, Anna, Sipeki, Szabolcs, Nyitray, László, Vértessy, Beáta G., Buday, László
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 22.03.2019; American Society for Biochemistry and Molecular Biology
• Subjects: 3BP-2; ABI2; ABL tyrosine kinase; Amino Acid Sequence; Crystallography, X-Ray; Dimerization; Humans; ligand binding; Ligands; nuclear magnetic resonance (NMR); Nuclear Magnetic Resonance, Biomolecular; Phosphorylation; phosphotyrosine signaling; post translational modification (PTM); Protein Binding; Protein Conformation; protein phosphorylation; Protein-Tyrosine Kinases - chemistry; Protein-Tyrosine Kinases - metabolism; Proto-Oncogene Proteins c-abl - chemistry; Proto-Oncogene Proteins c-abl - metabolism; Scattering, Small Angle; Signal Transduction; small-angle X-ray scattering (SAXS); Src homology 3 domain (SH3 domain); src Homology Domains; Tyrosine - metabolism; X-ray crystallography; X-ray crystallography; phosphotyrosine signaling; ABL tyrosine kinase; ABI2; small-angle X-ray scattering (SAXS); nuclear magnetic resonance (NMR); post translational modification (PTM); Src homology 3 domain (SH3 domain); 3BP-2; protein phosphorylation; ligand binding
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.RA118.004732

Src homology 3 (SH3) domains bind proline-rich linear motifs in eukaryotes. By mediating inter- and intramolecular interactions, they regulate the functions of many proteins involved in a wide variety of signal transduction pathways. Phosphorylation at different tyrosine residues in SH3 domains has been reported previously. In several cases, the functional consequences have also been investigated. However, a full understanding of the effects of tyrosine phosphorylation on the ligand interactions and cellular functions of SH3 domains requires detailed structural, atomic-resolution studies along with biochemical and biophysical analyses. Here, we present the first crystal structures of tyrosine-phosphorylated human SH3 domains derived from the Abelson-family kinases ABL1 and ABL2 at 1.6 and 1.4 Å resolutions, respectively. The structures revealed that simultaneous phosphorylation of Tyr89 and Tyr134 in ABL1 or the homologous residues Tyr116 and Tyr161 in ABL2 induces only minor structural perturbations. Instead, the phosphate groups sterically blocked the ligand-binding grooves, thereby strongly inhibiting the interaction with proline-rich peptide ligands. Although some crystal contact surfaces involving phosphotyrosines suggested the possibility of tyrosine phosphorylation–induced dimerization, we excluded this possibility by using small-angle X-ray scattering (SAXS), dynamic light scattering (DLS), and NMR relaxation analyses. Extensive analysis of relevant databases and literature revealed not only that the residues phosphorylated in our model systems are well-conserved in other human SH3 domains, but that the corresponding tyrosines are known phosphorylation sites in vivo in many cases. We conclude that tyrosine phosphorylation might be a mechanism involved in the regulation of the human SH3 interactome.