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

J Biol Chem. 2019 Mar 22;294(12):4608-4620. doi: 10.1074/jbc.RA118.004732. Epub 2019 Jan 18.


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.

Keywords: 3BP-2; ABI2; ABL tyrosine kinase; Src homology 3 domain (SH3 domain); X-ray crystallography; ligand binding; nuclear magnetic resonance (NMR); phosphotyrosine signaling; post translational modification (PTM); protein phosphorylation; small-angle X-ray scattering (SAXS).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Crystallography, X-Ray
  • Dimerization
  • Humans
  • Ligands
  • Nuclear Magnetic Resonance, Biomolecular
  • Phosphorylation
  • Protein Binding
  • Protein Conformation
  • Protein-Tyrosine Kinases / chemistry
  • Protein-Tyrosine Kinases / metabolism
  • Proto-Oncogene Proteins c-abl / chemistry
  • Proto-Oncogene Proteins c-abl / metabolism
  • Scattering, Small Angle
  • Tyrosine / metabolism*
  • src Homology Domains*


  • Ligands
  • Tyrosine
  • ARG tyrosine kinase
  • Protein-Tyrosine Kinases
  • ABL1 protein, human
  • Proto-Oncogene Proteins c-abl

Associated data

  • PDB/1QWE
  • PDB/4JJC
  • PDB/5NP2
  • PDB/5NP3
  • PDB/5NP5
  • PDB/1ABO