3EG1

Crystal structure of the N114Q mutant of ABL-SH3 domain complexed with a designed high-affinity peptide ligand: implications for SH3-ligand interactions

Summary for 3EG1

• Entry DOI: 10.2210/pdb3eg1/pdb
• Related: 1BBZ 2O88 3EG0 3EG2 3EG3
• Descriptor: Proto-oncogene tyrosine-protein kinase ABL1, p41 peptide, SULFATE ION, ... (4 entities in total)
• Functional Keywords: beta, sh3 domain, atp-binding, cell adhesion, cytoskeleton, kinase, lipoprotein, magnesium, manganese, metal-binding, myristate, nucleotide-binding, nucleus, phosphoprotein, proto-oncogene, sh2 domain, transferase, tyrosine-protein kinase, signaling protein, transferase-signaling protein complex, transferase/signaling protein
• Biological source: Homo sapiens (human); More
• Cellular location: Cytoplasm, cytoskeleton. Isoform IB: Nucleus membrane; Lipid-anchor: P00519
• Total number of polymer chains: 4
• Total formula weight: 16309.86

Authors

Camara-Artigas, A. (deposition date: 2008-09-10, release date: 2009-09-15, Last modification date: 2024-10-16)

Primary citation

Palencia, A.,Camara-Artigas, A.,Pisabarro, M.T.,Martinez, J.C.,Luque, I.
Role of interfacial water molecules in proline-rich ligand recognition by the Src homology 3 domain of Abl.
J.Biol.Chem., 285:2823-2833, 2010

PubMed Abstract: The interaction of Abl-Src homology 3 domain (SH3) with the high affinity peptide p41 is the most notable example of the inconsistency existing between the currently accepted description of SH3 complexes and their binding thermodynamic signature. We had previously hypothesized that the presence of interfacial water molecules is partially responsible for this thermodynamic behavior. We present here a thermodynamic, structural, and molecular dynamics simulation study of the interaction of p41 with Abl-SH3 and a set of mutants designed to alter the water-mediated interaction network. Our results provide a detailed description of the dynamic properties of the interfacial water molecules and a molecular interpretation of the thermodynamic effects elicited by the mutations in terms of the modulation of the water-mediated hydrogen bond network. In the light of these results, a new dual binding mechanism is proposed that provides a better description of proline-rich ligand recognition by Abl-SH3 and that has important implications for rational design.

PubMed: 19906645
DOI: 10.1074/jbc.M109.048033

Experimental method

X-RAY DIFFRACTION (1.85 Å)