4ZNX

Crystal structure of the Fyn-SH3 domain in complex with the high affinity peptide APP12

Summary for 4ZNX

• Entry DOI: 10.2210/pdb4znx/pdb
• Related: 3UA6 3UA7 4EIK
• Descriptor: Tyrosine-protein kinase Fyn, APP12 (3 entities in total)
• Functional Keywords: beta shandwich, signaling protein
• Biological source: Homo sapiens (Human); More
• Cellular location: Cytoplasm: P06241
• Total number of polymer chains: 8
• Total formula weight: 32039.45

Authors

Camara-Artigas, A. (deposition date: 2015-05-05, release date: 2016-06-29, Last modification date: 2024-01-10)

Primary citation

Camara-Artigas, A.,Ortiz-Salmeron, E.,Andujar-Sanchez, M.,Bacarizo, J.,Martin-Garcia, J.M.
The role of water molecules in the binding of class I and II peptides to the SH3 domain of the Fyn tyrosine kinase.
Acta Crystallogr.,Sect.F, 72:707-712, 2016

PubMed Abstract: Interactions of proline-rich motifs with SH3 domains are present in signal transduction and other important cell processes. Analysis of structural and thermodynamic data suggest a relevant role of water molecules in these protein-protein interactions. To determine whether or not the SH3 domain of the Fyn tyrosine kinase shows the same behaviour, the crystal structures of its complexes with two high-affinity synthetic peptides, VSL12 and APP12, which are class I and II peptides, respectively, have been solved. In the class I complexes two water molecules were found at the binding interface that were not present in the class II complexes. The structures suggest a role of these water molecules in facilitating conformational changes in the SH3 domain to allow the binding of the class I or II peptides. In the third binding pocket these changes modify the cation-π and salt-bridge interactions that determine the affinity of the binding. Comparison of the water molecules involved in the binding of the peptides with previous reported hydration spots suggests a different pattern for the SH3 domains of the Src tyrosine kinase family.

PubMed: 27599862
DOI: 10.1107/S2053230X16012310

Experimental method

X-RAY DIFFRACTION (2.1 Å)