4F59

Triple mutant Src SH2 domain

Summary for 4F59

• Entry DOI: 10.2210/pdb4f59/pdb
• Related: 4F5A 4F5B
• Descriptor: Proto-oncogene tyrosine-protein kinase Src (2 entities in total)
• Functional Keywords: sh2 domain, cell signalling, phosphotyrosine binding, protein binding
• Biological source: Homo sapiens (human)
• Cellular location: Cell membrane: P12931
• Total number of polymer chains: 1
• Total formula weight: 12699.32

Authors

Kaneko, T.,Huang, H.,Cao, X.,Li, C.,Voss, C.,Sidhu, S.S.,Li, S.S. (deposition date: 2012-05-12, release date: 2012-10-03, Last modification date: 2024-02-28)

Primary citation

Kaneko, T.,Huang, H.,Cao, X.,Li, X.,Li, C.,Voss, C.,Sidhu, S.S.,Li, S.S.
Superbinder SH2 Domains Act as Antagonists of Cell Signaling.
Sci.Signal., 5:ra68-ra68, 2012

PubMed Abstract: Protein-ligand interactions mediated by modular domains, which often play important roles in regulating cellular functions, are generally of moderate affinities. We examined the Src homology 2 (SH2) domain, a modular domain that recognizes phosphorylated tyrosine (pTyr) residues, to investigate how the binding affinity of a modular domain for its ligand influences the structure and cellular function of the protein. We used the phage display method to perform directed evolution of the pTyr-binding residues in the SH2 domain of the tyrosine kinase Fyn and identified three amino acid substitutions that critically affected binding. We generated three SH2 domain triple-point mutants that were "superbinders" with much higher affinities for pTyr-containing peptides than the natural domain. Crystallographic analysis of one of these superbinders revealed that the superbinder SH2 domain recognized the pTyr moiety in a bipartite binding mode: A hydrophobic surface encompassed the phenyl ring, and a positively charged site engaged the phosphate. When expressed in mammalian cells, the superbinder SH2 domains blocked epidermal growth factor receptor signaling and inhibited anchorage-independent cell proliferation, suggesting that pTyr superbinders might be explored for therapeutic applications and useful as biological research tools. Although the SH2 domain fold can support much higher affinity for its ligand than is observed in nature, our results suggest that natural SH2 domains are not optimized for ligand binding but for specificity and flexibility, which are likely properties important for their function in signaling and regulatory processes.

PubMed: 23012655
DOI: 10.1126/scisignal.2003021

Experimental method

X-RAY DIFFRACTION (1.71 Å)