PDBsum entry 4f5b

Protein binding

PDB id: 4f5b

Contents

Protein chain

108 a.a.

Ligands

PTR

Waters ×123

PDB id:

4f5b

Name:

Protein binding

Title:

Triple mutant src sh2 domain bound to phosphotyrosine

Structure:

Proto-oncogene tyrosine-protein kinase src. Chain: a. Fragment: sh2 domain. Synonym: proto-oncogenE C-src, pp60c-src, p60-src. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: src, src1. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.57Å R-factor: 0.200 R-free: 0.230

Authors:

T.Kaneko,H.Huang,X.Cao,C.Li,C.Voss,S.S.Sidhu,S.S.Li

Key ref:

T.Kaneko et al. (2012). Superbinder SH2 domains act as antagonists of cell signaling. Sci Signal, 5, ra68. PubMed id: 23012655

Date:

12-May-12 Release date: 03-Oct-12

Protein chain

P12931  (SRC_HUMAN) -  Proto-oncogene tyrosine-protein kinase Src from Homo sapiens

Seq: 536 a.a.

Struc: 108 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.7.10.2 - non-specific protein-tyrosine kinase.
• Reaction: L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] + ADP + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

Sci Signal 5:ra68 (2012)

PubMed id: 23012655

Superbinder SH2 domains act as antagonists of cell signaling.

T.Kaneko, H.Huang, X.Cao, X.Li, C.Li, C.Voss, S.S.Sidhu, S.S.Li.

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.