3BUW

Crystal structure of c-Cbl-TKB domain complexed with its binding motif in Syk

Summary for 3BUW

• Entry DOI: 10.2210/pdb3buw/pdb
• Related: 3BUM 3BUN 3BUO 3BUX
• Descriptor: 13-meric peptide from Tyrosine-protein kinase SYK, E3 ubiquitin-protein ligase CBL (3 entities in total)
• Functional Keywords: cbl, tkb, ligase, signal transduction, proto-oncogene, complex, alternative splicing, atp-binding, host-virus interaction, kinase, nucleotide-binding, phosphoprotein, polymorphism, sh2 domain, transferase, tyrosine-protein kinase, ubl conjugation, calcium, cytoplasm, metal-binding, ubl conjugation pathway, zinc, zinc-finger, ligase-signaling protein complex, ligase/signaling protein
• Biological source: Homo sapiens (human); More
• Cellular location: Cell membrane : P43405; Cytoplasm: P22681
• Total number of polymer chains: 4
• Total formula weight: 79471.31

Authors

Ng, C.,Jackson, R.A.,Buschdorf, J.P.,Sun, Q.,Guy, G.R.,Sivaraman, J. (deposition date: 2008-01-03, release date: 2008-02-26, Last modification date: 2024-11-13)

Primary citation

Ng, C.,Jackson, R.A.,Buschdorf, J.P.,Sun, Q.,Guy, G.R.,Sivaraman, J.
Structural basis for a novel intrapeptidyl H-bond and reverse binding of c-Cbl-TKB domain substrates
Embo J., 27:804-816, 2008

PubMed Abstract: The c-Cbl tyrosine kinase binding domain (Cbl-TKB), essentially an 'embedded' SH2 domain, has a critical role in targeting proteins for ubiquitination. To address how this domain can bind to disparate recognition mofits and to determine whether this results in variations in substrate-binding affinity, we compared crystal structures of the Cbl-TKB domain complexed with phosphorylated peptides of Sprouty2, Sprouty4, epidermal growth factor receptor, Syk, and c-Met receptors and validated the binding with point-mutational analyses using full-length proteins. An obligatory, intrapeptidyl H-bond between the phosphotyrosine and the conserved asparagine or adjacent arginine is essential for binding and orients the peptide into a positively charged pocket on c-Cbl. Surprisingly, c-Met bound to Cbl in the reverse direction, which is unprecedented for SH2 domain binding. The necessity of this intrapeptidyl H-bond was confirmed with isothermal titration calorimetry experiments that also showed Sprouty2 to have the highest binding affinity to c-Cbl; this may enable the selective sequestration of c-Cbl from other target proteins.

PubMed: 18273061
DOI: 10.1038/emboj.2008.18

Experimental method

X-RAY DIFFRACTION (1.45 Å)