3BUX

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

Summary for 3BUX

• Entry DOI: 10.2210/pdb3bux/pdb
• Related: 3BUM 3BUN 3BUO 3BUW
• Descriptor: 13-meric peptide from Hepatocyte growth factor receptor, E3 ubiquitin-protein ligase CBL (3 entities in total)
• Functional Keywords: cbl, tkb, ligase, signal transduction, proto-oncogene, complex, atp-binding, glycoprotein, kinase, membrane, nucleotide-binding, phosphoprotein, receptor, transferase, transmembrane, tyrosine-protein kinase, calcium, cytoplasm, metal-binding, sh2 domain, ubl conjugation pathway, zinc, zinc-finger, ligase-signaling protein complex, ligase/signaling protein
• Biological source: Homo sapiens (human); More
• Cellular location: Membrane; Single-pass type I membrane protein. Isoform 3: Secreted: P08581; Cytoplasm: P22681
• Total number of polymer chains: 4
• Total formula weight: 79575.25

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: 2024-10-16)

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 (1.35 Å)