Allosteric signal propagation pathways of unphosphorylated RING-type E3 ubiquitin ligase c-Cbl

Ubiquitin serves as a tag to selectively label proteins for degradation. E1, E2, and E3 ligases are enzymes acting sequentially in the protein degradation cascade to transfer ubiquitin to the target protein to be degraded. c-Cbl (Casitas B-lineage lymphoma) is one of the RING-type E3 ligases that negatively regulates protein tyrosine kinase signal transduction. X-ray structures show that in the absence of E2, c-Cbl adopts a closed conformation, while the RING domain is partially open upon the substrate (Zap-70) bound to the tyrosine kinase–binding domain (TKBD) of c-Cbl. The substrate-binding is the first step of c-Cbl activation. The partial opening of the RING domain induced by the binding of Zap-70 to TKBD triggers the subsequent binding of the RING domain to E2 ligase. To investigate the allosteric signal transduction from the TKBD-Zap-70 binding site to the RING domain, mutual information has been employed to detect and quantify correlated motions from molecular dynamics trajectories of the protein-substrate complex. The optimal and suboptimal communication paths involving correlated motions have been determined. Two major allosteric signal propagation pathways have been first identified in our study; one path goes through the linker between TKBD and the RING domain whereas the other path bypasses the linker. This study would provide new insights into our understanding of the regulation of RING E3s.

Figure. Two major pathways of allosteric signal transduction from the substrate-binding site to the RING.