IN LAYMAN TERMS: Substrate specificity is a function of availability (exposed surfaces)....I presume each of the ligases act in concert to modify the conformer to an opitmal exposed substrate binding area for other set to act on......This is known in the case of multi tier regulation of signal transduction...

Thanks for your comments dear Jacqueline and Fazil. It is not the mechanism or E1, E2 and E3 complex I mean, It is just E3 ligases and their binding site. We have studied the regulation of a protein through degradation and I can say that we have found that two different E3 ligases (maybe even 3) can bind the same region of the protein, and this binding is regulated by phosphorylation of a specific site. The binding of these E3 ligases can be completely independent of each other because the different signaling pathway. Now it sound more complicated than before, because the binding of all these (2-3) E3-ligases are dependent on the same P-site. If it was different p-sites then it was easier to understand. I hope you understand me now the difficulty and the confusing question..

Thanks for making it more clear Fuad, does the 3 different ligases belong to the same catalytic group? Or is there any difference in catalysis of enzymatic reaction even though the recognition and binding site are same?

Hi Fazil, 2 of the E3-Ligases belongs to Cullin-based E3-ligases and one to HECT-based E3-ligases. According to binding site , both Cullin based Ligases are dependent to the same p-Site and one of them can binds to 2 different region meanwhile the third HECT E3Ligase is dependent to another p-site which is very near but still bind to the same region as Cullin-based Ligase. As you see it is complicated because the mechanisms are still unclear and we still work on that.