Cells are equipped with an efficient quality control system to selectively eliminate abnormally folded and damaged proteins. Initially the cell tries to refold the unfolded proteins with the help of molecular chaperones, and failure to refold leads to their degradation by the ubiquitin proteasome system. But how this proteolytic machinery recognizes the abnormally folded proteins is poorly understood. Here, we report that E6-AP, a HECT domain family ubiquitin ligase implicated in Angelman syndrome, interacts with the substrate binding domain of Hsp70/Hsc70 chaperones and promotes the degradation of chaperone bound substrates. The expression of E6-AP was dramatically induced under a variety of stresses, and overexpression of E6-AP was found to protect against endoplasmic reticulum stress-induced cell death. The inhibition of proteasome function not only increases the expression of E6-AP but also causes its redistribution around microtubule-organizing center, a subcellular structure for the degradation of the cytoplasmic misfolded proteins. E6-AP is also recruited to aggresomes containing the cystic fibrosis transmembrane conductance regulator or expanded polyglutamine proteins. Finally, we demonstrate that E6-AP ubiquitinates misfolded luciferase that is bound by Hsp70. Our results suggest that E6-AP functions as a cellular quality control ubiquitin ligase and, therefore, can be implicated not only in the pathogenesis of Angelman syndrome but also in the biology of neurodegenerative disorders involving protein aggregation.