Recently, we showed that the ubiquitin ligase E6AP stabilizes β-catenin and activates its transcriptional activity. These activities were enhanced by the human papillomavirus (HPV) E6 protein. In the present study, we explored the function of E6AP, which increases β-catenin stabilization and transcriptional activation. Here, we report that E6AP interacts with β-catenin and mediates its nonproteolytic ubiquitylation, as evidenced in transiently transfected cell-based and in vitro reconstitution ubiquitylation assays. Overexpression of E6AP increased β-catenin polyubiquitylation and, consistent with that, knockdown or knock-out of E6AP expression reduced β-catenin polyubiquitylation. The ubiquitylation of β-catenin by E6AP was dependent on its E3 ubiquitin ligase activity, but it was proteasome-independent and did not require HPV-E6, phosphorylation of β-catenin by glycogen synthase kinase 3β (GSK3β) or activity of the β-catenin 'destruction complex'. We also show that transcriptional activation of β-catenin by E6AP is coupled with β-catenin protein stabilization, but not its ubiquitylation. In contrast to β-catenin ubiquitylation, β-catenin protein stability and its transcriptional activity were absolutely dependent on the activity of the destruction complex and phosphorylation by GSK3β. Collectively, our data uncover a dual role for E6AP in the regulation of β-catenin ubiquitylation, stability and transcriptional activity, with HPV-E6 enhancing only part of E6AP activities.