This article presents structural insights into the functional mechanism of the ubiquitin ligase E6AP, which is involved in Angelman syndrome and Autism spectrum disorder, and is hijacked by high-risk HPV E6 to ubiquitinate p53, contributing to cancer development. The study reveals that E6AP exists as a monomer and E6AP/E6 complex as a dimer, with the α1-helix of E6AP transforming into a longer helical structure upon complex formation. This structural change facilitates the dimerization of E6AP/E6, enabling the attachment and detachment of substrates to the catalytic C-lobe of E6AP, thus promoting ubiquitin transfer. The findings, supported by mutagenesis analysis, suggest that the α1-helix controls the transition between the inactive monomer and active dimer of E6AP. The study also shows that the dimerization of the E6AP/E6 protomer is essential for p53 ubiquitination. Structural analysis of the E6AP/E6 complex reveals that the two protomers interact through the α1-helix and N-helix, with the C-lobe of E6AP interacting with E6. The dynamic nature of the E6AP/E6 complex allows for the proximity of the C-lobe to E2 for ubiquitin acceptance or to substrates for ubiquitin donation. The study further demonstrates that the E6AP/E6 complex undergoes conformational changes, with the C-lobe of E6AP swaying towards E6 or p53, leading to the transition from Det to Att conformations. The results highlight the importance of the α1-helix in mediating dimerization and function of E6AP, and how mutations in this region can affect E6AP activity. The study also shows that the E6AP/E6 complex can auto-ubiquitinate, and that the stability of the extended α1-helix is crucial for E6AP function. The findings provide a structural understanding of the physiological and pathophysiological mechanisms of E6AP function.This article presents structural insights into the functional mechanism of the ubiquitin ligase E6AP, which is involved in Angelman syndrome and Autism spectrum disorder, and is hijacked by high-risk HPV E6 to ubiquitinate p53, contributing to cancer development. The study reveals that E6AP exists as a monomer and E6AP/E6 complex as a dimer, with the α1-helix of E6AP transforming into a longer helical structure upon complex formation. This structural change facilitates the dimerization of E6AP/E6, enabling the attachment and detachment of substrates to the catalytic C-lobe of E6AP, thus promoting ubiquitin transfer. The findings, supported by mutagenesis analysis, suggest that the α1-helix controls the transition between the inactive monomer and active dimer of E6AP. The study also shows that the dimerization of the E6AP/E6 protomer is essential for p53 ubiquitination. Structural analysis of the E6AP/E6 complex reveals that the two protomers interact through the α1-helix and N-helix, with the C-lobe of E6AP interacting with E6. The dynamic nature of the E6AP/E6 complex allows for the proximity of the C-lobe to E2 for ubiquitin acceptance or to substrates for ubiquitin donation. The study further demonstrates that the E6AP/E6 complex undergoes conformational changes, with the C-lobe of E6AP swaying towards E6 or p53, leading to the transition from Det to Att conformations. The results highlight the importance of the α1-helix in mediating dimerization and function of E6AP, and how mutations in this region can affect E6AP activity. The study also shows that the E6AP/E6 complex can auto-ubiquitinate, and that the stability of the extended α1-helix is crucial for E6AP function. The findings provide a structural understanding of the physiological and pathophysiological mechanisms of E6AP function.