The protein Kinase A (PKA) pathway was found to selectively regulate the function of oncogenic but not non-oncogenic E6 proteins. High risk E6 proteins are phosphorylated at their Dlg/PDZ binding motif at the C-terminus by a PKA like activity. This PKA and PDZ binding module is found only for human PV, is strictly conserved in all the transforming HPVs and is absent in all the low risk HPV types. We present evidence of a conditional regulation of E6 induced degradation of Dlg. HPV18E6 positive but not HPV negative keratinocytes exhibit increased Dlg steady state levels under conditions of high PKA activity, with a concomitant increase in the presence of Dlg at tight junctions. In vitro binding experiments show that E6 phosphorylation by PKA reduces its binding to Dlg and molecular modelling can explain this observation in a structural context. E6 dependent degradation of Dlg in cells with high PKA levels is inhibited and this is dependent on phosphorylation of the PDZ binding site in E6. In contrast, the degradation of p53 induced by E6 is not affected by PKA. We propose a differential regulation of E6 for the ubiquitin mediated degradation of specific E6 target proteins.