DNA replication of papillomaviruses requires the viral El and E2 proteins. These proteins bind cooperatively to the viral origin of replication (ori), which contains binding sites for both proteins, forming an E1-E2-ori complex which is essential for initiation of DNA replication. To map the domains in E2 that are involved in the interaction with El, we have used chimeric bovine papillomavirus (BPV)/human papillomavirus type 11 (HPV-11) E2 proteins, The results from this study show that both the DNA binding domain and the transactivation domain from BPV E2 independently can interact with BPV E1. However, the roles of these two interactions are different: the interaction between El and the activation domain of E2 is necessary and sufficient for cooperativity in binding and for DNA replication; the interaction between Fl and the DNA binding domain of E2 is required only when the binding sites for El and E2 are adjacent to each other, and the function of this interaction appears to be to facilitate the interaction between El and the transactivation domain of E2. These results indicate that the cooperative binding of El and E2 to the BPV ori takes place via a novel two-stage mechanism where one interaction serves as a trigger for the formation of the second, productive, interaction between the two proteins.