The E2 proteins of papillomaviruses are able to transactivate the viral enhancers by interacting with the sequence ACCGN4CGGT found in all papillomavirus long control regions. Analysis of the alignment of the amino acid sequences of 10 E2 proteins reveals three distinct regions: two partially conserved domains at the N and C termini of the proteins and a region variable in size and sequence in the middle. A computer prediction of the secondary structure of the 10 sequences outlines interesting conserved features, including two long amphiphilic alpha helices at the N terminus. To analyse the respective roles of the different segments of these proteins, we constructed a set of in-frame deletion and insertion mutations in the E2 coding sequences of the bovine papillomavirus type 1 (BPV1) and cottontail rabbit papillomavirus (CRPV). The test of their capacity to trans-activate or repress different viral constructs shows that the C-terminal domain of the E2 proteins is involved exclusively in DNA binding whereas the N-terminal domain is probably required for interaction with other components of the transcriptional machinery. The inner variable domain may confer flexibility to the protein such that it will facilitate contacts of the two others with their respective targets.