The E2 protein of papillomavirus is the key regulator of viral transcription and replication. Dimerization, which takes place via its conserved C-terminal DNA-binding domain (DBD), is critical for these functions. The presence and conservation of two histidines (H290 and H320) at or near the dimer interface suggests the importance of their roles in protein structure and stability that was explored by mutating them to neutral alanine. The H290A mutant but not the H320A mutant showed a significant change in the secondary as well as tertiary structure, as monitored by far- and near-UV circular dichroism and fluorescence. We show that the wild-type DBD was more stable than either of the two histidine mutants at pH 7.5 but that the order of stability changed with pH, where, at pH 4.5, the H290A mutant was most stable. Although H290 is important for pH dependence of the stability, it is not critical for dimerization or folding. The determination of pKa values for the solvent-exposed histidine residues shows that the surface properties of the protein change with pH, suggesting different interactions that can be made by the protein in response to cellular acidification. Moreover, identification of residues crucial for E2 stability will help in the design of modified proteins with desired characteristics.