The E2 protein of papillomaviruses is a site-specific DNA binding nuclear protein. It functions as the primary replication origin recognition protein and assists in the assembly of the preinitiation complex. It also helps regulate transcription from the native viral promoter. The E2 protein consists of an amino-terminal (N) trans-acting domain, a central hinge (H) domain, and a carboxyl-terminal (C) protein dimerization and DNA binding domain. The hinge is highly divergent among papillomaviruses, and little is known about its functions. We fused the enhanced green fluorescent protein (GFP) with the full-length human papillomavirus type 11 (HPV-11) E2 protein and showed that the resultant fusion, called gfpE2, maintained transcription and replication functions of the wild-type protein and formed similar subnuclear foci. Using a series of GFP fusion proteins, we showed that the hinge conferred strong nuclear localization, whereas the N or C domain was present in both cytoplasm and nucleus. Biochemical fractionation demonstrated that the N domain and hinge, but not the C domain, independently associated with the nuclear matrix. Mutational analyses showed that a cluster of basic amino acid residues, which is conserved among many mucosotropic papillomaviruses, was required for efficient nuclear localization and nuclear matrix association. This mutation no longer repressed the HPV-11 upstream regulatory region-controlled reporter expression. However, a very small fraction of this mutant colocalized with E1 in the nucleus, perhaps by a piggyback mechanism, and was able to support transient replication. We propose that the hinge is critical for the diverse regulatory functions of the HPV-11 E2 protein during mRNA transcription and viral DNA replication.The papillomavirus E2 protein is a multifunctional nuclear phosphoprotein with a molecular mass of approximately 40 kDa. With high affinity and specificity, it functions as a dimer, binding to multiple copies of a consensus E2 binding site (E2BS), ACCN 6 GGT, located in the upstream regulatory region (URR) and regulating both viral DNA replication and mRNA transcription from the viral E6 promoter located immediately upstream of the E6 gene. The E2 protein is the primary origin recognition protein and helps recruit the viral replication initiator E1 protein (8,30,40,55,64,66,70). It also plays a role in the assembly of the preinitiation complex (39; K.-Y. Lee, T. R. Broker, and L. T. Chow, unpublished data). In vitro, E2 is able to exclude nucleosome formation on the origin, which would otherwise inhibit the initiation of DNA replication (36). Furthermore, E2 modulates the native human papillomavirus (HPV) URR-E6 promoter or a surrogate promoter linked to the URR or to one or more copies of synthetic E2BS (16-18, 26, 59, 62, 63). The bovine papillomavirus type 1 (BPV-1) E2 protein tethers the BPV-1 DNA to mitotic chromosomes, ensuring plasmid segregation during mitosis (28,35,58). Moreover, the BPV-1 E2 has been postulated to play a role in virion morphogenesis (14).The fu...