Human and animal papillomavirus DNA replicates as multicopy nuclear plasmids. Replication requires two viral proteins, the origin-recognition protein E2 and the replicative DNA helicase E1. Using genetic, biochemical, and immunofluorescence assays, we demonstrated that efficient nuclear import of the human papillomavirus (HPV) type 11 E1 protein depends on a codominant bipartite nuclear localization sequence (NLS) and on phosphorylation of the serine residues S89 and S93 by the mitogen-activated protein kinases (MAPKs), extracellular signal-regulated kinase, and c-Jun N-terminal protein kinase. The NLS and the MAPK substrates are located within a 50-amino-acid-long peptide near the amino terminus, previously designated the localization regulatory region (LRR). The downstream NLS overlaps the cyclin-binding motif RRL, which is necessary for phosphorylation by the cyclin-dependent kinases to inactivate a dominant nuclear export sequence, also in the LRR. Alanine mutations of the MAPK substrates significantly impaired nuclear import, whereas phosphomimetic mutations partially restored nuclear import. We further identified two MAPK docking motifs near the C terminus of E1 that are conserved among E1 proteins of many HPVs and bovine papillomavirus type 1. Mutations of these MAPK docking motifs or addition of specific MAPK inhibitors significantly reduced nuclear import. Interestingly, a fraction of the NLS-minus E1 protein was cotransported with the E2 protein into the nucleus and supported transient viral DNA replication. In contrast, E1 proteins mutated in the MAPK docking motifs were completely inactive in transient replication, an indication that additional properties were adversely affected by those changes.Infections by human papillomaviruses (HPVs) can cause benign, hyperproliferative lesions of cutaneous or mucosal epithelium. The virus has a double-stranded circular DNA genome approximately 7,900 bp in length, which replicates as extrachromosomal nuclear plasmids. A low copy number of the viral DNA is maintained in the cycling basal and parabasal keratinocytes of squamous epithelium. Viral DNA amplification to produce progeny virions occurs only in postmitotic, suprabasal cells undergoing terminal differentiation (for a review, see reference 15). Initiation of replication from the origin (ori) of various HPV genotypes and bovine papillomavirus type 1 (BPV-1) depends on the virus-encoded ori binding protein E2 and the replicative DNA helicase E1 (for reviews, see references 16 and 63). The ori consists of several E2 protein binding sites flanking a cluster of E1 protein binding sites. The structures and functions of the E1 and E2 proteins of human and animal papillomaviruses are largely conserved, but significant differences are also noted. In brief, the 42-kDa E2 protein binds as dimers to the palindromic ori sequences, ACCGNNNNCGGT, and recruits the 70-kDa E1 protein via an interaction between the carboxyl terminus of E1 and the amino terminus of E2 (16). E1 then assembles into a dihexameric helicase (28,44...