title: Mapping of Functional Subdomains in the Terminal Protein Domain of Hepatitis B Virus Polymerase.
abstract: Hepatitis B virus (HBV) encodes a multifunction reverse transcriptase or polymerase (P), which is composed of several domains. The terminal protein (TP) domain is unique to HBV and related hepadnaviruses and is required for specifically binding to the viral pregenomic RNA (pgRNA). Subsequently, the TP domain is necessary for pgRNA packaging into viral nucleocapsids and the initiation of viral reverse transcription for conversion of the pgRNA to viral DNA. Uniquely, the HBV P protein initiates reverse transcription via a protein priming mechanism using the TP domain as a primer. No structural homologs or high-resolution structure exists for the TP domain. Secondary structure prediction identified three disordered loops in TP with highly conserved sequences. A meta-analysis of mutagenesis studies indicated these predicted loops are almost exclusively where functionally important residues are located. Newly constructed TP mutations revealed a priming loop in TP which plays a specific role in protein-primed DNA synthesis beyond simply harboring the site of priming. Substitutions of potential sites of phosphorylation surrounding the priming site demonstrated that these residues are involved in interactions critical for priming but are unlikely to be phosphorylated during viral replication. Furthermore, the first 13 and 66 TP residues were shown to be dispensable for protein priming and pgRNA binding, respectively. Combining current and previous mutagenesis work with sequence analysis has increased our understanding of TP structure and functions by mapping specific functions to distinct predicted secondary structures and will facilitate antiviral targeting of this unique domain.
  
  
  OBJECTIVE
  HBV is a major cause of viral hepatitis, liver cirrhosis, and hepatocellular carcinoma. One important feature of this virus is its polymerase, the enzyme used to create the DNA genome from a specific viral RNA by reverse transcription. One region of this polymerase, the TP domain, is required for association with the viral RNA and production of the DNA genome. Targeting the TP domain for antiviral development is difficult due to the lack of homology to other proteins and high-resolution structure. This study mapped the TP functions according to predicted secondary structure, where it folds into alpha helices or unstructured loops. Three predicted loops were found to be the most important regions functionally and the most conserved evolutionarily. Identification of these functional subdomains in TP will facilitate its targeting for antiviral development.
authors.affiliation: Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA dnc142@psu.edu.
authors.forename: Daniel N
authors.initials: DN
authors.lastname: Clark
authors.affiliation: Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA.
authors.forename: John M
authors.initials: JM
authors.lastname: Flanagan
authors.affiliation: Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA.
authors.forename: Jianming
authors.initials: J
authors.lastname: Hu
mesh_terms: D000595:Amino Acid Sequence; D017124:Conserved Sequence; D015684:Gene Products, pol / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D006515:Hepatitis B virus / Q000235:genetics* / Q000378:metabolism*; D006801:Humans; D008958:Models, Molecular; D009154:Mutation; D010641:Phenotype; D000072756:Protein Conformation, alpha-Helical; D054730:Protein Interaction Domains and Motifs; D012333:RNA, Messenger / Q000235:genetics; D012367:RNA, Viral; D016601:RNA-Binding Proteins
chemical_list: D015684:Gene Products, pol; C066027:P protein, Hepatitis B virus; D012333:RNA, Messenger; D012367:RNA, Viral; D016601:RNA-Binding Proteins
keywords: DNA polymerase; RNA binding; hepadnavirus; hepatitis B virus; protein priming; reverse transcriptase; terminal protein