title: Path of an RNA ligand around the surface of the vaccinia VP39 subunit of its cognate VP39-VP55 protein heterodimer.
abstract: VP39 is a vaccinia virus-encoded RNA modifying protein with roles in the modification of both mRNA ends. At the 3' end it acts as a processivity factor for the vaccinia poly(A) polymerase (VP55), promoting poly(A) tail elongation. Despite VP39's three-dimensional structure having been elucidated along with details of its mode of mRNA 5' end binding, the VP39-VP55 heterodimer's molecular mechanism of processivity is largely unknown. Here, the area immediately above almost the entire surface of the VP39 subunit was probed using chemical reporters, and the path of a previously unidentified RNA binding site was revealed. The path was indicated to fall within a cleft formed by the intersubunit interface and was consistent with both a previously reported model of the heterodimer-nucleic acid ternary complex and the known function of the heterodimer in processive poly(A) tail elongation.
authors.affiliation: Department of Medical Biochemistry and Genetics/Institute of Biosciences and Technology, Texas A&M University System Health Science Center, Houston, TX 77030, USA.
authors.forename: Akihiro
authors.initials: A
authors.lastname: Oguro
authors.forename: Lela
authors.initials: L
authors.lastname: Johnson
authors.forename: Paul D
authors.initials: PD
authors.lastname: Gershon
mesh_terms: D001665:Binding Sites; D019281:Dimerization; D008024:Ligands; D009690:Nucleic Acid Conformation; D017354:Point Mutation / Q000235:genetics; D011062:Polynucleotide Adenylyltransferase / Q000737:chemistry / Q000378:metabolism*; D012315:RNA Caps / Q000378:metabolism*; D012367:RNA, Viral / Q000378:metabolism*; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D008024:Ligands; D012315:RNA Caps; D012367:RNA, Viral; C088682:VP39 protein, Vaccinia virus; D014764:Viral Proteins; D011062:Polynucleotide Adenylyltransferase