title: New tools provide a second look at HDV ribozyme structure, dynamics and cleavage.
abstract: The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA enzyme essential for processing viral transcripts during rolling circle viral replication. The first crystal structure of the cleaved ribozyme was solved in 1998, followed by structures of uncleaved, mutant-inhibited and ion-complexed forms. Recently, methods have been developed that make the task of modeling RNA structure and dynamics significantly easier and more reliable. We have used ERRASER and PHENIX to rebuild and re-refine the cleaved and cis-acting C75U-inhibited structures of the HDV ribozyme. The results correct local conformations and identify alternates for RNA residues, many in functionally important regions, leading to improved R values and model validation statistics for both structures. We compare the rebuilt structures to a higher resolution, trans-acting deoxy-inhibited structure of the ribozyme, and conclude that although both inhibited structures are consistent with the currently accepted hammerhead-like mechanism of cleavage, they do not add direct structural evidence to the biochemical and modeling data. However, the rebuilt structures (PDBs: 4PR6, 4PRF) provide a more robust starting point for research on the dynamics and catalytic mechanism of the HDV ribozyme and demonstrate the power of new techniques to make significant improvements in RNA structures that impact biologically relevant conclusions.
authors.affiliation: Department of Biochemistry, Duke University, Durham, NC 27710, USA.
authors.forename: Gary J
authors.initials: GJ
authors.lastname: Kapral
authors.affiliation: Department of Biochemistry, Duke University, Durham, NC 27710, USA Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27710, USA.
authors.forename: Swati
authors.initials: S
authors.lastname: Jain
authors.affiliation: Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA.
authors.forename: Jonas
authors.initials: J
authors.lastname: Noeske
authors.affiliation: Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA.
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Doudna
authors.affiliation: Department of Biochemistry, Duke University, Durham, NC 27710, USA.
authors.forename: David C
authors.initials: DC
authors.lastname: Richardson
authors.affiliation: Department of Biochemistry, Duke University, Durham, NC 27710, USA jsr@kinemage.biochem.duke.edu.
authors.forename: Jane S
authors.initials: JS
authors.lastname: Richardson
mesh_terms: D020029:Base Pairing; D003698:Hepatitis Delta Virus / Q000201:enzymology*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D059367:RNA Cleavage; D016337:RNA, Catalytic / Q000737:chemistry* / Q000378:metabolism; D017412:Ribonucleoprotein, U1 Small Nuclear / Q000737:chemistry / Q000378:metabolism
chemical_list: D016337:RNA, Catalytic; D017412:Ribonucleoprotein, U1 Small Nuclear; C075339:U1A protein