title: Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot.
abstract: A hairpin-type messenger RNA pseudoknot from pea enation mosaic virus RNA1 (PEMV-1) regulates the efficiency of programmed -1 ribosomal frameshifting. The solution structure and 15N relaxation rates reveal that the PEMV-1 pseudoknot is a compact-folded structure composed almost entirely of RNA triple helix. A three nucleotide reverse turn in loop 1 positions a protonated cytidine, C(10), in the correct orientation to form an A((n-1)).C(+).G-C(n) major groove base quadruple, like that found in the beet western yellows virus pseudoknot and the hepatitis delta virus ribozyme, despite distinct structural contexts. A novel loop 2-loop 1 A.U Hoogsteen base-pair stacks on the C(10)(+).G(28) base-pair of the A(12).C(10)(+).G(28)-C(13) quadruple and forms a wedge between the pseudoknot stems stabilizing a bent and over-rotated global conformation. Substitution of key nucleotides that stabilize the unique conformation of the PEMV-1 pseudoknot greatly reduces ribosomal frameshifting efficacy.
authors.affiliation: Department of Biochemistry and Biophysics, Center for Advanced Biomolecular Research, 2128 TAMU, Texas A&M University, 77843-2128, College Station, TX, USA.
authors.forename: Paul L
authors.initials: PL
authors.lastname: Nixon
authors.forename: Anupama
authors.initials: A
authors.lastname: Rangan
authors.forename: Y-G
authors.initials: YG
authors.lastname: Kim
authors.forename: Alexander
authors.initials: A
authors.lastname: Rich
authors.forename: David W
authors.initials: DW
authors.lastname: Hoffman
authors.forename: Mirko
authors.initials: M
authors.lastname: Hennig
authors.forename: David P
authors.initials: DP
authors.lastname: Giedroc
mesh_terms: D020029:Base Pairing; D018965:Frameshifting, Ribosomal; D005786:Gene Expression Regulation; D017793:Luteovirus / Q000737:chemistry* / Q000235:genetics; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D018532:Pisum sativum / Q000737:chemistry / Q000821:virology*; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012996:Solutions; D013816:Thermodynamics
chemical_list: D012333:RNA, Messenger; D012367:RNA, Viral; D012996:Solutions