Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot

J Mol Biol. 2002 Sep 20;322(3):621-33. doi: 10.1016/s0022-2836(02)00779-9.

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Pairing
  • Frameshifting, Ribosomal*
  • Gene Expression Regulation
  • Luteovirus / chemistry*
  • Luteovirus / genetics
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Nucleic Acid Conformation
  • Peas / chemistry
  • Peas / virology*
  • RNA, Messenger / chemistry*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • RNA, Viral / chemistry*
  • RNA, Viral / genetics
  • RNA, Viral / metabolism
  • Solutions
  • Thermodynamics

Substances

  • RNA, Messenger
  • RNA, Viral
  • Solutions

Associated data

  • PDB/1KPY
  • PDB/1KPZ