1KPY

PEMV-1 P1-P2 Frameshifting Pseudoknot, 15 Lowest Energy Structures

Summary for 1KPY

• Entry DOI: 10.2210/pdb1kpy/pdb
• Related: 1KPZ
• NMR Information: BMRB: 5278
• Descriptor: P1-P2 frameshifting pseudoknot (1 entity in total)
• Functional Keywords: pseudoknot, frameshifting, luteovirus, triple helix, protonated cytidine, ribonucleic acid, rna
• Total number of polymer chains: 1
• Total formula weight: 10640.45

Authors

Nixon, P.L.,Giedroc, D.P. (deposition date: 2002-01-03, release date: 2002-01-11, Last modification date: 2024-05-01)

Primary citation

Nixon, P.L.,Rangan, A.,Kim, Y.-G.,Rich, A.,Hoffman, D.W.,Hennig, M.,Giedroc, D.P.
Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot
J.Mol.Biol., 322:621-633, 2002

PubMed 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.

PubMed: 12225754
DOI: 10.1016/S0022-2836(02)00779-9

Experimental method

SOLUTION NMR