1kpz
From Proteopedia
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PEMV-1 P1-P2 Frameshifting Pseudoknot Regularized Average Structure
Overview
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.
About this Structure
1KPZ is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot., Nixon PL, Rangan A, Kim YG, Rich A, Hoffman DW, Hennig M, Giedroc DP, J Mol Biol. 2002 Sep 20;322(3):621-33. PMID:12225754
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