PDBsum entry 1kpy

RNA

PDB id: 1kpy

Contents

DNA/RNA

PDB id:

1kpy

Name:

RNA

Title:

Pemv-1 p1-p2 frameshifting pseudoknot, 15 lowest energy structures

Structure:

P1-p2 frameshifting pseudoknot. Chain: a. Engineered: yes. Other_details: pea enation mosaic virus type i RNA

Source:

Synthetic: yes. Other_details: naturally occuring sequence of the p1-p2 frameshifting pseudoknot from pea enation mosaic virus type i. In vitro sp6 transcription.

NMR struc:

15 models

Authors:

P.L.Nixon,D.P.Giedroc

Key ref:

P.L.Nixon et al. (2002). Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot. J Mol Biol, 322, 621-633. PubMed id: 12225754 DOI: 10.1016/S0022-2836(02)00779-9

Date:

03-Jan-02 Release date: 11-Jan-02

DNA/RNA chain

U-C-C-G-G-U-_CH-G-A-C-U-C-C-G-G-A-G-A-A-A-C-A-A-A-G-U-C-A 28 bases

DOI no: 10.1016/S0022-2836(02)00779-9

J Mol Biol 322:621-633 (2002)

PubMed id: 12225754

Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot.

P.L.Nixon, A.Rangan, Y.G.Kim, A.Rich, D.W.Hoffman, M.Hennig, D.P.Giedroc.

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.

Selected figure(s)

Figure 6.
Figure 6. (a) Stereo view of the A[(n -1)]·C^+·G-C[n] base quadruple in the average structure of the PEMV-1 pseudoknot formed by loop 1 and stem 2 (A[12]·C[10]^+·G[28]-C[13]). C[10] is shown in red, the accepting Watson-Crick pair in blue, and A[12] of stem 2 which forms the third hydrogen bond to C[10]^+. (b) The three-base reverse turn places C[10] in the proper orientation to form the A[(n -1)]·C^+·G-C[n] base quadruple. C[10] is shown in red, U[9] from the Hoogsteen wedge pair in yellow and G[11], which forms the closing base-pair of stem 2, in blue. (c) Superposition of the bases from the A[(n -1)]·C^+·G-C[n] quadruples from the BWYV pseudoknot (white, 437D),[9.] the HDV ribozyme (red, 1CX0) [22.] and the average structure of the PEMV-1 pseudoknot (blue). (d) Overlay of the heavy atoms of the base quadruples and intervening nucleotide from the HDV ribozyme (red, residues 141-144, 161 of 1CX0) [22.] and the PEMV-1 pseudoknot (blue, residues 10-13, 28).

Figure 8.
Figure 8. (a) Overlay of the 15 lowest energy structures of the PEMV-1 pseudoknot with loop 2 (green) and U[14] (purple) highlighted. (b) Details of the A[25], A[26], and A[27] non-canonical base-pairings between loop 2 (green) and stem 1 (blue) nucleotides. A[25] forms an N1-2' OH hydrogen bond with the sugar of C[16], A[27] forms the analogous interaction with the sugar of C[15], and A[26] forms a pair of reciprocal hydrogen bonds with G[8] from stem 1 (A[26] amino to G[8] N3, G[8] amino to A[26] N1, shown with donors in red, acceptors in blue).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 322, 621-633) copyright 2002.

Figures were selected by an automated process.