1e95

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SOLUTION STRUCTURE OF THE PSEUDOKNOT OF SRV-1 RNA, INVOLVED IN RIBOSOMAL FRAMESHIFTING

Overview

RNA pseudoknots play important roles in many biological processes. In the, simian retrovirus type-1 (SRV-1) a pseudoknot together with a, heptanucleotide slippery sequence are responsible for programmed ribosomal, frameshifting, a translational recoding mechanism used to control, expression of the Gag-Pol polyprotein from overlapping gag and pol open, reading frames. Here we present the three-dimensional structure of the, SRV-1 pseudoknot determined by NMR. The structure has a classical H-type, fold and forms a triple helix by interactions between loop 2 and the minor, groove of stem 1 involving base-base and base-sugar interactions and a, ribose zipper motif, not identified in pseudoknots so far. Further, stabilization is provided by a stack of five adenine bases and a uracil in, loop 2, enforcing a cytidine to bulge. The two stems of the pseudoknot, stack upon each other, demonstrating that a pseudoknot without an, intercalated base at the junction can induce efficient frameshifting., Results of mutagenesis data are explained in context with the present, three-dimensional structure. The two base-pairs at the junction of stem 1, and 2 have a helical twist of approximately 49 degrees, allowing proper, alignment and close approach of the three different strands at the, junction. In addition to the overwound junction the structure is somewhat, kinked between stem 1 and 2, assisting the single adenosine in spanning, the major groove of stem 2. Geometrical models are presented that reveal, the importance of the magnitude of the helical twist at the junction in, determining the overall architecture of classical pseudoknots, in, particular related to the opening of the minor groove of stem 1 and the, orientation of stem 2, which determines the number of loop 1 nucleotides, that span its major groove.

About this Structure

1E95 is a Single protein structure of sequence from Simian retrovirus type-1. Full crystallographic information is available from OCA.

Reference

Solution structure of the pseudoknot of SRV-1 RNA, involved in ribosomal frameshifting., Michiels PJ, Versleijen AA, Verlaan PW, Pleij CW, Hilbers CW, Heus HA, J Mol Biol. 2001 Jul 27;310(5):1109-23. PMID:11501999

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