Solution structure of the pseudoknot of SRV-1 RNA, involved in ribosomal frameshifting

RNA pseudoknots play important roles in many biological processes. In the s imian retrovirus type-1 (SRV-1) a pseucloknot together with a heptanucleoti de 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 p resent the three-dimensional structure of the SRV-1 pseucloknot 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 ba se-base and base-sugar interactions and a ribose zipper motif, not identifi ed in pseudoknots so far. Further stabilization is provided by a stack of f ive adenine bases and a, uracil in loop 2, enforcing a cytidine to bulge. T he two stems of the pseudoknot stack upon each other, demonstrating that a pseucloknot without an intercalated base at the junction can induce efficie nt frameshifting. Results of mutagenesis data are explained in context with the present three-dimensional structure. The two base-pairs at the junctio n of stem 1 and 2 have a helical twist of approximately 49', allowing prope r alignment and close approach of the three different strands at the juncti on. 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 importa nce of the magnitude of the helical twist at the junction in determining th e overall architecture of classical pseudoknots, in particular related to t he opening of the minor groove of stem 1 and the orientation of stern 2, wh ich determines the number of loop 1 nucleotides that span its major groove. (C) 2001 Academic Press.