1kpd

From Proteopedia

A MUTANT RNA PSEUDOKNOT THAT PROMOTES RIBOSOMAL FRAMESHIFTING IN MOUSE MAMMARY TUMOR VIRUS, NMR, MINIMIZED AVERAGE STRUCTURE

Overview

A single A-->G mutation that changes a potential A.U base pair to a G.U, pair at the junction of the stems and loops of a non-frameshifting, pseudoknot dramatically increases its frameshifting efficiency in mouse, mammary tumor virus. The structure of the non-frameshifting pseudoknot APK, has been found to be very different from that of pseudoknots that cause, efficient frameshifting [Kang,H., Hines,J.V. and Tinoco,I. (1995) J. Mol., Biol. , 259, 135-147]. The 3-dimensional structure of the mutant, pseudoknot was determined by restrained molecular dynamics based on, NMR-derived interproton distance and torsion angle constraints. One, striking feature of the mutant pseudoknot compared with the parent, pseudoknot is that a G.U base pair forms at the top of stem 2, thus, leaving only 1 nt at the junction of the two stems. The conformation is, very different from that of the previously determined non-frameshifting, parent pseudoknot, which lacks the A.U base pair at the top of the stem, and has 2 nt between the stems. However, the conformation is quite similar, to that of efficient frameshifting pseudoknots whose structures were, previously determined by NMR. A single adenylate residue intervenes, between the two stems and interrupts their coaxial stacking. This unpaired, nucleotide produces a bent structure. The structural similarity among the, efficient frameshifting pseudoknots indicates that a specific conformation, is required for ribosomal frameshifting, further implying a specific, interaction of the pseudoknot with the ribosome.

About this Structure

1KPD is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

A mutant RNA pseudoknot that promotes ribosomal frameshifting in mouse mammary tumor virus., Kang H, Tinoco I Jr, Nucleic Acids Res. 1997 May 15;25(10):1943-9. PMID:9115361

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