1kpd: Difference between revisions
New page: left|200px<br /><applet load="1kpd" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kpd" /> '''A MUTANT RNA PSEUDOKNOT THAT PROMOTES RIBOSO... |
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'''A MUTANT RNA PSEUDOKNOT THAT PROMOTES RIBOSOMAL FRAMESHIFTING IN MOUSE MAMMARY TUMOR VIRUS, NMR, MINIMIZED AVERAGE STRUCTURE'''<br /> | '''A MUTANT RNA PSEUDOKNOT THAT PROMOTES RIBOSOMAL FRAMESHIFTING IN MOUSE MAMMARY TUMOR VIRUS, NMR, MINIMIZED AVERAGE STRUCTURE'''<br /> | ||
==Overview== | ==Overview== | ||
A single A-->G mutation that changes a potential A.U base pair to a G.U | 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== | ==About this Structure== | ||
1KPD is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | 1KPD is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KPD OCA]. | ||
==Reference== | ==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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9115361 9115361] | 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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9115361 9115361] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Junior, I | [[Category: Junior, I Tinoco.]] | ||
[[Category: Kang, H.]] | [[Category: Kang, H.]] | ||
[[Category: ribonucleic acid]] | [[Category: ribonucleic acid]] | ||
[[Category: rna pseudoknot]] | [[Category: rna pseudoknot]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:36:36 2008'' | ||
Revision as of 11:36, 21 February 2008
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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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