1kpy: Difference between revisions

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'''PEMV-1 P1-P2 Frameshifting Pseudoknot, 15 Lowest Energy Structures'''<br />

==Overview==

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.

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.

==About this Structure==

1KPY 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://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=1KPY OCA].

1KPY 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=1KPY OCA].

==Reference==

Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot., Nixon PL, Rangan A, Kim YG, Rich A, Hoffman DW, Hennig M, Giedroc DP, J Mol Biol. 2002 Sep 20;322(3):621-33. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12225754 12225754]

[[Category: Protein complex]]

[[Category: Giedroc, D.P.]]

[[Category: Giedroc, D P.]]

[[Category: Nixon, P.L.]]

[[Category: Nixon, P L.]]

[[Category: frameshifting]]

[[Category: luteovirus]]

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[[Category: triple helix]]

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@@ Line 1: / Line 1: @@
-[[Image:1kpy.gif|left|200px]]<br /><applet load="1kpy" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1kpy.gif|left|200px]]<br /><applet load="1kpy" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1kpy" />
 '''PEMV-1 P1-P2 Frameshifting Pseudoknot, 15 Lowest Energy Structures'''<br />
 ==Overview==
-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.
+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.
 ==About this Structure==
-KPY 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KPY OCA].
+KPY 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=1KPY OCA].
 ==Reference==
 Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot., Nixon PL, Rangan A, Kim YG, Rich A, Hoffman DW, Hennig M, Giedroc DP, J Mol Biol. 2002 Sep 20;322(3):621-33. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12225754 12225754]
 [[Category: Protein complex]]
-[[Category: Giedroc, D.P.]]
+[[Category: Giedroc, D P.]]
-[[Category: Nixon, P.L.]]
+[[Category: Nixon, P L.]]
 [[Category: frameshifting]]
 [[Category: luteovirus]]
@@ Line 22: / Line 22: @@
 [[Category: triple helix]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 01:44:24 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:36:42 2008''