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| <!--
| | ==PEMV-1 P1-P2 Frameshifting Pseudoknot, 15 Lowest Energy Structures== |
| The line below this paragraph, containing "STRUCTURE_1kpy", creates the "Structure Box" on the page.
| | <StructureSection load='1kpy' size='340' side='right'caption='[[1kpy]]' scene=''> |
| You may change the PDB parameter (which sets the PDB file loaded into the applet)
| | == Structural highlights == |
| or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| | <table><tr><td colspan='2'>[[1kpy]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KPY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KPY FirstGlance]. <br> |
| or leave the SCENE parameter empty for the default display.
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| -->
| | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CH:N3-PROTONATED+CYTIDINE-5-MONOPHOSPHATE'>CH</scene></td></tr> |
| {{STRUCTURE_1kpy| PDB=1kpy | SCENE= }}
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kpy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kpy OCA], [https://pdbe.org/1kpy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kpy RCSB], [https://www.ebi.ac.uk/pdbsum/1kpy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kpy ProSAT]</span></td></tr> |
| | | </table> |
| '''PEMV-1 P1-P2 Frameshifting Pseudoknot, 15 Lowest Energy Structures'''
| | __TOC__ |
| | | </StructureSection> |
| | | [[Category: Large Structures]] |
| ==Overview== | | [[Category: Giedroc DP]] |
| 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.
| | [[Category: Nixon PL]] |
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| ==About this Structure==
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| 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://www.ncbi.nlm.nih.gov/pubmed/12225754 12225754]
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| [[Category: Giedroc, D P.]] | |
| [[Category: Nixon, P L.]] | |
| [[Category: Frameshifting]]
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| [[Category: Luteovirus]] | |
| [[Category: Nmr]]
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| [[Category: Protonated cytidine]]
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| [[Category: Pseudoknot]] | |
| [[Category: Ribonucleic acid]] | |
| [[Category: Triple helix]] | |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 23:01:43 2008''
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