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| - | [[Image:1kpz.gif|left|200px]] | |
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| - | {{Structure
| + | ==PEMV-1 P1-P2 Frameshifting Pseudoknot Regularized Average Structure== |
| - | |PDB= 1kpz |SIZE=350|CAPTION= <scene name='initialview01'>1kpz</scene>
| + | <StructureSection load='1kpz' size='340' side='right'caption='[[1kpz]]' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=CH:N3-PROTONATED+CYTIDINE-5'-MONOPHOSPHATE'>CH</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene>
| + | <table><tr><td colspan='2'>[[1kpz]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KPZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KPZ FirstGlance]. <br> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| - | |GENE=
| + | <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> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kpz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kpz OCA], [https://pdbe.org/1kpz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kpz RCSB], [https://www.ebi.ac.uk/pdbsum/1kpz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kpz ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=[[1kpy|1KPY]]
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kpz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kpz OCA], [http://www.ebi.ac.uk/pdbsum/1kpz PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1kpz RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''PEMV-1 P1-P2 Frameshifting Pseudoknot Regularized Average Structure'''
| + | [[Category: Giedroc DP]] |
| - | | + | [[Category: Nixon PL]] |
| - | | + | |
| - | ==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.
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| - | | + | |
| - | ==About this Structure==
| + | |
| - | 1KPZ is a [[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=1KPZ OCA].
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| - | | + | |
| - | ==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: Protein complex]] | + | |
| - | [[Category: Giedroc, D P.]] | + | |
| - | [[Category: Nixon, P L.]] | + | |
| - | [[Category: frameshifting]]
| + | |
| - | [[Category: luteovirus]]
| + | |
| - | [[Category: nmr]]
| + | |
| - | [[Category: protonated cytidine]]
| + | |
| - | [[Category: pseudoknot]]
| + | |
| - | [[Category: ribonucleic acid]]
| + | |
| - | [[Category: triple helix]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:51:55 2008''
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