2tpk

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[[Image:2tpk.jpg|left|200px]]
 
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{{Structure
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==AN INVESTIGATION OF THE STRUCTURE OF THE PSEUDOKNOT WITHIN THE GENE 32 MESSENGER RNA OF BACTERIOPHAGE T2 USING HETERONUCLEAR NMR METHODS==
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|PDB= 2tpk |SIZE=350|CAPTION= <scene name='initialview01'>2tpk</scene>
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<StructureSection load='2tpk' size='340' side='right'caption='[[2tpk]]' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
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<table><tr><td colspan='2'>[[2tpk]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2TPK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2TPK FirstGlance]. <br>
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|ACTIVITY=
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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|GENE=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2tpk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2tpk OCA], [https://pdbe.org/2tpk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2tpk RCSB], [https://www.ebi.ac.uk/pdbsum/2tpk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2tpk ProSAT]</span></td></tr>
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|DOMAIN=
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</table>
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|RELATEDENTRY=
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<div style="background-color:#fffaf0;">
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2tpk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2tpk OCA], [http://www.ebi.ac.uk/pdbsum/2tpk PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2tpk RCSB]</span>
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== Publication Abstract from PubMed ==
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}}
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'''AN INVESTIGATION OF THE STRUCTURE OF THE PSEUDOKNOT WITHIN THE GENE 32 MESSENGER RNA OF BACTERIOPHAGE T2 USING HETERONUCLEAR NMR METHODS'''
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==Overview==
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The RNA pseudoknot located at the 5' end of the gene 32 messenger RNA of bacteriophage T2 contains two A-form helical stems connected by two loops, in an H-type pseudoknot topology. A combination of multidimensional NMR methods and isotope labeling were used to investigate the pseudoknot structure, resulting in a more detailed structural model than provided by earlier homonuclear NMR studies. Of particular significance, the interface between the stacked helical stems within the pseudoknot motif is described in detail. The two stems are stacked in a coaxial manner, with an approximately 18 degrees rotation of stem1 relative to stem2 about an axis that is parallel to the helical axis. This rotation serves to relieve what would otherwise be a relatively close phosphate-phosphate contact at the junction of the two stems, while preserving the stabilizing effects of base stacking. The ability of the NMR data to determine pseudoknot bending was critically assessed. The data were found to be a modestly precise indicator of pseudoknot bending, with the angle between the helical axes of stem1 and stem2 being in the range of 15+/-15 degrees. Pseudoknot models with bend angles within this range are equally consistent with the data, since they differ by only small amounts in the relatively short-range interproton distances from which the structure was derived. The gene 32 messenger RNA pseudoknot was compared with other RNA structures with coaxial or near-coaxial stacked helical stems.
The RNA pseudoknot located at the 5' end of the gene 32 messenger RNA of bacteriophage T2 contains two A-form helical stems connected by two loops, in an H-type pseudoknot topology. A combination of multidimensional NMR methods and isotope labeling were used to investigate the pseudoknot structure, resulting in a more detailed structural model than provided by earlier homonuclear NMR studies. Of particular significance, the interface between the stacked helical stems within the pseudoknot motif is described in detail. The two stems are stacked in a coaxial manner, with an approximately 18 degrees rotation of stem1 relative to stem2 about an axis that is parallel to the helical axis. This rotation serves to relieve what would otherwise be a relatively close phosphate-phosphate contact at the junction of the two stems, while preserving the stabilizing effects of base stacking. The ability of the NMR data to determine pseudoknot bending was critically assessed. The data were found to be a modestly precise indicator of pseudoknot bending, with the angle between the helical axes of stem1 and stem2 being in the range of 15+/-15 degrees. Pseudoknot models with bend angles within this range are equally consistent with the data, since they differ by only small amounts in the relatively short-range interproton distances from which the structure was derived. The gene 32 messenger RNA pseudoknot was compared with other RNA structures with coaxial or near-coaxial stacked helical stems.
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==About this Structure==
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An examination of coaxial stacking of helical stems in a pseudoknot motif: the gene 32 messenger RNA pseudoknot of bacteriophage T2.,Holland JA, Hansen MR, Du Z, Hoffman DW RNA. 1999 Feb;5(2):257-71. PMID:10024177<ref>PMID:10024177</ref>
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2TPK 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=2TPK OCA].
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==Reference==
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An examination of coaxial stacking of helical stems in a pseudoknot motif: the gene 32 messenger RNA pseudoknot of bacteriophage T2., Holland JA, Hansen MR, Du Z, Hoffman DW, RNA. 1999 Feb;5(2):257-71. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10024177 10024177]
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[[Category: Protein complex]]
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[[Category: Du, Z.]]
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[[Category: Hansen, M R.]]
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[[Category: Hoffman, D W.]]
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[[Category: Holland, J A.]]
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[[Category: pseudoknot]]
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[[Category: ribonucleic acid]]
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[[Category: rna]]
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[[Category: t2]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:03:59 2008''
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2tpk" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Du Z]]
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[[Category: Hansen MR]]
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[[Category: Hoffman DW]]
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[[Category: Holland JA]]

Current revision

AN INVESTIGATION OF THE STRUCTURE OF THE PSEUDOKNOT WITHIN THE GENE 32 MESSENGER RNA OF BACTERIOPHAGE T2 USING HETERONUCLEAR NMR METHODS

PDB ID 2tpk

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