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2dd2

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(New page: 200px<br /><applet load="2dd2" size="350" color="white" frame="true" align="right" spinBox="true" caption="2dd2" /> '''An alternating sheared AA pair in 5'GGUGAAGG...)
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[[Image:2dd2.gif|left|200px]]<br /><applet load="2dd2" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2dd2" />
 
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'''An alternating sheared AA pair in 5'GGUGAAGGCU/3'PCCGAAGCCG: I. The major conformation with A6/A15/A16 stack'''<br />
 
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==Overview==
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==An alternating sheared AA pair in 5'GGUGAAGGCU/3'PCCGAAGCCG: I. The major conformation with A6/A15/A16 stack==
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A previous NMR structure of the duplex 5'GGU GGA GGCU/PCCG AAG CCG5', revealed an unusually stable RNA internal loop with three consecutive, sheared GA pairs. Here, we report NMR studies of two duplexes, 5'GGU GGA, GGCU/PCCA AAG CCG5' (replacing the UG pair with a UA closing pair) and, 5'GGU GAA GGCU/PCCG AAG CCG5' (replacing the middle GA pair with an AA, pair). An unusually stable loop with three consecutive sheared GA pairs, forms in the duplex 5'GGU GGA GGCU/PCCA AAG CCG5'. The structure contrasts, with that reported for this loop in the crystal structure of the large, ribosomal subunit of Deinococcus radiodurans [Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Franceschi, F., and Yonath, A. (2001) Cell 107, 679-688]. The middle AA pair in the duplex, 5'GGU GAA GGCU/PCCG AAG CCG5' rapidly exchanges orientations, resulting in, alternative base stacking and pseudosymmetry with exclusively sheared, pairs. The U GAA G/G AAG C internal loop is 2.1 kcal/mol less stable than, the U GGA G/G AAG C internal loop at 37 degrees C. Structural, energetic, and dynamic consequences upon functional group substitutions within, related 3 x 3 and 3 x 6 internal loops are also reported.
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<StructureSection load='2dd2' size='340' side='right'caption='[[2dd2]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2dd2]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DD2 FirstGlance]. <br>
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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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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=P5P:PURINE+RIBOSIDE-5-MONOPHOSPHATE'>P5P</scene></td></tr>
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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=2dd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dd2 OCA], [https://pdbe.org/2dd2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dd2 RCSB], [https://www.ebi.ac.uk/pdbsum/2dd2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dd2 ProSAT]</span></td></tr>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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A previous NMR structure of the duplex 5'GGU GGA GGCU/PCCG AAG CCG5' revealed an unusually stable RNA internal loop with three consecutive sheared GA pairs. Here, we report NMR studies of two duplexes, 5'GGU GGA GGCU/PCCA AAG CCG5' (replacing the UG pair with a UA closing pair) and 5'GGU GAA GGCU/PCCG AAG CCG5' (replacing the middle GA pair with an AA pair). An unusually stable loop with three consecutive sheared GA pairs forms in the duplex 5'GGU GGA GGCU/PCCA AAG CCG5'. The structure contrasts with that reported for this loop in the crystal structure of the large ribosomal subunit of Deinococcus radiodurans [Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Franceschi, F., and Yonath, A. (2001) Cell 107, 679-688]. The middle AA pair in the duplex 5'GGU GAA GGCU/PCCG AAG CCG5' rapidly exchanges orientations, resulting in alternative base stacking and pseudosymmetry with exclusively sheared pairs. The U GAA G/G AAG C internal loop is 2.1 kcal/mol less stable than the U GGA G/G AAG C internal loop at 37 degrees C. Structural, energetic, and dynamic consequences upon functional group substitutions within related 3 x 3 and 3 x 6 internal loops are also reported.
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==About this Structure==
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An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA.,Chen G, Kennedy SD, Qiao J, Krugh TR, Turner DH Biochemistry. 2006 Jun 6;45(22):6889-903. PMID:16734425<ref>PMID:16734425</ref>
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2DD2 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=2DD2 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA., Chen G, Kennedy SD, Qiao J, Krugh TR, Turner DH, Biochemistry. 2006 Jun 6;45(22):6889-903. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16734425 16734425]
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</div>
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[[Category: Protein complex]]
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<div class="pdbe-citations 2dd2" style="background-color:#fffaf0;"></div>
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[[Category: Chen, G.]]
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== References ==
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[[Category: Kennedy, S.D.]]
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<references/>
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[[Category: Krugh, T.R.]]
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__TOC__
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[[Category: Turner, D.H.]]
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</StructureSection>
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[[Category: a-minor motif]]
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[[Category: Large Structures]]
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[[Category: alternating]]
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[[Category: Chen G]]
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[[Category: conformation exchange]]
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[[Category: Kennedy SD]]
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[[Category: dynamics]]
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[[Category: Krugh TR]]
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[[Category: kink-turn]]
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[[Category: Turner DH]]
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[[Category: rna secondary structure]]
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[[Category: sheared aa pair]]
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[[Category: sheared ga pair]]
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[[Category: thermodynamics]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 19:00:47 2008''
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Current revision

An alternating sheared AA pair in 5'GGUGAAGGCU/3'PCCGAAGCCG: I. The major conformation with A6/A15/A16 stack

PDB ID 2dd2

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