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| | ==An alternating sheared AA pair in 5'GGUGAAGGCU/3'PCCGAAGCCG: II. The minor conformation with A6/A5/A16 stack== | | ==An alternating sheared AA pair in 5'GGUGAAGGCU/3'PCCGAAGCCG: II. The minor conformation with A6/A5/A16 stack== |
| - | <StructureSection load='2dd3' size='340' side='right' caption='[[2dd3]], [[NMR_Ensembles_of_Models | 18 NMR models]]' scene=''> | + | <StructureSection load='2dd3' size='340' side='right'caption='[[2dd3]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2dd3]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DD3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2dd3]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DD3 FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=P5P:PURINE+RIBOSIDE-5-MONOPHOSPHATE'>P5P</scene></td></tr> | + | </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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2dd1|2dd1]], [[2dd2|2dd2]], [[1xv0|1xv0]]</td></tr> | + | <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> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dd3 OCA], [http://pdbe.org/2dd3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dd3 RCSB], [http://www.ebi.ac.uk/pdbsum/2dd3 PDBsum]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dd3 OCA], [https://pdbe.org/2dd3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dd3 RCSB], [https://www.ebi.ac.uk/pdbsum/2dd3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dd3 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Chen, G]] | + | [[Category: Large Structures]] |
| - | [[Category: Kennedy, S D]] | + | [[Category: Chen G]] |
| - | [[Category: Krugh, T R]] | + | [[Category: Kennedy SD]] |
| - | [[Category: Turner, D H]] | + | [[Category: Krugh TR]] |
| - | [[Category: Alternating sheared aa pair]] | + | [[Category: Turner DH]] |
| - | [[Category: Kink-turn motif]]
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| - | [[Category: Rapid conformation exchange]]
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| - | [[Category: Rna]]
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| - | [[Category: Rna secondary structure prediction]]
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| - | [[Category: Sequence specific a-minor motif]]
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| - | [[Category: Thermodynamic]]
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| Structural highlights
Publication Abstract from PubMed
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Chen G, Kennedy SD, Qiao J, Krugh TR, Turner DH. An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA. Biochemistry. 2006 Jun 6;45(22):6889-903. PMID:16734425 doi:10.1021/bi0524464
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