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==NMR solution structure of the d3'-hairpin from the Sc.ai5gamma group II intron including the EBS1:dIBS1 RNA:DNA hybrid==
==NMR solution structure of the d3'-hairpin from the Sc.ai5gamma group II intron including the EBS1:dIBS1 RNA:DNA hybrid==
<StructureSection load='2m1v' size='340' side='right'caption='[[2m1v]], [[NMR_Ensembles_of_Models | 18 NMR models]]' scene=''>
<StructureSection load='2m1v' size='340' side='right'caption='[[2m1v]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2m1v]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M1V OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2M1V FirstGlance]. <br>
<table><tr><td colspan='2'>[[2m1v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M1V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2M1V FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2k65|2k65]], [[2k66|2k66]], [[2m23|2m23]], [[2m24|2m24]]</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2m1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m1v OCA], [http://pdbe.org/2m1v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2m1v RCSB], [http://www.ebi.ac.uk/pdbsum/2m1v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2m1v ProSAT]</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=2m1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m1v OCA], [https://pdbe.org/2m1v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2m1v RCSB], [https://www.ebi.ac.uk/pdbsum/2m1v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2m1v ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Group II intron ribozymes catalyze the cleavage of (and their reinsertion into) DNA and RNA targets using a Mg2+-dependent reaction. The target is cleaved 3' to the last nucleotide of the intron binding site (IBS)1, one of three regions that form base pairs with the intron's exon binding sites (EBS)1-3. We solved the NMR solution structure of the d3'-hairpin of the Sc.ai5gamma intron containing EBS1 in its 11 nt loop in complex with the dIBS1 DNA 7mer and compare it to the analogous RNA.RNA contact. The EBS1.dIBS1 helix is slightly flexible and non-symmetric. NMR data reveal two major-groove binding sites for divalent metal ions at the EBS1.dIBS1 helix and Surface Plasmon Resonance experiments show that low concentrations of Mg2+ considerably enhance the affinity of dIBS1 for EBS1. Our results indicate that identification of both RNA and DNA IBS1 targets, presentation of the scissile bond, and stabilization of the structure by metal ions are governed by the overall structure of EBS1.dIBS1 and the surrounding loop nucleotides but are irrespective of different EBS1.(d)IBS1 geometries and interstrand affinities.
The Role of Magnesium(II) for DNA Cleavage Site Recognition in Group II Intron Ribozymes -- Solution Structure and Metal Ion Binding Sites of the RNA.DNA Complex.,Skilandat M, Sigel RK J Biol Chem. 2014 Jun 3. pii: jbc.M113.542381. PMID:24895129<ref>PMID:24895129</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2m1v" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Sigel, R K.O]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Skilandat, M]]
[[Category: Synthetic construct]]
[[Category: Dna]]
[[Category: Sigel RKO]]
[[Category: Dna-rna complex]]
[[Category: Skilandat M]]
[[Category: Group ii intron]]
[[Category: Hybrid]]
[[Category: Retrohoming]]
[[Category: Reverse splicing]]
[[Category: Ribozyme]]
[[Category: Rna]]

Latest revision as of 06:58, 1 May 2024

NMR solution structure of the d3'-hairpin from the Sc.ai5gamma group II intron including the EBS1:dIBS1 RNA:DNA hybrid

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