6ez0: Difference between revisions

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New page: '''Unreleased structure''' The entry 6ez0 is ON HOLD Authors: Description: Category: Unreleased Structures
 
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'''Unreleased structure'''


The entry 6ez0 is ON HOLD
==Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding==
<StructureSection load='6ez0' size='340' side='right'caption='[[6ez0]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6ez0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EZ0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6EZ0 FirstGlance]. <br>
</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=U37:URIDINE+5-MONOTHIOPHOSPHATE'>U37</scene></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=6ez0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ez0 OCA], [https://pdbe.org/6ez0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ez0 RCSB], [https://www.ebi.ac.uk/pdbsum/6ez0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ez0 ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Group II introns are large self-splicing ribozymes that require high amounts of monovalent and divalent metal ions for folding and catalysis under in vitro conditions. Domain 6 of these ribozymes contains a highly conserved adenosine whose 2'-OH acts as a nucleophile during self-cleavage via the branching pathway. We have previously suggested a divalent metal ion that binds to the major groove at the GU wobble pair above the branch-A in a minimal, but active branch domain construct (D6-27) from the yeast mitochondrial intron Sc.ai5gamma. Here we characterize metal ion binding to the phosphate oxygens at the branch site. In vitro transcription yielded a D6-27 construct where all R P oxygens of the uridine phosphate groups are replaced by sulfur (alpha-thio-D6-27). We determined its NMR structure, the second RNA-only structure containing thiophosphate groups. [(31)P] resonances were assigned and chemical shift changes monitored upon titration with Cd(2+). In addition, the two uridines flanking the branch-point, U19 and U21 were specifically thioated by chemical synthesis (thio-U19-D6-27 and thio-U19/U21-D6-27), enabling us to study Cd(2+) binding at the R P-, as well as the S P- position of the corresponding phosphate oxygens. Our studies reveal that both non-bridging phosphate oxygens of U19 are involved in metal ion coordination, whereas only the major groove phosphate oxygen of U21 is influenced. Together with NOE data of a hexaamminecobalt(III) titration, this suggests a single metal ion binding site at the GU wobble pair above the branch point in the major groove of D6 of this group II intron ribozyme.


Authors:  
Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding.,Erat MC, Besic E, Oberhuber M, Johannsen S, Sigel RKO J Biol Inorg Chem. 2017 Dec 7. pii: 10.1007/s00775-017-1519-3. doi:, 10.1007/s00775-017-1519-3. PMID:29218637<ref>PMID:29218637</ref>


Description:  
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
<div class="pdbe-citations 6ez0" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Ribozyme 3D structures|Ribozyme 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Besic E]]
[[Category: Erat MC]]
[[Category: Johannsen S]]
[[Category: Oberhuber M]]
[[Category: Sigel RKO]]
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