View source for 5dun


==The crystal structure of OMe substituted twister ribozyme==
<StructureSection load='5dun' size='340' side='right'caption='[[5dun]], [[Resolution|resolution]] 2.64&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5dun]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DUN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DUN FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.64&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</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=5dun FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dun OCA], [https://pdbe.org/5dun PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dun RCSB], [https://www.ebi.ac.uk/pdbsum/5dun PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dun ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Nucleolytic ribozymes catalyze site-specific cleavage of their phosphodiester backbones. A minimal version of the twister ribozyme is reported that lacks the phylogenetically conserved stem P1 while retaining wild-type activity. Atomic mutagenesis revealed that nitrogen atoms N1 and N3 of the adenine-6 at the cleavage site are indispensable for cleavage. By NMR spectroscopy, a pKa value of 5.1 was determined for a (13) C2-labeled adenine at this position in the twister ribozyme, which is significantly shifted compared to the pKa of the same adenine in the substrate alone. This finding pinpoints at a potential role for adenine-6 in the catalytic mechanism besides the previously identified invariant guanine-48 and a Mg(2+) ion, both of which are directly coordinated to the non-bridging oxygen atoms of the scissile phosphate; for the latter, additional evidence stems from the observation that Mn(2+) or Cd(2+) accelerated cleavage of phosphorothioate substrates. The relevance of this metal ion binding site is further emphasized by a new 2.6 A X-ray structure of a 2'-OCH3 -U5 modified twister ribozyme.

A Mini-Twister Variant and Impact of Residues/Cations on the Phosphodiester Cleavage of this Ribozyme Class.,Kosutic M, Neuner S, Ren A, Flur S, Wunderlich C, Mairhofer E, Vusurovic N, Seikowski J, Breuker K, Hobartner C, Patel DJ, Kreutz C, Micura R Angew Chem Int Ed Engl. 2015 Dec 7;54(50):15128-33. doi: 10.1002/anie.201506601. , Epub 2015 Oct 16. PMID:26473980<ref>PMID:26473980</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5dun" style="background-color:#fffaf0;"></div>

==See Also==
*[[Ribozyme 3D structures|Ribozyme 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Synthetic construct]]
[[Category: Micura R]]
[[Category: Patel DJ]]
[[Category: Rajashankar KR]]
[[Category: Ren A]]