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==Crystal structure of a hammerhead ribozyme with pseudoknot==
<StructureSection load='8ydc' size='340' side='right'caption='[[8ydc]], [[Resolution|resolution]] 2.89&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[8ydc]] is a 2 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=8YDC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8YDC 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]] 2.89&#8491;</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=8ydc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ydc OCA], [https://pdbe.org/8ydc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ydc RCSB], [https://www.ebi.ac.uk/pdbsum/8ydc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ydc ProSAT]</span></td></tr>
</table>
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== Publication Abstract from PubMed ==
We have determined the crystal structure of a pseudoknot (PK)-containing hammerhead ribozyme that closely resembles the pistol ribozyme, with essentially identical secondary structure and connectivity. The activity is more sensitive to deletion of the G8 2'OH than to the absence of magnesium ions, indicating that the catalytic mechanism is the same as the extended hammerhead, and distinct from the pistol ribozyme. Here we show that nucleophilic attack is almost perfectly in-line, and the G8 2'OH is well positioned to act as general acid, being directed towards the O5' leaving group, and 2.9 A away from it. Despite the similarity in overall structure to the pistol ribozyme, the local structure close to the cleavage site differs, and the PK hammerhead retains its unique mechanistic identity and demonstrates enhanced activity over other hammerhead ribozymes under standard conditions.

The structure and catalytic mechanism of a pseudoknot-containing hammerhead ribozyme.,Zhan X, Wilson TJ, Li Z, Zhang J, Yang Y, Lilley DMJ, Liu Y Nat Commun. 2024 Aug 5;15(1):6628. doi: 10.1038/s41467-024-50892-y. PMID:39103372<ref>PMID:39103372</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 8ydc" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Synthetic construct]]
[[Category: Liu Y]]
[[Category: Zhan X]]