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==Crystal structure of a self-alkylating ribozyme - alkylated form with biotinylated epoxide substrate==
<StructureSection load='6xjq' size='340' side='right'caption='[[6xjq]], [[Resolution|resolution]] 1.71&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6xjq]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XJQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XJQ 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]] 1.708&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=V4J:2-{[(4R)-4-hydroxyhexyl]oxy}ethyl+5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoate'>V4J</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=6xjq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xjq OCA], [https://pdbe.org/6xjq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xjq RCSB], [https://www.ebi.ac.uk/pdbsum/6xjq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xjq ProSAT]</span></td></tr>
</table>
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== Publication Abstract from PubMed ==
Ribozymes that react with small-molecule probes have important applications in transcriptomics and chemical biology, such as RNA labeling and imaging. Understanding the structural basis for these RNA-modifying reactions will enable the development of better tools for studying RNA. Nevertheless, high-resolution structures and underlying catalytic mechanisms for members of this ribozyme class remain elusive. Here, we focus on a self-alkylating ribozyme that catalyzes nitrogen-carbon bond formation between a specific guanine and a 2,3-disubstituted epoxide substrate and report the crystal structures of a self-alkylating ribozyme, including both alkylated and apo forms, at 1.71-A and 2.49-A resolution, respectively. The ribozyme assumes an elongated hairpin-like architecture preorganized to accommodate the epoxide substrate in a hook-shaped conformation. Observed reactivity of substrate analogs together with an inverse, log-linear pH dependence of the reaction rate suggests a requirement for epoxide protonation, possibly assisted by the ether oxygens within the substrate.

Structural basis for substrate binding and catalysis by a self-alkylating ribozyme.,Krochmal D, Shao Y, Li NS, DasGupta S, Shelke SA, Koirala D, Piccirilli JA Nat Chem Biol. 2022 Apr;18(4):376-384. doi: 10.1038/s41589-021-00950-z. Epub 2022 , Jan 20. PMID:35058645<ref>PMID:35058645</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 6xjq" style="background-color:#fffaf0;"></div>

==See Also==
*[[Ribozyme 3D structures|Ribozyme 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Aeropyrum pernix]]
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Koirala D]]
[[Category: Piccirilli JA]]