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6xjy
From Proteopedia
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| - | '''Unreleased structure''' | ||
| - | + | ==Crystal structure of a self-alkylating ribozyme - short time incubation with the epoxide substrate== | |
| + | <StructureSection load='6xjy' size='340' side='right'caption='[[6xjy]], [[Resolution|resolution]] 2.16Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[6xjy]] 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=6XJY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XJY 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]] 2.156Å</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=6xjy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xjy OCA], [https://pdbe.org/6xjy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xjy RCSB], [https://www.ebi.ac.uk/pdbsum/6xjy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xjy ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == 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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| - | [[Category: Koirala | + | <div class="pdbe-citations 6xjy" style="background-color:#fffaf0;"></div> |
| - | [[Category: Piccirilli | + | |
| + | ==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]] | ||
Current revision
Crystal structure of a self-alkylating ribozyme - short time incubation with the epoxide substrate
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