This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
6xjw
From Proteopedia
(Difference between revisions)
| Line 1: | Line 1: | ||
| - | ==== | + | ==Crystal structure of a self-alkylating ribozyme - alkylated form without biotin moiety== |
| - | <StructureSection load='6xjw' size='340' side='right'caption='[[6xjw]]' scene=''> | + | <StructureSection load='6xjw' size='340' side='right'caption='[[6xjw]], [[Resolution|resolution]] 1.92Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6xjw]] 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=6XJW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XJW FirstGlance]. <br> |
| - | </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=6xjw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xjw OCA], [https://pdbe.org/6xjw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xjw RCSB], [https://www.ebi.ac.uk/pdbsum/6xjw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xjw ProSAT]</span></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.918Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=97C:2-{[(4R)-4-hydroxyhexyl]oxy}ethyl+pentanoate'>97C</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=6xjw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xjw OCA], [https://pdbe.org/6xjw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xjw RCSB], [https://www.ebi.ac.uk/pdbsum/6xjw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xjw ProSAT]</span></td></tr> | ||
</table> | </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> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6xjw" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[Ribozyme 3D structures|Ribozyme 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Aeropyrum pernix]] | ||
| + | [[Category: Homo sapiens]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: | + | [[Category: Koirala D]] |
| + | [[Category: Piccirilli JA]] | ||
Current revision
Crystal structure of a self-alkylating ribozyme - alkylated form without biotin moiety
| |||||||||||
