5k7e: Difference between revisions
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==The structure of pistol ribozyme, soaked with Mn2+== | ==The structure of pistol ribozyme, soaked with Mn2+== | ||
<StructureSection load='5k7e' size='340' side='right' caption='[[5k7e]], [[Resolution|resolution]] 3.27Å' scene=''> | <StructureSection load='5k7e' size='340' side='right'caption='[[5k7e]], [[Resolution|resolution]] 3.27Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5k7e]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K7E OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[5k7e]] 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=5K7E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K7E FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.27Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5k7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k7e OCA], [https://pdbe.org/5k7e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k7e RCSB], [https://www.ebi.ac.uk/pdbsum/5k7e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k7e ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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==See Also== | ==See Also== | ||
*[[Ribozyme|Ribozyme]] | *[[Ribozyme 3D structures|Ribozyme 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Synthetic construct]] | ||
[[Category: | [[Category: Patel D]] | ||
[[Category: | [[Category: Ren A]] | ||
Latest revision as of 12:53, 27 September 2023
The structure of pistol ribozyme, soaked with Mn2+The structure of pistol ribozyme, soaked with Mn2+
Structural highlights
Publication Abstract from PubMedThe field of small self-cleaving nucleolytic ribozymes has been invigorated by the recent discovery of the twister, twister-sister, pistol and hatchet ribozymes. We report the crystal structure of a pistol ribozyme termed env25, which adopts a compact tertiary architecture stabilized by an embedded pseudoknot fold. The G-U cleavage site adopts a splayed-apart conformation with in-line alignment of the modeled 2'-O of G for attack on the adjacent to-be-cleaved P-O5' bond. Highly conserved residues G40 (N1 position) and A32 (N3 and 2'-OH positions) are aligned to act as a general base and a general acid, respectively, to accelerate cleavage chemistry, with their roles confirmed by cleavage assays on variants, and an increased pKa of 4.7 for A32. Our structure of the pistol ribozyme defined how the overall and local topologies dictate the in-line alignment at the G-U cleavage site, with cleavage assays on variants revealing key residues that participate in acid-base-catalyzed cleavage chemistry. Pistol ribozyme adopts a pseudoknot fold facilitating site-specific in-line cleavage.,Ren A, Vusurovic N, Gebetsberger J, Gao P, Juen M, Kreutz C, Micura R, Patel DJ Nat Chem Biol. 2016 Jul 11. doi: 10.1038/nchembio.2125. PMID:27398999[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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