6t3k: Difference between revisions
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==Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of K+, Mg2+ and 5'-exon== | |||
<StructureSection load='6t3k' size='340' side='right'caption='[[6t3k]], [[Resolution|resolution]] 3.44Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6t3k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Oceanobacillus_iheyensis Oceanobacillus iheyensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T3K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6T3K 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]] 3.44Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</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=6t3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t3k OCA], [https://pdbe.org/6t3k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6t3k RCSB], [https://www.ebi.ac.uk/pdbsum/6t3k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6t3k ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Group II introns are ubiquitous self-splicing ribozymes and retrotransposable elements evolutionarily and chemically related to the eukaryotic spliceosome, with potential applications as gene-editing tools. Recent biochemical and structural data have captured the intron in multiple conformations at different stages of catalysis. Here, we employ enzymatic assays, X-ray crystallography, and molecular simulations to resolve the spatiotemporal location and function of conformational changes occurring between the first and the second step of splicing. We show that the first residue of the highly-conserved catalytic triad is protonated upon 5'-splice-site scission, promoting a reversible structural rearrangement of the active site (toggling). Protonation and active site dynamics induced by the first step of splicing facilitate the progression to the second step. Our insights into the mechanism of group II intron splicing parallels functional data on the spliceosome, thus reinforcing the notion that these evolutionarily-related molecular machines share the same enzymatic strategy. | |||
Visualizing group II intron dynamics between the first and second steps of splicing.,Manigrasso J, Chillon I, Genna V, Vidossich P, Somarowthu S, Pyle AM, De Vivo M, Marcia M Nat Commun. 2020 Jun 5;11(1):2837. doi: 10.1038/s41467-020-16741-4. PMID:32503992<ref>PMID:32503992</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 6t3k" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Ribozyme 3D structures|Ribozyme 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Oceanobacillus iheyensis]] | |||
[[Category: Marcia M]] | |||
[[Category: Pyle AM]] | |||
Latest revision as of 15:53, 24 January 2024
Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of K+, Mg2+ and 5'-exonStructure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of K+, Mg2+ and 5'-exon
Structural highlights
Publication Abstract from PubMedGroup II introns are ubiquitous self-splicing ribozymes and retrotransposable elements evolutionarily and chemically related to the eukaryotic spliceosome, with potential applications as gene-editing tools. Recent biochemical and structural data have captured the intron in multiple conformations at different stages of catalysis. Here, we employ enzymatic assays, X-ray crystallography, and molecular simulations to resolve the spatiotemporal location and function of conformational changes occurring between the first and the second step of splicing. We show that the first residue of the highly-conserved catalytic triad is protonated upon 5'-splice-site scission, promoting a reversible structural rearrangement of the active site (toggling). Protonation and active site dynamics induced by the first step of splicing facilitate the progression to the second step. Our insights into the mechanism of group II intron splicing parallels functional data on the spliceosome, thus reinforcing the notion that these evolutionarily-related molecular machines share the same enzymatic strategy. Visualizing group II intron dynamics between the first and second steps of splicing.,Manigrasso J, Chillon I, Genna V, Vidossich P, Somarowthu S, Pyle AM, De Vivo M, Marcia M Nat Commun. 2020 Jun 5;11(1):2837. doi: 10.1038/s41467-020-16741-4. PMID:32503992[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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