5y87: Difference between revisions

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<StructureSection load='5y87' size='340' side='right'caption='[[5y87]], [[Resolution|resolution]] 2.13&Aring;' scene=''>
<StructureSection load='5y87' size='340' side='right'caption='[[5y87]], [[Resolution|resolution]] 2.13&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5y87]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y87 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5Y87 FirstGlance]. <br>
<table><tr><td colspan='2'>[[5y87]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Metagenome Metagenome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y87 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y87 FirstGlance]. <br>
</td></tr><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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.132&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5y87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y87 OCA], [http://pdbe.org/5y87 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y87 RCSB], [http://www.ebi.ac.uk/pdbsum/5y87 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y87 ProSAT]</span></td></tr>
<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'>[https://proteopedia.org/fgij/fg.htm?mol=5y87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y87 OCA], [https://pdbe.org/5y87 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y87 RCSB], [https://www.ebi.ac.uk/pdbsum/5y87 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y87 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Here we report on the crystal structure and cleavage assays of a four-way junctional twister-sister self-cleaving ribozyme. Notably, 11 conserved spatially separated loop nucleotides are brought into close proximity at the ribozyme core through long-range interactions mediated by hydrated Mg2+ cations. The C62-A63 step at the cleavage site adopts a splayed-apart orientation, with flexible C62 directed outwards, whereas A63 is directed inwards and anchored by stacking and hydrogen-bonding interactions. Structure-guided studies of key base, sugar, and phosphate mutations in the twister-sister ribozyme, suggest contributions to the cleavage chemistry from interactions between a guanine at the active site and the non-bridging oxygen of the scissile phosphate, a feature found previously also for the related twister ribozyme. Our four-way junctional pre-catalytic structure differs significantly in the alignment at the cleavage step (splayed-apart vs. base-stacked) and surrounding residues and hydrated Mg2+ ions relative to a reported three-way junctional pre-catalytic structure of the twister-sister ribozyme.
Structure-based insights into self-cleavage by a four-way junctional twister-sister ribozyme.,Zheng L, Mairhofer E, Teplova M, Zhang Y, Ma J, Patel DJ, Micura R, Ren A Nat Commun. 2017 Oct 30;8(1):1180. doi: 10.1038/s41467-017-01276-y. PMID:29081514<ref>PMID:29081514</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5y87" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Ribozyme|Ribozyme]]
*[[Ribozyme 3D structures|Ribozyme 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Micura, R L]]
[[Category: Metagenome]]
[[Category: Ren, A]]
[[Category: Micura RL]]
[[Category: Zheng, L]]
[[Category: Ren A]]
[[Category: Catalysis]]
[[Category: Zheng L]]
[[Category: Mn2+ soaking]]
[[Category: Riboyzme]]
[[Category: Rna]]
[[Category: Self-cleaving]]
[[Category: Twister-sister]]

Latest revision as of 13:22, 27 March 2024

Structure-based Insights into Self-Cleavage by a Four-way Junctional Twister-Sister RibozymeStructure-based Insights into Self-Cleavage by a Four-way Junctional Twister-Sister Ribozyme

Structural highlights

5y87 is a 4 chain structure with sequence from Metagenome. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.132Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

5y87, resolution 2.13Å

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