2oeu: Difference between revisions
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New page: left|200px<br /><applet load="2oeu" size="350" color="white" frame="true" align="right" spinBox="true" caption="2oeu, resolution 2.00Å" /> '''Full-length hammerhe... |
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== | ==Full-length hammerhead ribozyme with Mn(II) bound== | ||
<StructureSection load='2oeu' size='340' side='right'caption='[[2oeu]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
[ | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2oeu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OEU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OEU 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]] 2Å</td></tr> | |||
[ | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</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=2oeu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oeu OCA], [https://pdbe.org/2oeu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oeu RCSB], [https://www.ebi.ac.uk/pdbsum/2oeu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oeu ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Although the hammerhead ribozyme is regarded as a prototype for understanding RNA catalysis, the mechanistic roles of associated metal ions and water molecules in the cleavage reaction remain controversial. We have investigated the catalytic potential of observed divalent metal ions and water molecules bound to a 2 A structure of the full-length hammerhead ribozyme by using X-ray crystallography in combination with molecular dynamics simulations. A single Mn(2+) is observed to bind directly to the A9 phosphate in the active site, accompanying a hydrogen-bond network involving a well-ordered water molecule spanning N1 of G12 (the general base) and 2'-O of G8 (previously implicated in general acid catalysis) that we propose, based on molecular dynamics calculations, facilitates proton transfer in the cleavage reaction. Phosphate-bridging metal interactions and other mechanistic hypotheses are also tested with this approach. | |||
Solvent structure and hammerhead ribozyme catalysis.,Martick M, Lee TS, York DM, Scott WG Chem Biol. 2008 Apr;15(4):332-42. PMID:18420140<ref>PMID:18420140</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2oeu" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Ribozyme 3D structures|Ribozyme 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Martick M]] | |||
[[Category: Scott WG]] | |||
Latest revision as of 10:36, 30 August 2023
Full-length hammerhead ribozyme with Mn(II) bound
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