5eao: Difference between revisions
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New page: '''Unreleased structure''' The entry 5eao is ON HOLD Authors: Mir, A., Golden, B.L. Description: Category: Unreleased Structures Category: Mir, A Category: Golden, B.L |
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The | ==Two active site divalent ion in the crystal structure of the hammerhead ribozyme bound to a transition state analog-Mg2+== | ||
<StructureSection load='5eao' size='340' side='right'caption='[[5eao]], [[Resolution|resolution]] 2.99Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5eao]] 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=5EAO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EAO 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]] 2.988Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CVC:[(1~{R},5~{R},6~{R},8~{R})-6-(4-AZANYL-2-OXIDANYLIDENE-PYRIMIDIN-1-YL)-3,3-BIS(OXIDANYL)-2,4,7-TRIOXA-3$L^{4}-VANADABICYCLO[3.3.0]OCTAN-8-YL]METHYL+DIHYDROGEN+PHOSPHATE'>CVC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=5eao FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eao OCA], [https://pdbe.org/5eao PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5eao RCSB], [https://www.ebi.ac.uk/pdbsum/5eao PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5eao ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The crystal structure of the hammerhead ribozyme bound to the pentavalent transition state analogue vanadate reveals significant rearrangements relative to the previously determined structures. The active site contracts, bringing G10.1 closer to the cleavage site and repositioning a divalent metal ion such that it could, ultimately, interact directly with the scissile phosphate. This ion could also position a water molecule to serve as a general acid in the cleavage reaction. A second divalent ion is observed coordinated to O6 of G12. This metal ion is well-placed to help tune the pKA of G12. On the basis of this crystal structure as well as a wealth of biochemical studies, we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid. | |||
Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue.,Mir A, Golden BL Biochemistry. 2016 Feb 2;55(4):633-6. doi: 10.1021/acs.biochem.5b01139. Epub 2016, Jan 19. PMID:26551631<ref>PMID:26551631</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5eao" style="background-color:#fffaf0;"></div> | ||
[[Category: Golden | |||
==See Also== | |||
*[[Ribozyme 3D structures|Ribozyme 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Synthetic construct]] | |||
[[Category: Golden BL]] | |||
[[Category: Mir A]] | |||
Latest revision as of 09:19, 5 July 2023
Two active site divalent ion in the crystal structure of the hammerhead ribozyme bound to a transition state analog-Mg2+Two active site divalent ion in the crystal structure of the hammerhead ribozyme bound to a transition state analog-Mg2+
Structural highlights
Publication Abstract from PubMedThe crystal structure of the hammerhead ribozyme bound to the pentavalent transition state analogue vanadate reveals significant rearrangements relative to the previously determined structures. The active site contracts, bringing G10.1 closer to the cleavage site and repositioning a divalent metal ion such that it could, ultimately, interact directly with the scissile phosphate. This ion could also position a water molecule to serve as a general acid in the cleavage reaction. A second divalent ion is observed coordinated to O6 of G12. This metal ion is well-placed to help tune the pKA of G12. On the basis of this crystal structure as well as a wealth of biochemical studies, we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid. Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue.,Mir A, Golden BL Biochemistry. 2016 Feb 2;55(4):633-6. doi: 10.1021/acs.biochem.5b01139. Epub 2016, Jan 19. PMID:26551631[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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