5t5a: Difference between revisions

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<StructureSection load='5t5a' size='340' side='right'caption='[[5t5a]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='5t5a' size='340' side='right'caption='[[5t5a]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5t5a]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T5A OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5T5A FirstGlance]. <br>
<table><tr><td colspan='2'>[[5t5a]] is a 1 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=5T5A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T5A FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CBV:5-BROMOCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>CBV</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CBV:5-BROMOCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>CBV</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'>[http://proteopedia.org/fgij/fg.htm?mol=5t5a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t5a OCA], [http://pdbe.org/5t5a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t5a RCSB], [http://www.ebi.ac.uk/pdbsum/5t5a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t5a ProSAT]</span></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=5t5a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t5a OCA], [https://pdbe.org/5t5a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t5a RCSB], [https://www.ebi.ac.uk/pdbsum/5t5a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t5a ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The TS ribozyme (originally called "twister sister") is a catalytic RNA. We present a crystal structure of the ribozyme in a pre-reactive conformation. Two co-axial helical stacks are organized by a three-way junction and two tertiary contacts. Five divalent metal ions are directly coordinated to RNA ligands, making important contributions to the RNA architecture. The scissile phosphate lies in a quasihelical loop region that is organized by a network of hydrogen bonding. A divalent metal ion is directly bound to the nucleobase 5' to the scissile phosphate, with an inner-sphere water molecule positioned to interact with the O2' nucleophile. The rate of ribozyme cleavage correlated in a log-linear manner with divalent metal ion pKa, consistent with proton transfer in the transition state, and we propose that the bound metal ion is a likely general base for the cleavage reaction. Our data indicate that the TS ribozyme functions predominantly as a metalloenzyme.
The structure of a nucleolytic ribozyme that employs a catalytic metal ion.,Liu Y, Wilson TJ, Lilley DM Nat Chem Biol. 2017 Mar 6. doi: 10.1038/nchembio.2333. PMID:28263963<ref>PMID:28263963</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5t5a" 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: Lilley, D M.J]]
[[Category: Metagenome]]
[[Category: Liu, Y]]
[[Category: Lilley DMJ]]
[[Category: Wilson, T J]]
[[Category: Liu Y]]
[[Category: Rna]]
[[Category: Wilson TJ]]
[[Category: Rna junction catalysis]]
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