4qjh

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==Crystal Structure of the Twister Ribozyme with the Nucleotide 5'- to the Cleavage Site Ordered at 4.1 A Resolution==
==Crystal Structure of the Twister Ribozyme with the Nucleotide 5'- to the Cleavage Site Ordered at 4.1 A Resolution==
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<StructureSection load='4qjh' size='340' side='right' caption='[[4qjh]], [[Resolution|resolution]] 3.88&Aring;' scene=''>
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<StructureSection load='4qjh' size='340' side='right'caption='[[4qjh]], [[Resolution|resolution]] 3.88&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4qjh]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QJH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QJH FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4qjh]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QJH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QJH FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.88&#8491;</td></tr>
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<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4qjd|4qjd]]</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4qjh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qjh OCA], [https://pdbe.org/4qjh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qjh RCSB], [https://www.ebi.ac.uk/pdbsum/4qjh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qjh ProSAT]</span></td></tr>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4qjh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qjh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qjh RCSB], [http://www.ebi.ac.uk/pdbsum/4qjh PDBsum]</span></td></tr>
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</table>
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<table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Twister is a recently discovered RNA motif that is estimated to have one of the fastest known catalytic rates of any naturally occurring small self-cleaving ribozyme. We determined the 4.1-A resolution crystal structure of a twister sequence from an organism that has not been cultured in isolation, and it shows an ordered scissile phosphate and nucleotide 5' to the cleavage site. A second crystal structure of twister from Orzyza sativa determined at 3.1-A resolution exhibits a disordered scissile phosphate and nucleotide 5' to the cleavage site. The core of twister is stabilized by base pairing, a large network of stacking interactions, and two pseudoknots. We observe three nucleotides that appear to mediate catalysis: a guanosine that we propose deprotonates the 2'-hydroxyl of the nucleotide 5' to the cleavage site and a conserved adenosine. We suggest the adenosine neutralizes the negative charge on a nonbridging phosphate oxygen atom at the cleavage site. The active site also positions the labile linkage for in-line nucleophilic attack, and thus twister appears to simultaneously use three strategies proposed for small self-cleaving ribozymes. The twister crystal structures (i) show its global structure, (ii) demonstrate the significance of the double pseudoknot fold, (iii) provide a possible hypothesis for enhanced catalysis, and (iv) illuminate the roles of all 10 highly conserved nucleotides of twister that participate in the formation of its small and stable catalytic pocket.
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Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme.,Eiler D, Wang J, Steitz TA Proc Natl Acad Sci U S A. 2014 Aug 25. pii: 201414571. PMID:25157168<ref>PMID:25157168</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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==See Also==
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</div>
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*[[Ribozyme 3D structures|Ribozyme 3D structures]]
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Eiler, D R.]]
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[[Category: Large Structures]]
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[[Category: Steitz, T A.]]
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[[Category: Eiler DR]]
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[[Category: Wang, J.]]
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[[Category: Steitz TA]]
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[[Category: Rna]]
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[[Category: Wang J]]
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[[Category: Small self-cleaving ribozyme]]
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Current revision

Crystal Structure of the Twister Ribozyme with the Nucleotide 5'- to the Cleavage Site Ordered at 4.1 A Resolution

PDB ID 4qjh

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