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==Class II ligase ribozyme product-template duplex, structure 1==
==Class II ligase ribozyme product-template duplex, structure 1==
<StructureSection load='3ftm' size='340' side='right' caption='[[3ftm]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
<StructureSection load='3ftm' size='340' side='right'caption='[[3ftm]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3ftm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FTM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FTM FirstGlance]. <br>
<table><tr><td colspan='2'>[[3ftm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FTM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FTM FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <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]] 2.7&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3fs0|3fs0]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ftm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ftm OCA], [http://pdbe.org/3ftm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ftm RCSB], [http://www.ebi.ac.uk/pdbsum/3ftm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ftm 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=3ftm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ftm OCA], [https://pdbe.org/3ftm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ftm RCSB], [https://www.ebi.ac.uk/pdbsum/3ftm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ftm ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Ribozyme-catalyzed RNA synthesis is central to the RNA world hypothesis. No natural RNA polymerase ribozymes have been discovered. However, ribozymes that catalyze the requisite chemistry, generating a new phosphodiester through attack of a terminal hydroxyl of an RNA on the alpha-phosphate of a triphosphate-activated oligonucleotide, have been isolated by in vitro selection. These experiments often yield ribozymes that generate 2'-5' phosphodiesters rather than conventional 3'-5' linkages. We have determined crystal structures of the duplex formed by the template segment of a representative 2'-5' RNA ligase ribozyme, the class II ligase, and its ligation product. The structures reveal a product-template duplex with a G x A pair at the ligation junction. This sheared pair is flanked on one side by a minor groove-broadening wedge comprised of two unpaired nucleotides. The reported structure of an independently isolated 3'-5' ligase ribozyme, the L1 ligase, shows a product-template duplex that shares the G x A pair with the class II ligase. However, this G x A pair is flanked by G x U wobbles, rather than an unpaired wedge. We demonstrate that these structural differences of the substrate-template duplexes are largely responsible for the divergent regioselectivity of the two ribozymes, independent of their catalytic moieties, by constructing chimeras. The L1 ligase with a class II substrate-template duplex shows a 30-fold increase in 2'-5' bond synthesis, while the class II ligase with an L1 substrate-template duplex produces 3'-5' bonds exclusively. These results demonstrate how local geometry inherent to the substrate-template duplexes controls the regioselectivity of ribozyme-catalyzed RNA ligation reactions.
Structure-guided engineering of the regioselectivity of RNA ligase ribozymes.,Pitt JN, Ferre-D'Amare AR J Am Chem Soc. 2009 Mar 18;131(10):3532-40. PMID:19220054<ref>PMID:19220054</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3ftm" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Ribozyme|Ribozyme]]
*[[Ribozyme 3D structures|Ribozyme 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Amare, A R.Ferre-D]]
[[Category: Large Structures]]
[[Category: Pitt, J N]]
[[Category: Ferre-D'Amare AR]]
[[Category: 2'-5ss']]
[[Category: Pitt JN]]
[[Category: 2-5]]
[[Category: Ligase]]
[[Category: Ribozyme]]
[[Category: Rna]]

Latest revision as of 12:51, 21 February 2024

Class II ligase ribozyme product-template duplex, structure 1Class II ligase ribozyme product-template duplex, structure 1

Structural highlights

3ftm is a 4 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.7Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

3ftm, resolution 2.70Å

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