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==Crystal structure of guanine riboswitch C61U/G37A double mutant bound to thio-guanine==
==Crystal structure of guanine riboswitch C61U/G37A double mutant bound to thio-guanine==
<StructureSection load='3rkf' size='340' side='right' caption='[[3rkf]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
<StructureSection load='3rkf' size='340' side='right'caption='[[3rkf]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3rkf]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RKF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RKF FirstGlance]. <br>
<table><tr><td colspan='2'>[[3rkf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RKF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RKF FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DX4:2-AMINO-1,9-DIHYDRO-6H-PURINE-6-THIONE'>DX4</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</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]] 2.5&#8491;</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=3rkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rkf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rkf RCSB], [http://www.ebi.ac.uk/pdbsum/3rkf PDBsum]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DX4:2-AMINO-1,9-DIHYDRO-6H-PURINE-6-THIONE'>DX4</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</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=3rkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rkf OCA], [https://pdbe.org/3rkf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rkf RCSB], [https://www.ebi.ac.uk/pdbsum/3rkf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rkf ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Riboswitch RNAs fold into complex tertiary structures upon binding to their cognate ligand. Ligand recognition is accomplished by key residues in the binding pocket. In addition, it often crucially depends on the stability of peripheral structural elements. The ligand-bound complex of the guanine-sensing riboswitch from Bacillus subtilis, for example, is stabilized by extensive interactions between apical loop regions of the aptamer domain. Previously, we have shown that destabilization of this tertiary loop-loop interaction abrogates ligand binding of the G37A/C61U-mutant aptamer domain (Gsw(loop)) in the absence of Mg(2+). However, if Mg(2+) is available, ligand-binding capability is restored by a population shift of the ground-state RNA ensemble toward RNA conformations with pre-formed loop-loop interactions. Here, we characterize the striking influence of long-range tertiary structure on RNA folding kinetics and on ligand-bound complex structure, both by X-ray crystallography and time-resolved NMR. The X-ray structure of the ligand-bound complex reveals that the global architecture is almost identical to the wild-type aptamer domain. The population of ligand-binding competent conformations in the ground-state ensemble of Gsw(loop) is tunable through variation of the Mg(2+) concentration. We quantitatively describe the influence of distinct Mg(2+) concentrations on ligand-induced folding trajectories both by equilibrium and time-resolved NMR spectroscopy at single-residue resolution.
Influence of ground-state structure and Mg2+ binding on folding kinetics of the guanine-sensing riboswitch aptamer domain.,Buck J, Wacker A, Warkentin E, Wohnert J, Wirmer-Bartoschek J, Schwalbe H Nucleic Acids Res. 2011 Sep 2. PMID:21890900<ref>PMID:21890900</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[Riboswitch|Riboswitch]]
*[[Riboswitch 3D structures|Riboswitch 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Buck, J]]
[[Category: Bacillus subtilis]]
[[Category: Schwalbe, H]]
[[Category: Large Structures]]
[[Category: Wacker, A]]
[[Category: Buck J]]
[[Category: Warkentin, E]]
[[Category: Schwalbe H]]
[[Category: Wirmer-Bartoschek, J]]
[[Category: Wacker A]]
[[Category: Woehnert, J]]
[[Category: Warkentin E]]
[[Category: M-rna]]
[[Category: Wirmer-Bartoschek J]]
[[Category: Riboswitch]]
[[Category: Woehnert J]]
[[Category: Rna]]
[[Category: Thioguanine]]
[[Category: Three-way junction]]

Latest revision as of 15:27, 14 March 2024

Crystal structure of guanine riboswitch C61U/G37A double mutant bound to thio-guanineCrystal structure of guanine riboswitch C61U/G37A double mutant bound to thio-guanine

Structural highlights

3rkf is a 4 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

3rkf, resolution 2.50Å

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