View source for 5nef


==The structure of the G. violaceus guanidine II riboswitch P1 stem-loop with guanidine==
<StructureSection load='5nef' size='340' side='right'caption='[[5nef]], [[Resolution|resolution]] 1.91&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5nef]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gloeobacter_violaceus Gloeobacter violaceus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NEF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NEF 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]] 1.91&#8491;</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=GAI:GUANIDINE'>GAI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5nef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nef OCA], [https://pdbe.org/5nef PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nef RCSB], [https://www.ebi.ac.uk/pdbsum/5nef PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nef ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The guanidine-II (mini-ykkC) riboswitch is the smallest of the guanidine-responsive riboswitches, comprising two stem loops of similar sequence. We have solved high-resolution crystal structures of both stem loops for the riboswitch from Gloeobacter violaceus. The stem loops have a strong propensity to dimerize by intimate loop-loop interaction. The dimerization creates specific binding pockets for two guanidine molecules, explaining their cooperative binding. Within the binding pockets the ligands are hydrogen bonded to a guanine at O6 and N7, and to successive backbone phosphates. Additionally they are each stacked upon a guanine nucleobase. One side of the pocket has an opening to the solvent, slightly lowering the specificity of ligand binding, and structures with bound methylguanidine, aminoguanidine, and agmatine show how this is possible.

The Structure of the Guanidine-II Riboswitch.,Huang L, Wang J, Lilley DMJ Cell Chem Biol. 2017 Jun 22;24(6):695-702.e2. doi:, 10.1016/j.chembiol.2017.05.014. Epub 2017 May 18. PMID:28529131<ref>PMID:28529131</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5nef" style="background-color:#fffaf0;"></div>

==See Also==
*[[Riboswitch 3D structures|Riboswitch 3D structures]]
== References ==
<references/>
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</StructureSection>
[[Category: Gloeobacter violaceus]]
[[Category: Large Structures]]
[[Category: Huang L]]
[[Category: Lilley DMJ]]
[[Category: Wang J]]