4fel: Difference between revisions
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New page: '''Unreleased structure''' The entry 4fel is ON HOLD Authors: Stoddard, C.D., Trausch, J. J., Widmann, J., Marcano, J., Knight, R., Batey, R.T. Description: Crystal structure of the U2... |
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The | ==Crystal structure of the U25A/A46G mutant of the xpt-pbuX guanine riboswitch aptamer domain in complex with hypoxanthine== | ||
<StructureSection load='4fel' size='340' side='right'caption='[[4fel]], [[Resolution|resolution]] 1.60Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4fel]] is a 1 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=4FEL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FEL 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]] 1.6Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</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=4fel FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fel OCA], [https://pdbe.org/4fel PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fel RCSB], [https://www.ebi.ac.uk/pdbsum/4fel PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fel ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Direct sensing of intracellular metabolite concentrations by riboswitch RNAs provides an economical and rapid means to maintain metabolic homeostasis. Since many organisms employ the same class of riboswitch to control different genes or transcription units, it is likely that functional variation exists in riboswitches such that activity is tuned to meet cellular needs. Using a bioinformatic approach, we have identified a region of the purine riboswitch aptamer domain that displays conservation patterns linked to riboswitch activity. Aptamer domain compositions within this region can be divided into nine classes that display a spectrum of activities. Naturally occurring compositions in this region favor rapid association rate constants and slow dissociation rate constants for ligand binding. Using X-ray crystallography and chemical probing, we demonstrate that both the free and bound states are influenced by the composition of this region and that modest sequence alterations have a dramatic impact on activity. The introduction of non-natural compositions result in the inability to regulate gene expression in vivo, suggesting that aptamer domain activity is highly plastic and thus readily tunable to meet cellular needs. | |||
Nucleotides Adjacent to the Ligand-Binding Pocket are Linked to Activity Tuning in the Purine Riboswitch.,Stoddard CD, Widmann J, Trausch JJ, Marcano-Velazquez JG, Knight R, Batey RT J Mol Biol. 2013 Feb 26. pii: S0022-2836(13)00125-3. doi:, 10.1016/j.jmb.2013.02.023. PMID:23485418<ref>PMID:23485418</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4fel" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Riboswitch 3D structures|Riboswitch 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bacillus subtilis]] | |||
[[Category: Large Structures]] | |||
[[Category: Batey RT]] | |||
[[Category: Knight R]] | |||
[[Category: Marcano J]] | |||
[[Category: Stoddard CD]] | |||
[[Category: Trausch JJ]] | |||
[[Category: Widmann J]] | |||
Latest revision as of 10:55, 13 August 2026
Crystal structure of the U25A/A46G mutant of the xpt-pbuX guanine riboswitch aptamer domain in complex with hypoxanthine
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