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==Crystal structure of the AU25A/A46G/C74U mutant xpt-pbuX guanine riboswitch aptamer domain in complex with 2,6-diaminopurine== | |||
<StructureSection load='4feo' size='340' side='right' caption='[[4feo]], [[Resolution|resolution]] 1.60Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4feo]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FEO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FEO FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6AP:9H-PURINE-2,6-DIAMINE'>6AP</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr> | |||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1u8d|1u8d]], [[4fe5|4fe5]], [[4fej|4fej]], [[4fel|4fel]], [[4fen|4fen]], [[4fep|4fep]]</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=4feo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4feo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4feo RCSB], [http://www.ebi.ac.uk/pdbsum/4feo PDBsum]</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> | |||
[[Category: Batey, R T | |||
[[Category: Knight, R | ==See Also== | ||
[[Category: Marcano, J | *[[Riboswitch|Riboswitch]] | ||
[[Category: Stoddard, C D | == References == | ||
[[Category: Trausch, J J | <references/> | ||
[[Category: Widmann, J | __TOC__ | ||
</StructureSection> | |||
[[Category: Batey, R T]] | |||
[[Category: Knight, R]] | |||
[[Category: Marcano, J]] | |||
[[Category: Stoddard, C D]] | |||
[[Category: Trausch, J J]] | |||
[[Category: Widmann, J]] | |||
[[Category: 6-diaminopurine]] | [[Category: 6-diaminopurine]] | ||
[[Category: Genetic regulatory element]] | [[Category: Genetic regulatory element]] | ||
[[Category: Rna]] | [[Category: Rna]] | ||
[[Category: Three-way junction with distal tertiary interaction]] | [[Category: Three-way junction with distal tertiary interaction]] | ||
Revision as of 17:30, 4 January 2015
Crystal structure of the AU25A/A46G/C74U mutant xpt-pbuX guanine riboswitch aptamer domain in complex with 2,6-diaminopurineCrystal structure of the AU25A/A46G/C74U mutant xpt-pbuX guanine riboswitch aptamer domain in complex with 2,6-diaminopurine
Structural highlights
Publication Abstract from PubMedDirect 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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