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< | ==Crystal structure of a F. nucleatum FMN riboswitch - Free state== | ||
<StructureSection load='2yif' size='340' side='right'caption='[[2yif]], [[Resolution|resolution]] 3.30Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2yif]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Fusobacterium_nucleatum_subsp._nucleatum_ATCC_25586 Fusobacterium nucleatum subsp. nucleatum ATCC 25586]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YIF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YIF 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]] 3.298Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <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'>[https://proteopedia.org/fgij/fg.htm?mol=2yif FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yif OCA], [https://pdbe.org/2yif PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yif RCSB], [https://www.ebi.ac.uk/pdbsum/2yif PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yif ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Understanding the nature of the free state of riboswitch aptamers is important for illuminating common themes in gene regulation by riboswitches. Prior evidence indicated the flavin mononucleotide (FMN)-binding riboswitch aptamer adopted a 'bound-like' structure in absence of FMN, suggesting only local conformational changes upon ligand binding. In the scope of pinpointing the general nature of such changes at the nucleotide level, we performed SHAPE mapping experiments using the aptamer domain of two phylogenetic variants, both in absence and in presence of FMN. We also solved the crystal structures of one of these domains both free (3.3 A resolution) and bound to FMN (2.95 A resolution). Our comparative study reveals that structural rearrangements occurring upon binding are restricted to a few of the joining regions that form the binding pocket in both RNAs. This type of binding event with minimal structural perturbations is reminiscent of binding events by conformational selection encountered in other riboswitches and various RNAs. | |||
Molecular sensing by the aptamer domain of the FMN riboswitch: a general model for ligand binding by conformational selection.,Vicens Q, Mondragon E, Batey RT Nucleic Acids Res. 2011 Oct 1;39(19):8586-98. Epub 2011 Jul 10. PMID:21745821<ref>PMID:21745821</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2yif" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Riboswitch 3D structures|Riboswitch 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Fusobacterium nucleatum subsp. nucleatum ATCC 25586]] | ||
[[ | [[Category: Large Structures]] | ||
[[Category: Batey RT]] | |||
== | [[Category: Mondragon E]] | ||
< | [[Category: Vicens Q]] | ||
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Latest revision as of 13:53, 20 December 2023
Crystal structure of a F. nucleatum FMN riboswitch - Free stateCrystal structure of a F. nucleatum FMN riboswitch - Free state
Structural highlights
Publication Abstract from PubMedUnderstanding the nature of the free state of riboswitch aptamers is important for illuminating common themes in gene regulation by riboswitches. Prior evidence indicated the flavin mononucleotide (FMN)-binding riboswitch aptamer adopted a 'bound-like' structure in absence of FMN, suggesting only local conformational changes upon ligand binding. In the scope of pinpointing the general nature of such changes at the nucleotide level, we performed SHAPE mapping experiments using the aptamer domain of two phylogenetic variants, both in absence and in presence of FMN. We also solved the crystal structures of one of these domains both free (3.3 A resolution) and bound to FMN (2.95 A resolution). Our comparative study reveals that structural rearrangements occurring upon binding are restricted to a few of the joining regions that form the binding pocket in both RNAs. This type of binding event with minimal structural perturbations is reminiscent of binding events by conformational selection encountered in other riboswitches and various RNAs. Molecular sensing by the aptamer domain of the FMN riboswitch: a general model for ligand binding by conformational selection.,Vicens Q, Mondragon E, Batey RT Nucleic Acids Res. 2011 Oct 1;39(19):8586-98. Epub 2011 Jul 10. PMID:21745821[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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