7d81: Difference between revisions
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<StructureSection load='7d81' size='340' side='right'caption='[[7d81]], [[Resolution|resolution]] 2.10Å' scene=''> | <StructureSection load='7d81' size='340' side='right'caption='[[7d81]], [[Resolution|resolution]] 2.10Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[7d81]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D81 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[7d81]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acidobacteriaceae_bacterium_KBS_83 Acidobacteriaceae bacterium KBS 83]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D81 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7D81 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 2.1Å</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=7d81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d81 OCA], [https://pdbe.org/7d81 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7d81 RCSB], [https://www.ebi.ac.uk/pdbsum/7d81 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7d81 ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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</div> | </div> | ||
<div class="pdbe-citations 7d81" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 7d81" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Riboswitch 3D structures|Riboswitch 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Acidobacteriaceae bacterium KBS 83]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Chen | [[Category: Chen H]] | ||
[[Category: Ren | [[Category: Ren AM]] | ||
Latest revision as of 19:28, 29 November 2023
Crystal Structure of the Domain2 of NAD+ Riboswitch with nicotinamide adenine dinucleotide (NAD+)Crystal Structure of the Domain2 of NAD+ Riboswitch with nicotinamide adenine dinucleotide (NAD+)
Structural highlights
Publication Abstract from PubMedRiboswitches are important gene regulatory elements frequently encountered in bacterial mRNAs. The recently discovered nadA riboswitch contains two similar, tandemly arrayed aptamer domains, with the first domain possessing high affinity for nicotinamide adenine dinucleotide (NAD+). The second domain which comprises the ribosomal binding site in a putative regulatory helix, however, has withdrawn from detection of ligand-induced structural modulation thus far, and therefore, the identity of the cognate ligand and the regulation mechanism have remained unclear. Here, we report crystal structures of both riboswitch domains, each bound to NAD+. Furthermore, we demonstrate that ligand binding to domain 2 requires significantly higher concentrations of NAD+ (or ADP retaining analogs) compared to domain 1. Using a fluorescence spectroscopic approach, we further shed light on the structural features which are responsible for the different ligand affinities, and describe the Mg2+-dependent, distinct folding and pre-organization of their binding pockets. Finally, we speculate about possible scenarios for nadA RNA gene regulation as a putative two-concentration sensor module for a time-controlled signal that is primed and stalled by the gene regulation machinery at low ligand concentrations (domain 1), and finally triggers repression of translation as soon as high ligand concentrations are reached in the cell (domain 2). Structural distinctions between NAD+ riboswitch domains 1 and 2 determine differential folding and ligand binding.,Chen H, Egger M, Xu X, Flemmich L, Krasheninina O, Sun A, Micura R, Ren A Nucleic Acids Res. 2020 Dec 2;48(21):12394-12406. doi: 10.1093/nar/gkaa1029. PMID:33170270[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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