7d7x: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-'''Unreleased structure'''
-The entry 7d7x is ON HOLD
+==Crystal Structure of the Domain1 of NAD+ Riboswitch with adenosine diphosphate (ADP)==
+<StructureSection load='7d7x' size='340' side='right'caption='[[7d7x]], [[Resolution|resolution]] 2.63&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[7d7x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D7X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7D7X 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]] 2.631&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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=7d7x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d7x OCA], [https://pdbe.org/7d7x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7d7x RCSB], [https://www.ebi.ac.uk/pdbsum/7d7x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7d7x ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Riboswitches 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 The second domain which comprises the ribosomal binding site in a putative regulatory helix, however, has withdrawn from detection of ligand-induced structural modulation thus far, and therefore, the identity of the cognate ligand and the regulation mechanism have remained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).
-Authors:
+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<ref>PMID:33170270</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 7d7x" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Riboswitch 3D structures|Riboswitch 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Synthetic construct]]
+[[Category: Chen H]]
+[[Category: Ren AM]]