5t83: Difference between revisions

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<StructureSection load='5t83' size='340' side='right'caption='[[5t83]], [[Resolution|resolution]] 2.71&Aring;' scene=''>
<StructureSection load='5t83' size='340' side='right'caption='[[5t83]], [[Resolution|resolution]] 2.71&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5t83]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T83 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T83 FirstGlance]. <br>
<table><tr><td colspan='2'>[[5t83]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfobacillus_acidophilus_DSM_10332 Sulfobacillus acidophilus DSM 10332]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T83 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T83 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GAI:GUANIDINE'>GAI</scene>, <scene name='pdbligand=IRI:IRIDIUM+HEXAMMINE+ION'>IRI</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPK:SPERMINE+(FULLY+PROTONATED+FORM)'>SPK</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</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]] 2.71&#8491;</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=5t83 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t83 OCA], [http://pdbe.org/5t83 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t83 RCSB], [http://www.ebi.ac.uk/pdbsum/5t83 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t83 ProSAT]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GAI:GUANIDINE'>GAI</scene>, <scene name='pdbligand=IRI:IRIDIUM+HEXAMMINE+ION'>IRI</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPK:SPERMINE+(FULLY+PROTONATED+FORM)'>SPK</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</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=5t83 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t83 OCA], [https://pdbe.org/5t83 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t83 RCSB], [https://www.ebi.ac.uk/pdbsum/5t83 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t83 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The guanidine-I riboswitch is a conserved RNA element with approximately 2,000 known examples across four phyla of bacteria. It exists upstream of nitrogen metabolism and multidrug resistance transporter genes and alters expression through the specific recognition of a free guanidinium cation. Here we report the structure of a guanidine riboswitch aptamer from Sulfobacillus acidophilus at 2.7 A resolution. Helices P1, P1a, P1b, and P2 form a coaxial stack that acts as a scaffold for ligand binding. A previously unidentified P3 helix docks into P1a to form the guanidinium binding pocket, which is completely enclosed. Every functional group of the ligand is recognized through hydrogen bonding to guanine bases and phosphate oxygens. Guanidinium binding is further stabilized through cation-pi interactions with guanine bases. This allows the riboswitch to recognize guanidinium while excluding other bacterial metabolites with a guanidino group, including the amino acid arginine.
Structural Basis for Ligand Binding to the Guanidine-I Riboswitch.,Reiss CW, Xiong Y, Strobel SA Structure. 2017 Jan 3;25(1):195-202. doi: 10.1016/j.str.2016.11.020. Epub 2016, Dec 22. PMID:28017522<ref>PMID:28017522</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5t83" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Riboswitch|Riboswitch]]
*[[Riboswitch 3D structures|Riboswitch 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Reiss, C W]]
[[Category: Sulfobacillus acidophilus DSM 10332]]
[[Category: Strobel, S A]]
[[Category: Reiss CW]]
[[Category: Xiong, Y]]
[[Category: Strobel SA]]
[[Category: A-minor]]
[[Category: Xiong Y]]
[[Category: Guanidine]]
[[Category: Riboswitch]]
[[Category: Rna]]
[[Category: S-turn]]

Latest revision as of 17:19, 6 March 2024

Structure of a guanidine-I riboswitch from S. acidophilusStructure of a guanidine-I riboswitch from S. acidophilus

Structural highlights

5t83 is a 1 chain structure with sequence from Sulfobacillus acidophilus DSM 10332. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.71Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

5t83, resolution 2.71Å

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