3suy: Difference between revisions

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 <StructureSection load='3suy' size='340' side='right'caption='[[3suy]], [[Resolution|resolution]] 3.21&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3suy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SUY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SUY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3suy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Eubacterium_siraeum_V10Sc8a Eubacterium siraeum V10Sc8a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SUY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SUY FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</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]] 3.21&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3suh|3suh]], [[3sux|3sux]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</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=3suy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3suy OCA], [https://pdbe.org/3suy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3suy RCSB], [https://www.ebi.ac.uk/pdbsum/3suy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3suy ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Tetrahydrofolate (THF), a biologically active form of the vitamin folate (B(9)), is an essential cofactor in one-carbon transfer reactions. In bacteria, expression of folate-related genes is controlled by feedback modulation in response to specific binding of THF and related compounds to a riboswitch. Here, we present the X-ray structures of the THF-sensing domain from the Eubacterium siraeum riboswitch in the ligand-bound and unbound states. The structure reveals an "inverted" three-way junctional architecture, most unusual for riboswitches, with the junction located far from the regulatory helix P1 and not directly participating in helix P1 formation. Instead, the three-way junction, stabilized by binding to the ligand, aligns the riboswitch stems for long-range tertiary pseudoknot interactions that contribute to the organization of helix P1 and therefore stipulate the regulatory response of the riboswitch. The pterin moiety of the ligand docks in a semiopen pocket adjacent to the junction, where it forms specific hydrogen bonds with two moderately conserved pyrimidines. The aminobenzoate moiety stacks on a guanine base, whereas the glutamate moiety does not appear to make strong interactions with the RNA. In contrast to other riboswitches, these findings demonstrate that the THF riboswitch uses a limited number of available determinants for ligand recognition. Given that modern antibiotics target folate metabolism, the THF riboswitch structure provides insights on mechanistic aspects of riboswitch function and may help in manipulating THF levels in pathogenic bacteria.
-Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch.,Huang L, Ishibe-Murakami S, Patel DJ, Serganov A Proc Natl Acad Sci U S A. 2011 Sep 6;108(36):14801-6. Epub 2011 Aug 22. PMID:21873197<ref>PMID:21873197</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3suy" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Riboswitch 3D structures|Riboswitch 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Huang, L]]
+[[Category: Huang L]]
-[[Category: Patel, D J]]
+[[Category: Patel DJ]]
-[[Category: Serganov, A]]
+[[Category: Serganov A]]
-[[Category: Gene regulator]]
-[[Category: Pseudoknot]]
-[[Category: Rna]]
-[[Category: Three-way junction]]