3suy: Difference between revisions
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==Crystal structure of THF riboswitch, unbound status== | ==Crystal structure of THF riboswitch, unbound status== | ||
<StructureSection load='3suy' size='340' side='right' caption='[[3suy]], [[Resolution|resolution]] 3.21Å' scene=''> | <StructureSection load='3suy' size='340' side='right'caption='[[3suy]], [[Resolution|resolution]] 3.21Å' scene=''> | ||
== Structural highlights == | == 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 [ | <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> | ||
</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='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> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3suh|3suh]], [[3sux|3sux]]</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <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> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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==See Also== | ==See Also== | ||
*[[Riboswitch|Riboswitch]] | *[[Riboswitch 3D structures|Riboswitch 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Huang, L]] | [[Category: Huang, L]] | ||
[[Category: Patel, D J]] | [[Category: Patel, D J]] | ||
Revision as of 11:11, 29 June 2022
Crystal structure of THF riboswitch, unbound statusCrystal structure of THF riboswitch, unbound status
Structural highlights
Publication Abstract from PubMedTetrahydrofolate (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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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