5o69: Difference between revisions
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==The structure of the thermobifida fusca guanidine III riboswitch with agmatine.== | ==The structure of the thermobifida fusca guanidine III riboswitch with agmatine.== | ||
<StructureSection load='5o69' size='340' side='right' caption='[[5o69]], [[Resolution|resolution]] 2.32Å' scene=''> | <StructureSection load='5o69' size='340' side='right'caption='[[5o69]], [[Resolution|resolution]] 2.32Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5o69]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O69 OCA]. For a <b>guided tour on the structure components</b> use [http:// | <table><tr><td colspan='2'>[[5o69]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O69 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5O69 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AG2:AGMATINE'>AG2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AG2:AGMATINE'>AG2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | ||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CBV:5-BROMOCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>CBV</scene></td></tr> | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CBV:5-BROMOCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>CBV</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http:// | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5o69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o69 OCA], [http://pdbe.org/5o69 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o69 RCSB], [http://www.ebi.ac.uk/pdbsum/5o69 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o69 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Huang, L]] | [[Category: Huang, L]] | ||
[[Category: Lilley, D M.J]] | [[Category: Lilley, D M.J]] | ||
Revision as of 15:18, 26 August 2020
The structure of the thermobifida fusca guanidine III riboswitch with agmatine.The structure of the thermobifida fusca guanidine III riboswitch with agmatine.
Structural highlights
Publication Abstract from PubMedRiboswitches are structural elements found in mRNA molecules that couple small-molecule binding to regulation of gene expression, usually by controlling transcription or translation. We have determined high-resolution crystal structures of the ykkC guanidine III riboswitch from Thermobifida fusca. The riboswitch forms a classic H-type pseudoknot that includes a triple helix that is continuous with a central core of conserved nucleotides. These form a left-handed helical ramp of inter-nucleotide interactions, generating the guanidinium cation binding site. The ligand is hydrogen bonded to the Hoogsteen edges of two guanine bases. The binding pocket has a side opening that can accommodate a small side chain, shown by structures with bound methylguanidine, aminoguanidine, ethylguanidine, and agmatine. Comparison of the new structure with those of the guanidine I and II riboswitches reveals that evolution generated three different structural solutions for guanidine binding and subsequent gene regulation, although with some common elements. Structure of the Guanidine III Riboswitch.,Huang L, Wang J, Wilson TJ, Lilley DMJ Cell Chem Biol. 2017 Sep 28. pii: S2451-9456(17)30319-7. doi:, 10.1016/j.chembiol.2017.08.021. PMID:28988949[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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