5ny8: Difference between revisions
No edit summary |
No edit summary |
||
| Line 3: | Line 3: | ||
<StructureSection load='5ny8' size='340' side='right'caption='[[5ny8]], [[Resolution|resolution]] 2.04Å' scene=''> | <StructureSection load='5ny8' size='340' side='right'caption='[[5ny8]], [[Resolution|resolution]] 2.04Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5ny8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NY8 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[5ny8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermobifida_fusca Thermobifida fusca]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NY8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NY8 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.04Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGU:AMINOGUANIDINE'>AGU</scene>, <scene name='pdbligand=CBV:5-BROMOCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>CBV</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=5ny8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ny8 OCA], [https://pdbe.org/5ny8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ny8 RCSB], [https://www.ebi.ac.uk/pdbsum/5ny8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ny8 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
| Line 17: | Line 17: | ||
</div> | </div> | ||
<div class="pdbe-citations 5ny8" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 5ny8" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Riboswitch 3D structures|Riboswitch 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
| Line 22: | Line 25: | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Thermobifida fusca]] | ||
[[Category: | [[Category: Huang L]] | ||
[[Category: | [[Category: Lilley DMJ]] | ||
[[Category: | [[Category: Wang J]] | ||
Latest revision as of 15:15, 22 November 2023
The structure of the thermobifida fusca guanidine III riboswitch with aminoguanidineThe structure of the thermobifida fusca guanidine III riboswitch with aminoguanidine
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. See AlsoReferences
|
| ||||||||||||||||||