6dlr: Difference between revisions
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==PRPP Riboswitch bound to PRPP, iridium-hexamine soaked structure== | |||
<StructureSection load='6dlr' size='340' side='right'caption='[[6dlr]], [[Resolution|resolution]] 2.66Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6dlr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Syntrophothermus_lipocalidus_DSM_12680 Syntrophothermus lipocalidus DSM 12680]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DLR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DLR FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.656Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=IRI:IRIDIUM+HEXAMMINE+ION'>IRI</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PRP:ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC+ACID'>PRP</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=6dlr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dlr OCA], [https://pdbe.org/6dlr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dlr RCSB], [https://www.ebi.ac.uk/pdbsum/6dlr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dlr ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The ykkC family of bacterial riboswitches combines several widespread classes that have similar secondary structures and consensus motifs but control different genes in response to different cellular metabolites. Here we report the crystal structures of two distinct ykkC riboswitches specifically bound to their cognate ligand ppGpp, a second messenger involved in stress response, or PRPP, a precursor in purine biosynthesis. Both RNAs adopt similar structures and contain a conserved core previously observed in the guanidine-specific ykkC riboswitch. However, ppGpp and PRPP riboswitches uniquely employ an additional helical element that joins the ends of the ligand-sensing domains and creates a tunnel for direct and Mg(2+)-mediated binding of ligands. Mutational and footprinting experiments highlight the importance of conserved nucleotides forming the tunnel and long-distance contacts for ligand binding and genetic response. Our work provides new insights into the specificity of riboswitches and gives a unique opportunity for future studies of RNA evolution. | |||
ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands.,Peselis A, Serganov A Nat Chem Biol. 2018 Sep;14(9):887-894. doi: 10.1038/s41589-018-0114-4. Epub 2018 , Aug 17. PMID:30120360<ref>PMID:30120360</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 6dlr" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Riboswitch 3D structures|Riboswitch 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Syntrophothermus lipocalidus DSM 12680]] | |||
[[Category: Peselis A]] | |||
[[Category: Serganov A]] | |||
Latest revision as of 13:07, 22 May 2024
PRPP Riboswitch bound to PRPP, iridium-hexamine soaked structurePRPP Riboswitch bound to PRPP, iridium-hexamine soaked structure
Structural highlights
Publication Abstract from PubMedThe ykkC family of bacterial riboswitches combines several widespread classes that have similar secondary structures and consensus motifs but control different genes in response to different cellular metabolites. Here we report the crystal structures of two distinct ykkC riboswitches specifically bound to their cognate ligand ppGpp, a second messenger involved in stress response, or PRPP, a precursor in purine biosynthesis. Both RNAs adopt similar structures and contain a conserved core previously observed in the guanidine-specific ykkC riboswitch. However, ppGpp and PRPP riboswitches uniquely employ an additional helical element that joins the ends of the ligand-sensing domains and creates a tunnel for direct and Mg(2+)-mediated binding of ligands. Mutational and footprinting experiments highlight the importance of conserved nucleotides forming the tunnel and long-distance contacts for ligand binding and genetic response. Our work provides new insights into the specificity of riboswitches and gives a unique opportunity for future studies of RNA evolution. ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands.,Peselis A, Serganov A Nat Chem Biol. 2018 Sep;14(9):887-894. doi: 10.1038/s41589-018-0114-4. Epub 2018 , Aug 17. PMID:30120360[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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