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| | <StructureSection load='6dls' size='340' side='right'caption='[[6dls]], [[Resolution|resolution]] 2.88Å' scene=''> | | <StructureSection load='6dls' size='340' side='right'caption='[[6dls]], [[Resolution|resolution]] 2.88Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6dls]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DLS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DLS FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6dls]] 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=6DLS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DLS FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PRP:ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC+ACID'>PRP</scene>, <scene name='pdbligand=TL:THALLIUM+(I)+ION'>TL</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]] 2.885Å</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>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></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>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PRP:ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC+ACID'>PRP</scene>, <scene name='pdbligand=TL:THALLIUM+(I)+ION'>TL</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6dls FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dls OCA], [http://pdbe.org/6dls PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dls RCSB], [http://www.ebi.ac.uk/pdbsum/6dls PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dls ProSAT]</span></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=6dls FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dls OCA], [https://pdbe.org/6dls PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dls RCSB], [https://www.ebi.ac.uk/pdbsum/6dls PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dls ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Peselis, A]] | + | [[Category: Syntrophothermus lipocalidus DSM 12680]] |
| - | [[Category: Serganov, A]] | + | [[Category: Peselis A]] |
| - | [[Category: Non-coding]] | + | [[Category: Serganov A]] |
| - | [[Category: Riboswitch]]
| + | |
| - | [[Category: Rna]]
| + | |
| - | [[Category: Ykkc]]
| + | |
| Structural highlights
6dls is a 1 chain structure with sequence from Syntrophothermus lipocalidus DSM 12680. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.885Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Peselis A, Serganov A. ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands. Nat Chem Biol. 2018 Sep;14(9):887-894. doi: 10.1038/s41589-018-0114-4. Epub 2018 , Aug 17. PMID:30120360 doi:http://dx.doi.org/10.1038/s41589-018-0114-4
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