4qk8
From Proteopedia
(Difference between revisions)
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4qk8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoanaerobacter_pseudethanolicus Thermoanaerobacter pseudethanolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QK8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QK8 FirstGlance]. <br> | <table><tr><td colspan='2'>[[4qk8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoanaerobacter_pseudethanolicus Thermoanaerobacter pseudethanolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QK8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QK8 FirstGlance]. <br> | ||
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=23G:GUANOSINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>23G</scene>, <scene name='pdbligand=2BA:(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6-AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-3,5,10,12-TETROL+5,12-DIOXIDE'>2BA</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 3.05Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=23G:GUANOSINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>23G</scene>, <scene name='pdbligand=2BA:(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6-AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-3,5,10,12-TETROL+5,12-DIOXIDE'>2BA</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4qk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qk8 OCA], [https://pdbe.org/4qk8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qk8 RCSB], [https://www.ebi.ac.uk/pdbsum/4qk8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qk8 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=4qk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qk8 OCA], [https://pdbe.org/4qk8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qk8 RCSB], [https://www.ebi.ac.uk/pdbsum/4qk8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qk8 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | Bacterial second messenger cyclic di-AMP (c-di-AMP) is implicated in signaling DNA damage and cell wall stress through interactions with several protein receptors and a widespread ydaO-type riboswitch. We report the crystal structures of c-di-AMP riboswitches from Thermoanaerobacter pseudethanolicus and Thermovirga lienii determined at approximately 3.0-A resolution. In both species, the RNA adopts an unforeseen 'square'-shaped pseudosymmetrical architecture that features two three-way junctions, a turn and a pseudoknot, positioned in the square corners. Uncharacteristically for riboswitches, the structure is stapled by two ligand molecules that span the interior of the structure and employ similar noncanonical interactions for RNA recognition. Mutations in either ligand-binding site negatively affect c-di-AMP binding, suggesting that the riboswitch-triggered genetic response requires contribution of both ligands. Our data provide what are to our knowledge the first insights into specific sensing of c-di-AMP and a molecular mechanism underlying the common c-di-AMP-dependent control of essential cellular processes in bacteria. | ||
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| - | Structural insights into recognition of c-di-AMP by the ydaO riboswitch.,Gao A, Serganov A Nat Chem Biol. 2014 Sep;10(9):787-92. doi: 10.1038/nchembio.1607. Epub 2014 Aug, 3. PMID:25086507<ref>PMID:25086507</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 4qk8" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
*[[Riboswitch 3D structures|Riboswitch 3D structures]] | *[[Riboswitch 3D structures|Riboswitch 3D structures]] | ||
| - | == References == | ||
| - | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
Current revision
Thermoanaerobacter pseudethanolicus c-di-AMP riboswitch
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