4y1j: Difference between revisions

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 ==Lactococcus lactis yybP-ykoY Mn riboswitch A41U binding site mutant in presence of Mn2+==
-<StructureSection load='4y1j' size='340' side='right' caption='[[4y1j]], [[Resolution|resolution]] 2.24&Aring;' scene=''>
+<StructureSection load='4y1j' size='340' side='right'caption='[[4y1j]], [[Resolution|resolution]] 2.24&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4y1j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y1J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y1J FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4y1j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_lactis_subsp._lactis Lactococcus lactis subsp. lactis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y1J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y1J FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</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]] 2.24&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4y1i|4y1i]], [[4y1m|4y1m]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</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=4y1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y1j OCA], [http://pdbe.org/4y1j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y1j RCSB], [http://www.ebi.ac.uk/pdbsum/4y1j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4y1j 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=4y1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y1j OCA], [https://pdbe.org/4y1j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y1j RCSB], [https://www.ebi.ac.uk/pdbsum/4y1j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y1j ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Gene regulation in cis by riboswitches is prevalent in bacteria. The yybP-ykoY riboswitch family is quite widespread, yet its ligand and function remained unknown. Here, we characterize the Lactococcus lactis yybP-ykoY orphan riboswitch as a Mn(2+)-dependent transcription-ON riboswitch, with a approximately 30-40 muM affinity for Mn(2+). We further determined its crystal structure at 2.7 A to elucidate the metal sensing mechanism. The riboswitch resembles a hairpin, with two coaxially stacked helices tethered by a four-way junction and a tertiary docking interface. The Mn(2+)-sensing region, strategically located at the highly conserved docking interface, has two metal binding sites. Whereas one site tolerates the binding of either Mg(2+) or Mn(2+), the other site strongly prefers Mn(2+) due to a direct contact from the N7 of an invariable adenosine. Mutagenesis and a Mn(2+)-free E. coli yybP-ykoY structure further reveal that Mn(2+) binding is coupled with stabilization of the Mn(2+)-sensing region and the aptamer domain.
-Mn(2+)-Sensing Mechanisms of yybP-ykoY Orphan Riboswitches.,Price IR, Gaballa A, Ding F, Helmann JD, Ke A Mol Cell. 2015 Mar 19;57(6):1110-23. doi: 10.1016/j.molcel.2015.02.016. PMID:25794619<ref>PMID:25794619</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4y1j" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Riboswitch|Riboswitch]]
+*[[Riboswitch 3D structures|Riboswitch 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Ke, A]]
+[[Category: Lactococcus lactis subsp. lactis]]
-[[Category: Price, I R]]
+[[Category: Large Structures]]
-[[Category: Manganese-binding]]
+[[Category: Ke A]]
-[[Category: Mutant]]
+[[Category: Price IR]]
-[[Category: Riboswitch]]
-[[Category: Rna]]