2hoo: Difference between revisions

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 ==Crystal structure of an E. coli thi-box riboswitch bound to benfotiamine==
-<StructureSection load='2hoo' size='340' side='right' caption='[[2hoo]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+<StructureSection load='2hoo' size='340' side='right'caption='[[2hoo]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2hoo]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HOO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HOO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2hoo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HOO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HOO FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BFT:S-BENZOYLTHIAMINE+O-MONOPHOSPHATE'>BFT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2hoj|2hoj]], [[2hok|2hok]], [[2hol|2hol]], [[2hom|2hom]], [[2hop|2hop]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BFT:S-BENZOYLTHIAMINE+O-MONOPHOSPHATE'>BFT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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=2hoo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hoo OCA], [http://pdbe.org/2hoo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hoo RCSB], [http://www.ebi.ac.uk/pdbsum/2hoo PDBsum]</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=2hoo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hoo OCA], [https://pdbe.org/2hoo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hoo RCSB], [https://www.ebi.ac.uk/pdbsum/2hoo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hoo ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Riboswitches are noncoding mRNA elements that bind small-molecule metabolites with high affinity and specificity, and they regulate the expression of associated genes. The thi-box riboswitch can exhibit a 1000-fold higher affinity for thiamine pyrophosphate over closely related noncognate compounds such as thiamine monophosphate. To understand the chemical basis of thi-box pyrophosphate specificity, we have determined crystal structures of an E. coli thi-box bound to thiamine pyrophosphate, thiamine monophosphate, and the structural analogs benfotiamine and pyrithiamine. When bound to monophosphorylated compounds, the RNA elements that recognize the thiamine and phosphate moieties of the ligand move closer together. This allows the riboswitch to recognize the monophosphate in a manner similar to how it recognizes the beta-phosphate of thiamine pyrophosphate. In the pyrithiamine complex, the pyrophosphate binding site is largely unstructured. These results show how the riboswitch can bind to various metabolites, and why the thi-box preferentially binds thiamine pyrophosphate.
-Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition.,Edwards TE, Ferre-D'Amare AR Structure. 2006 Sep;14(9):1459-68. PMID:16962976<ref>PMID:16962976</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2hoo" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Riboswitch|Riboswitch]]
+*[[Riboswitch 3D structures|Riboswitch 3D structures]]
-*[[Ribozyme|Ribozyme]]
+*[[Ribozyme 3D structures|Ribozyme 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Amare, A R.Ferre-D]]
+[[Category: Escherichia coli]]
-[[Category: Edwards, T E]]
+[[Category: Large Structures]]
-[[Category: Benfotiamine]]
+[[Category: Edwards TE]]
-[[Category: Riboswitch]]
+[[Category: Ferre-D'Amare AR]]
-[[Category: Rna]]