2hol: Difference between revisions

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-[[Image:2hol.gif|left|200px]]
- {{Structure
+==Crystal structure of an E. coli thi-box riboswitch bound to thiamine pyrophosphate, barium ions==
-|PDB= 2hol |SIZE=350|CAPTION= <scene name='initialview01'>2hol</scene>, resolution 2.90&Aring;
+<StructureSection load='2hol' size='340' side='right'caption='[[2hol]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
+<table><tr><td colspan='2'>[[2hol]] 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=2HOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HOL FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2hol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hol OCA], [https://pdbe.org/2hol PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hol RCSB], [https://www.ebi.ac.uk/pdbsum/2hol PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hol ProSAT]</span></td></tr>
-|RELATEDENTRY=[[2hoj|2HOJ]], [[2hok|2HOK]], [[2hom|2HOM]], [[2hoo|2HOO]], [[2hop|2HOP]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2hol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hol OCA], [http://www.ebi.ac.uk/pdbsum/2hol PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2hol RCSB]</span>
-}}
-'''Crystal structure of an E. coli thi-box riboswitch bound to thiamine pyrophosphate, barium ions'''
+==See Also==
+*[[Riboswitch 3D structures|Riboswitch 3D structures]]
+*[[Ribozyme 3D structures|Ribozyme 3D structures]]
-==Overview==
+__TOC__
-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.
+</StructureSection>
+[[Category: Escherichia coli]]
-==About this Structure==
+[[Category: Large Structures]]
-HOL is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HOL OCA].
+[[Category: Edwards TE]]
+[[Category: Ferre-D'Amare AR]]
-==Reference==
-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:[http://www.ncbi.nlm.nih.gov/pubmed/16962976 16962976]
-[[Category: Protein complex]]
-[[Category: Amare, A R.Ferre-D.]]
-[[Category: Edwards, T E.]]
-[[Category: riboswitch]]
-[[Category: rna]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:33:09 2008''