3d2g: Difference between revisions

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-[[Image:3d2g.png|left|200px]]
-<!--
+==Structural basis of thiamine pyrophosphate analogues binding to the eukaryotic riboswitch==
-The line below this paragraph, containing "STRUCTURE_3d2g", creates the "Structure Box" on the page.
+<StructureSection load='3d2g' size='340' side='right'caption='[[3d2g]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3d2g]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D2G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D2G FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
-{{STRUCTURE_3d2g|  PDB=3d2g  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3d2g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d2g OCA], [https://pdbe.org/3d2g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d2g RCSB], [https://www.ebi.ac.uk/pdbsum/3d2g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d2g ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The thiamine pyrophosphate (TPP)-sensing riboswitch is the only riboswitch found in eukaryotes. In plants, TPP regulates its own production by binding to the 3' untranslated region of the mRNA encoding ThiC, a critical enzyme in thiamine biosynthesis, which promotes the formation of an unstable splicing variant. In order to better understand the molecular basis of TPP-analogue binding to the eukaryotic TPP-responsive riboswitch, we have determined the crystal structures of the Arabidopsis thaliana TPP-riboswitch in complex with oxythiamine pyrophosphate (OTPP) and with the antimicrobial compound pyrithiamine pyrophosphate (PTPP). The OTPP-riboswitch complex reveals that the pyrimidine ring of OTPP is stabilized in its enol form in order to retain key interactions with guanosine 28 of the riboswitch previously observed in the TPP complex. The structure of PTPP in complex with the riboswitch shows that the base moiety of guanosine 60 undergoes a conformational change to cradle the pyridine ring of the PTPP. Structural information from these complexes has implications for the design of novel antimicrobials targeting TPP-sensing riboswitches.
-===Structural basis of thiamine pyrophosphate analogues binding to the eukaryotic riboswitch===
+Structural basis of thiamine pyrophosphate analogues binding to the eukaryotic riboswitch.,Thore S, Frick C, Ban N J Am Chem Soc. 2008 Jul 2;130(26):8116-7. Epub 2008 Jun 6. PMID:18533652<ref>PMID:18533652</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3d2g" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18533652}}, adds the Publication Abstract to the page
+*[[Riboswitch 3D structures|Riboswitch 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18533652 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18533652}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[3d2g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D2G OCA].
-==Reference==
-<ref group="xtra">PMID:018533652</ref><references group="xtra"/>
-[[Category: Arabidopsis thaliana]]
-[[Category: Thore, S.]]
-[[Category: Antibiotic]]
 [[Category: Arabidopsis thaliana]]
-[[Category: Eukaryote]]
+[[Category: Large Structures]]
-[[Category: Riboswitch]]
+[[Category: Thore S]]
-[[Category: Rna]]
-[[Category: Thiamine analogue]]
-[[Category: Tpp]]