4znp: Difference between revisions

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 ==The structure of A pfI Riboswitch Bound to ZMP==
-<StructureSection load='4znp' size='340' side='right' caption='[[4znp]], [[Resolution|resolution]] 2.94&Aring;' scene=''>
+<StructureSection load='4znp' size='340' side='right'caption='[[4znp]], [[Resolution|resolution]] 2.94&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4znp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZNP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZNP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4znp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZNP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZNP FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMZ:AMINOIMIDAZOLE+4-CARBOXAMIDE+RIBONUCLEOTIDE'>AMZ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.94&#8491;</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=4znp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4znp OCA], [http://pdbe.org/4znp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4znp RCSB], [http://www.ebi.ac.uk/pdbsum/4znp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4znp ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMZ:AMINOIMIDAZOLE+4-CARBOXAMIDE+RIBONUCLEOTIDE'>AMZ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=4znp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4znp OCA], [https://pdbe.org/4znp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4znp RCSB], [https://www.ebi.ac.uk/pdbsum/4znp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4znp ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-ZTP, the pyrophosphorylated analog of ZMP (5-amino-4-imidazole carboxamide ribose-5'-monophosphate), was identified as an alarmone that senses 10-formyl-tetrahydroflate deficiency in bacteria. Recently, a pfl riboswitch was identified that selectively binds ZMP and regulates genes associated with purine biosynthesis and one-carbon metabolism. We report on the structure of the ZMP-bound Thermosinus carboxydivorans pfl riboswitch sensing domain, thereby defining the pseudoknot-based tertiary RNA fold, the binding-pocket architecture, and principles underlying ligand recognition specificity. Molecular recognition involves shape complementarity, with the ZMP 5-amino and carboxamide groups paired with the Watson-Crick edge of an invariant uracil, and the imidazole ring sandwiched between guanines, while the sugar hydroxyls form intermolecular hydrogen bond contacts. The burial of the ZMP base and ribose moieties, together with unanticipated coordination of the carboxamide by Mg(2+), contrasts with exposure of the 5'-phosphate to solvent. Our studies highlight the principles underlying RNA-based recognition of ZMP, a master regulator of one-carbon metabolism.
-Global RNA Fold and Molecular Recognition for a pfl Riboswitch Bound to ZMP, a Master Regulator of One-Carbon Metabolism.,Ren A, Rajashankar KR, Patel DJ Structure. 2015 Aug 4;23(8):1375-81. doi: 10.1016/j.str.2015.05.016. Epub 2015, Jun 25. PMID:26118534<ref>PMID:26118534</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4znp" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Riboswitch|Riboswitch]]
+*[[Riboswitch 3D structures|Riboswitch 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Patel, D J]]
+[[Category: Large Structures]]
-[[Category: Rajashankar, R K]]
+[[Category: Synthetic construct]]
-[[Category: Ren, A]]
+[[Category: Patel DJ]]
-[[Category: Aicar]]
+[[Category: Rajashankar RK]]
-[[Category: Complex]]
+[[Category: Ren A]]
-[[Category: One carbon mechanism]]
-[[Category: Riboswitch]]
-[[Category: Rna]]
-[[Category: Zmp]]
-[[Category: Ztp]]