2cd6: Difference between revisions

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 ==Refinement of RNase P P4 stemloop structure using residual dipolar coupling data, C70U mutant cobalt(III) hexammine complex==
-<StructureSection load='2cd6' size='340' side='right'caption='[[2cd6]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>
+<StructureSection load='2cd6' size='340' side='right'caption='[[2cd6]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2cd6]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CD6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CD6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2cd6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CD6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CD6 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2cd1|2cd1]], [[2cd3|2cd3]], [[2cd5|2cd5]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</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=2cd6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cd6 OCA], [https://pdbe.org/2cd6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cd6 RCSB], [https://www.ebi.ac.uk/pdbsum/2cd6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cd6 ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-We determined the solution structure of two 27-nt RNA hairpins and their complexes with cobalt(III)-hexammine (Co(NH3)3+(6)) by NMR spectroscopy. The RNA hairpins used in this study are the P4 region from Escherichia coli RNase P RNA and a C-to-U mutant that confers altered divalent metal-ion specificity (Ca2+ replaces Mg2+) for catalytic activity of this ribozyme. Co(NH3)3+(6) is a useful spectroscopic probe for Mg(H2O)2+(6)-binding sites because both complexes have octahedral symmetry and have similar radii. The thermodynamics of binding to both RNA hairpins was studied using chemical shift changes upon titration with Mg2+, Ca2+, and Co(NH3)3+(6). We found that the equilibrium binding constants for each of the metal ions was essentially unchanged when the P4 model RNA hairpin was mutated, although the NMR structures show that the RNA hairpins adopt different conformations. In the C-to-U mutant a C.G base pair is replaced by U.G, and the conserved bulged uridine in the P4 wild-type stem shifts in the 3' direction by 1 nt. Intermolecular NOE cross-peaks between Co(NH3)3+(6) and RNA protons were used to locate the site of Co(NH3)3+(6) binding to both RNA hairpins. The metal ion binds in the major groove near a bulge loop, but is shifted 5' by more than 1 bp in the mutant. The change of the metal-ion binding site provides a possible explanation for changes in catalytic activity of the mutant RNase P in the presence of Ca2+.
-Solution structure and metal-ion binding of the P4 element from bacterial RNase P RNA.,Schmitz M, Tinoco I Jr RNA. 2000 Sep;6(9):1212-25. PMID:10999599<ref>PMID:10999599</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2cd6" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Ribozyme|Ribozyme]]
+*[[Ribozyme 3D structures|Ribozyme 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Schmitz, M]]
+[[Category: Schmitz M]]
-[[Category: C70u mutant]]
-[[Category: Metal binding site]]
-[[Category: Metal complex]]
-[[Category: Nucleic acid]]
-[[Category: P4 stem]]
-[[Category: Ribonuclease p]]
-[[Category: Ribonucleic acid]]
-[[Category: Ribozyme]]
-[[Category: Transfer rna processing]]