3zd5: Difference between revisions

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-[[Image:3zd5.jpg|left|200px]]
-{{STRUCTURE_3zd5|  PDB=3zd5  |  SCENE=  }}
+==THE 2.2 A STRUCTURE OF A FULL-LENGTH CATALYTICALLY ACTIVE HAMMERHEAD RIBOZYME==
+<StructureSection load='3zd5' size='340' side='right'caption='[[3zd5]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3zd5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Schistosoma_mansoni Schistosoma mansoni]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2goz 2goz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZD5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZD5 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</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=3zd5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zd5 OCA], [https://pdbe.org/3zd5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zd5 RCSB], [https://www.ebi.ac.uk/pdbsum/3zd5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zd5 ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Minimal hammerhead ribozymes have been characterized extensively by static and time-resolved crystallography as well as numerous biochemical analyses, leading to mutually contradictory mechanistic explanations for catalysis. We present the 2.2 A resolution crystal structure of a full-length Schistosoma mansoni hammerhead ribozyme that permits us to explain the structural basis for its 1000-fold catalytic enhancement. The full-length hammerhead structure reveals how tertiary interactions occurring remotely from the active site prime this ribozyme for catalysis. G-12 and G-8 are positioned consistent with their previously suggested roles in acid-base catalysis, the nucleophile is aligned with a scissile phosphate positioned proximal to the A-9 phosphate, and previously unexplained roles of other conserved nucleotides become apparent within the context of a distinctly new fold that nonetheless accommodates the previous structural studies. These interactions permit us to explain the previously irreconcilable sets of experimental results in a unified, consistent, and unambiguous manner.
-===THE 2.2 A STRUCTURE OF A FULL-LENGTH CATALYTICALLY ACTIVE HAMMERHEAD RIBOZYME===
+Tertiary contacts distant from the active site prime a ribozyme for catalysis.,Martick M, Scott WG Cell. 2006 Jul 28;126(2):309-20. Epub 2006 Jul 20. PMID:16859740<ref>PMID:16859740</ref>
-{{ABSTRACT_PUBMED_16859740}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3zd5" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[3zd5]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2goz 2goz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZD5 OCA].
+*[[Ribozyme 3D structures|Ribozyme 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:016859740</ref><references group="xtra"/>
+__TOC__
-[[Category: Martick, M.]]
+</StructureSection>
-[[Category: Scott, W G.]]
+[[Category: Large Structures]]
-[[Category: A-form helix]]
+[[Category: Schistosoma mansoni]]
-[[Category: Catalytic rna]]
+[[Category: Martick M]]
-[[Category: Hammerhead rna]]
+[[Category: Scott WG]]
-[[Category: In-line attack]]
-[[Category: Rna]]
-[[Category: Stem-loop interaction]]
-[[Category: Uridine turn]]