1fg1: Difference between revisions

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 {{Theoretical_model}}
-{{Seed}}
-[[Image:1fg1.png|left|200px]]
-<!--
+==MODEL OF A HYPOTHESIZED HAMMERHEAD RIBOZYME CONFORMATIONAL CHANGE==
-The line below this paragraph, containing "STRUCTURE_1fg1", creates the "Structure Box" on the page.
+<StructureSection load='1fg1' size='340' side='right'caption='[[1fg1]]' 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'>For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FG1 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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=1fg1 FirstGlance], [https://www.ebi.ac.uk/pdbsum/1fg1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fg1 ProSAT]</span></td></tr>
--->
+</table>
-{{STRUCTURE_1fg1|  PDB=1fg1  |  SCENE=  }}
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We have constructed a model structure that we believe represents the strongest possible physically and chemically reasonable representation of a hypothesized catalytically active hammerhead ribozyme structure in which a single divalent metal ion bridges the A9 and scissile phosphate groups. It has been proposed that such a structure arises from a conformational change in which the so-called ground-state structure (as observed by X-ray crystallography) rearranges in such a way that the pro-R oxygen atoms of both the A9 and scissile phosphate groups are directly coordinated by a single divalent metal ion in the transition-state of the hammerhead ribozyme cleavage reaction. We show that even the small subset of possible model structures that are consistent with these requirements, and that are stereochemically and sterically reasonable, are contradicted by experimental evidence. We also demonstrate that even a minimal subset of assumptions, i.e. that stems I and II are helical and that the two phosphate groups are coordinated by a divalent metal ion in the standard octahedral geometry, are sufficient to lead to this contradiction. We therefore conclude that such a mechanism of hammerhead ribozyme catalysis is untenable, at least in its present formulation.
-===MODEL OF A HYPOTHESIZED HAMMERHEAD RIBOZYME CONFORMATIONAL CHANGE===
+Does a single metal ion bridge the A-9 and scissile phosphate groups in the catalytically active hammerhead ribozyme structure?,Murray JB, Scott WG J Mol Biol. 2000 Feb 11;296(1):33-41. PMID:10656816<ref>PMID:10656816</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_10656816}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1fg1" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 10656816 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_10656816}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Theoretical Model]]
-Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FG1 OCA].
+[[Category: Large Structures]]
-==Reference==
-<ref group="xtra">PMID:10656816</ref><references group="xtra"/>
 [[Category: Murray, J B]]
 [[Category: Scott, W G]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr  8 09:32:23 2010''