1vc6: Difference between revisions

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-[[Image:1vc6.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1vc6", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-{{STRUCTURE_1vc6|  PDB=1vc6  |  SCENE=  }}
-'''Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Product with C75U Mutaion, cleaved in Imidazole and Mg2+ solutions'''
+==Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Product with C75U Mutaion, cleaved in Imidazole and Mg2+ solutions==
+<StructureSection load='1vc6' size='340' side='right'caption='[[1vc6]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1vc6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VC6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VC6 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]] 2.8&#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></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=1vc6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vc6 OCA], [https://pdbe.org/1vc6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vc6 RCSB], [https://www.ebi.ac.uk/pdbsum/1vc6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vc6 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vc/1vc6_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1vc6 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Ribozymes enhance chemical reaction rates using many of the same catalytic strategies as protein enzymes. In the hepatitis delta virus (HDV) ribozyme, site-specific self-cleavage of the viral RNA phosphodiester backbone requires both divalent cations and a cytidine nucleotide. General acid-base catalysis, substrate destabilization and global and local conformational changes have all been proposed to contribute to the ribozyme catalytic mechanism. Here we report ten crystal structures of the HDV ribozyme in its pre-cleaved state, showing that cytidine is positioned to activate the 2'-OH nucleophile in the precursor structure. This observation supports its proposed role as a general base in the reaction mechanism. Comparison of crystal structures of the ribozyme in the pre- and post-cleavage states reveals a significant conformational change in the RNA after cleavage and that a catalytically critical divalent metal ion from the active site is ejected. The HDV ribozyme has remarkable chemical similarity to protein ribonucleases and to zymogens for which conformational dynamics are integral to biological activity. This finding implies that RNA structural rearrangements control the reactivity of ribozymes and ribonucleoprotein enzymes.
-==Overview==
+A conformational switch controls hepatitis delta virus ribozyme catalysis.,Ke A, Zhou K, Ding F, Cate JH, Doudna JA Nature. 2004 May 13;429(6988):201-5. PMID:15141216<ref>PMID:15141216</ref>
-Ribozymes enhance chemical reaction rates using many of the same catalytic strategies as protein enzymes. In the hepatitis delta virus (HDV) ribozyme, site-specific self-cleavage of the viral RNA phosphodiester backbone requires both divalent cations and a cytidine nucleotide. General acid-base catalysis, substrate destabilization and global and local conformational changes have all been proposed to contribute to the ribozyme catalytic mechanism. Here we report ten crystal structures of the HDV ribozyme in its pre-cleaved state, showing that cytidine is positioned to activate the 2'-OH nucleophile in the precursor structure. This observation supports its proposed role as a general base in the reaction mechanism. Comparison of crystal structures of the ribozyme in the pre- and post-cleavage states reveals a significant conformational change in the RNA after cleavage and that a catalytically critical divalent metal ion from the active site is ejected. The HDV ribozyme has remarkable chemical similarity to protein ribonucleases and to zymogens for which conformational dynamics are integral to biological activity. This finding implies that RNA structural rearrangements control the reactivity of ribozymes and ribonucleoprotein enzymes.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-VC6 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VC6 OCA].
+</div>
+<div class="pdbe-citations 1vc6" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-A conformational switch controls hepatitis delta virus ribozyme catalysis., Ke A, Zhou K, Ding F, Cate JH, Doudna JA, Nature. 2004 May 13;429(6988):201-5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15141216 15141216]
+*[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]]
+*[[Ribozyme 3D structures|Ribozyme 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Cate, J H.D.]]
+[[Category: Cate JHD]]
-[[Category: Ding, F.]]
+[[Category: Ding F]]
-[[Category: Doudna, J A.]]
+[[Category: Doudna JA]]
-[[Category: Ke, A.]]
+[[Category: Ke A]]
-[[Category: Zhou, K.]]
+[[Category: Zhou K]]
-[[Category: Hdv]]
-[[Category: Precursor]]
-[[Category: Ribozyme]]
-[[Category: Rna]]
-[[Category: U1a]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 12:21:33 2008''