1ykv: Difference between revisions

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-[[Image:1ykv.png|left|200px]]
-{{STRUCTURE_1ykv|  PDB=1ykv  |  SCENE=  }}
+==Crystal structure of the Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene==
+<StructureSection load='1ykv' size='340' side='right'caption='[[1ykv]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1ykv]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YKV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YKV 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]] 3.3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAI:(3AS,9AS)-2-PENTYL-4-HYDROXYMETHYL-3A,4,9,9A-TETRAHYDRO-4,9[1,2]-BENZENO-1H-BENZ[F]ISOINDOLE-1,3(2H)-DIONE'>DAI</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=1ykv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ykv OCA], [https://pdbe.org/1ykv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ykv RCSB], [https://www.ebi.ac.uk/pdbsum/1ykv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ykv ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The majority of structural efforts addressing RNA's catalytic function have focused on natural ribozymes, which catalyze phosphodiester transfer reactions. By contrast, little is known about how RNA catalyzes other types of chemical reactions. We report here the crystal structures of a ribozyme that catalyzes enantioselective carbon-carbon bond formation by the Diels-Alder reaction in the unbound state and in complex with a reaction product. The RNA adopts a lambda-shaped nested pseudoknot architecture whose preformed hydrophobic pocket is precisely complementary in shape to the reaction product. RNA folding and product binding are dictated by extensive stacking and hydrogen bonding, whereas stereoselection is governed by the shape of the catalytic pocket. Catalysis is apparently achieved by a combination of proximity, complementarity and electronic effects. We observe structural parallels in the independently evolved catalytic pocket architectures for ribozyme- and antibody-catalyzed Diels-Alder carbon-carbon bond-forming reactions.
-===Crystal structure of the Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene===
+Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation.,Serganov A, Keiper S, Malinina L, Tereshko V, Skripkin E, Hobartner C, Polonskaia A, Phan AT, Wombacher R, Micura R, Dauter Z, Jaschke A, Patel DJ Nat Struct Mol Biol. 2005 Mar;12(3):218-24. Epub 2005 Feb 20. PMID:15723077<ref>PMID:15723077</ref>
-{{ABSTRACT_PUBMED_15723077}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1ykv" style="background-color:#fffaf0;"></div>
-[[1ykv]] is a 4 chain structure of [[Ribozyme]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YKV OCA].
 ==See Also==
-*[[Ribozyme|Ribozyme]]
+*[[Ribozyme 3D structures|Ribozyme 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:015723077</ref><references group="xtra"/>
+__TOC__
-[[Category: Dauter, Z.]]
+</StructureSection>
-[[Category: Hobartner, C.]]
+[[Category: Large Structures]]
-[[Category: Jaschke, A.]]
+[[Category: Dauter Z]]
-[[Category: Keiper, S.]]
+[[Category: Hobartner C]]
-[[Category: Malinina, L.]]
+[[Category: Jaschke A]]
-[[Category: Micura, R.]]
+[[Category: Keiper S]]
-[[Category: Patel, D J.]]
+[[Category: Malinina L]]
-[[Category: Phan, A T.]]
+[[Category: Micura R]]
-[[Category: Polonskaia, A.]]
+[[Category: Patel DJ]]
-[[Category: Serganov, A.]]
+[[Category: Phan AT]]
-[[Category: Skripkin, E.]]
+[[Category: Polonskaia A]]
-[[Category: Tereshko, V.]]
+[[Category: Serganov A]]
-[[Category: Wombacher, R.]]
+[[Category: Skripkin E]]
-[[Category: Carbon-carbon bond]]
+[[Category: Tereshko V]]
-[[Category: Catalytic mechanism]]
+[[Category: Wombacher R]]
-[[Category: Diels-alder reaction]]
-[[Category: Ribozyme]]
-[[Category: Rna]]