1ykv: Difference between revisions

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-{{Seed}}
-[[Image:1ykv.png|left|200px]]
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+==Crystal structure of the Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene==
-The line below this paragraph, containing "STRUCTURE_1ykv", creates the "Structure Box" on the page.
+<StructureSection load='1ykv' size='340' side='right'caption='[[1ykv]], [[Resolution|resolution]] 3.30&Aring;' 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'>[[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>
-or leave the SCENE parameter empty for the default display.
+</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>
-{{STRUCTURE_1ykv|  PDB=1ykv  |  SCENE=  }}
+<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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1ykv" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15723077}}, adds the Publication Abstract to the page
+*[[Ribozyme 3D structures|Ribozyme 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15723077 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15723077}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YKV OCA].
+[[Category: Dauter Z]]
+[[Category: Hobartner C]]
-==Reference==
+[[Category: Jaschke A]]
-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:[http://www.ncbi.nlm.nih.gov/pubmed/15723077 15723077]
+[[Category: Keiper S]]
-[[Category: Dauter, Z.]]
+[[Category: Malinina L]]
-[[Category: Hobartner, C.]]
+[[Category: Micura R]]
-[[Category: Jaschke, A.]]
+[[Category: Patel DJ]]
-[[Category: Keiper, S.]]
+[[Category: Phan AT]]
-[[Category: Malinina, L.]]
+[[Category: Polonskaia A]]
-[[Category: Micura, R.]]
+[[Category: Serganov A]]
-[[Category: Patel, D J.]]
+[[Category: Skripkin E]]
-[[Category: Phan, A T.]]
+[[Category: Tereshko V]]
-[[Category: Polonskaia, A.]]
+[[Category: Wombacher R]]
-[[Category: Serganov, A.]]
-[[Category: Skripkin, E.]]
-[[Category: Tereshko, V.]]
-[[Category: Wombacher, R.]]
-[[Category: Carbon-carbon bond]]
-[[Category: Catalytic mechanism]]
-[[Category: Crystal structure]]
-[[Category: Diels-alder reaction]]
-[[Category: Ribozyme]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 11:38:36 2008''