1yls - Revision history

OCA at 08:58, 14 February 2024

OCA — Wed, 14 Feb 2024 08:58:16 GMT

←Older revision		Revision as of 08:58, 14 February 2024
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	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yls FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yls OCA], [https://pdbe.org/1yls PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yls RCSB], [https://www.ebi.ac.uk/pdbsum/1yls PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yls ProSAT]</span></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=1yls FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yls OCA], [https://pdbe.org/1yls PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yls RCSB], [https://www.ebi.ac.uk/pdbsum/1yls PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yls ProSAT]</span></td></tr>
	</table>		</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.
-
-	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®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1yls" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Ribozyme 3D structures\|Ribozyme 3D structures]]		*[[Ribozyme 3D structures\|Ribozyme 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:14, 9 August 2023

OCA — Wed, 09 Aug 2023 07:14:48 GMT

←Older revision		Revision as of 07:14, 9 August 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1yls]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YLS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YLS FirstGlance]. <br>		<table><tr><td colspan='2'>[[1yls]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YLS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YLS FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSL:(D)-2-METHYLSELENYL-2-DEOXYCYTIDINE-5-PHOSPHATE'>CSL</scene>, <scene name='pdbligand=~~UMS~~:2-~~METHYLSELENYL~~-2-~~DEOXYURIDINE~~-5-~~PHOSPHATE~~'>~~UMS~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSL:(D)-2-METHYLSELENYL-2-DEOXYCYTIDINE-5-PHOSPHATE'>CSL</scene>, <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>, <scene name='pdbligand=UMS:2-METHYLSELENYL-2-DEOXYURIDINE-5-PHOSPHATE'>UMS</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td><~~td class~~=~~"sblockDat"><div style~~=~~'overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1ykq\|1ykq]], [[1ykv\|1ykv]]~~</~~div~~></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=1yls FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yls OCA], [https://pdbe.org/1yls PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yls RCSB], [https://www.ebi.ac.uk/pdbsum/1yls PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yls ProSAT]</span></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=1yls FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yls OCA], [https://pdbe.org/1yls PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yls RCSB], [https://www.ebi.ac.uk/pdbsum/1yls PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yls ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 19:

	==See Also==		==See Also==
-	*[[Ribozyme\|Ribozyme]]	+	*[[Ribozyme 3D structures\|Ribozyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 26:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dauter, Z]]	+	[[Category: Dauter Z]]
-	[[Category: Hobartner, C]]	+	[[Category: Hobartner C]]
-	[[Category: Jaschke, A]]	+	[[Category: Jaschke A]]
-	[[Category: Keiper, S]]	+	[[Category: Keiper S]]
-	[[Category: Malinina, L]]	+	[[Category: Malinina L]]
-	[[Category: Micura, R]]	+	[[Category: Micura R]]
-	[[Category: Patel~~, D J~~]]	+	[[Category: Patel DJ]]
-	[[Category: Phan~~, A T~~]]	+	[[Category: Phan AT]]
-	[[Category: Polonskaia, A]]	+	[[Category: Polonskaia A]]
-	[[Category: Serganov, A]]	+	[[Category: Serganov A]]
-	[[Category: Skripkin, E]]	+	[[Category: Skripkin E]]
-	[[Category: Tereshko, V]]	+	[[Category: Tereshko V]]
-	[[Category: Wombacher, R]]	+	[[Category: Wombacher R]]
-	~~[[Category: Carbon-carbon bond formation]]~~	+
-	~~[[Category: Catalytic mechanism]]~~	+
-	~~[[Category: Diels-alder reaction]]~~	+
-	~~[[Category: Ribozyme]]~~	+
-	~~[[Category: Rna~~]]	+

OCA at 16:29, 3 November 2021

OCA — Wed, 03 Nov 2021 16:29:43 GMT

←Older revision		Revision as of 16:29, 3 November 2021
Line 3:		Line 3:
	<StructureSection load='1yls' size='340' side='right'caption='[[1yls]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1yls' size='340' side='right'caption='[[1yls]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yls]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YLS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1YLS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yls]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YLS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YLS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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>	+	</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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSL:(D)-2-METHYLSELENYL-2-DEOXYCYTIDINE-5-PHOSPHATE'>CSL</scene>, <scene name='pdbligand=UMS:2-METHYLSELENYL-2-DEOXYURIDINE-5-PHOSPHATE'>UMS</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSL:(D)-2-METHYLSELENYL-2-DEOXYCYTIDINE-5-PHOSPHATE'>CSL</scene>, <scene name='pdbligand=UMS:2-METHYLSELENYL-2-DEOXYURIDINE-5-PHOSPHATE'>UMS</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ykq\|1ykq]], [[1ykv\|1ykv]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ykq\|1ykq]], [[1ykv\|1ykv]]</div></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1yls FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yls OCA], [~~http~~://pdbe.org/1yls PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1yls RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1yls PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1yls ProSAT]</span></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=1yls FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yls OCA], [https://pdbe.org/1yls PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yls RCSB], [https://www.ebi.ac.uk/pdbsum/1yls PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yls ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 16:42, 29 January 2020

OCA — Wed, 29 Jan 2020 16:42:46 GMT

←Older revision		Revision as of 16:42, 29 January 2020
Line 1:		Line 1:

	==Crystal structure of selenium-modified Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene==		==Crystal structure of selenium-modified Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene==
-	<StructureSection load='1yls' size='340' side='right' caption='[[1yls]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='1yls' size='340' side='right'caption='[[1yls]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1yls]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YLS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YLS FirstGlance]. <br>		<table><tr><td colspan='2'>[[1yls]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YLS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YLS FirstGlance]. <br>
Line 25:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Dauter, Z]]		[[Category: Dauter, Z]]
	[[Category: Hobartner, C]]		[[Category: Hobartner, C]]

OCA at 06:29, 25 April 2018

OCA — Wed, 25 Apr 2018 06:29:28 GMT

←Older revision		Revision as of 06:29, 25 April 2018
Line 1:		Line 1:
		+
	==Crystal structure of selenium-modified Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene==		==Crystal structure of selenium-modified Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene==
	<StructureSection load='1yls' size='340' side='right' caption='[[1yls]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1yls' size='340' side='right' caption='[[1yls]], [[Resolution\|resolution]] 3.00Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSL:(D)-2-METHYLSELENYL-2-DEOXYCYTIDINE-5-PHOSPHATE'>CSL</scene>, <scene name='pdbligand=UMS:2-METHYLSELENYL-2-DEOXYURIDINE-5-PHOSPHATE'>UMS</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSL:(D)-2-METHYLSELENYL-2-DEOXYCYTIDINE-5-PHOSPHATE'>CSL</scene>, <scene name='pdbligand=UMS:2-METHYLSELENYL-2-DEOXYURIDINE-5-PHOSPHATE'>UMS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ykq\|1ykq]], [[1ykv\|1ykv]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ykq\|1ykq]], [[1ykv\|1ykv]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yls FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yls OCA], [http://pdbe.org/1yls PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yls RCSB], [http://www.ebi.ac.uk/pdbsum/1yls PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yls FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yls OCA], [http://pdbe.org/1yls PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yls RCSB], [http://www.ebi.ac.uk/pdbsum/1yls PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yls ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:46, 11 September 2015

OCA — Fri, 11 Sep 2015 09:46:30 GMT

←Older revision		Revision as of 09:46, 11 September 2015
Line 6:		Line 6:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSL:(D)-2-METHYLSELENYL-2-DEOXYCYTIDINE-5-PHOSPHATE'>CSL</scene>, <scene name='pdbligand=UMS:2-METHYLSELENYL-2-DEOXYURIDINE-5-PHOSPHATE'>UMS</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSL:(D)-2-METHYLSELENYL-2-DEOXYCYTIDINE-5-PHOSPHATE'>CSL</scene>, <scene name='pdbligand=UMS:2-METHYLSELENYL-2-DEOXYURIDINE-5-PHOSPHATE'>UMS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ykq\|1ykq]], [[1ykv\|1ykv]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ykq\|1ykq]], [[1ykv\|1ykv]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yls FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yls OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yls RCSB], [http://www.ebi.ac.uk/pdbsum/1yls PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yls FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yls OCA], [http://pdbe.org/1yls PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yls RCSB], [http://www.ebi.ac.uk/pdbsum/1yls PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 16:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1yls" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribozyme\|Ribozyme]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:02, 8 January 2015

OCA — Thu, 08 Jan 2015 10:02:27 GMT

←Older revision		Revision as of 10:02, 8 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1yls]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YLS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YLS FirstGlance]. <br>		<table><tr><td colspan='2'>[[1yls]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YLS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YLS FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSL:(D)-2-METHYLSELENYL-2-DEOXYCYTIDINE-5-PHOSPHATE'>CSL</scene>, <scene name='pdbligand=UMS:2-METHYLSELENYL-2-DEOXYURIDINE-5-PHOSPHATE'>UMS</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSL:(D)-2-METHYLSELENYL-2-DEOXYCYTIDINE-5-PHOSPHATE'>CSL</scene>, <scene name='pdbligand=UMS:2-METHYLSELENYL-2-DEOXYURIDINE-5-PHOSPHATE'>UMS</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ykq\|1ykq]], [[1ykv\|1ykv]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ykq\|1ykq]], [[1ykv\|1ykv]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yls FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yls OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yls RCSB], [http://www.ebi.ac.uk/pdbsum/1yls PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yls FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yls OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yls RCSB], [http://www.ebi.ac.uk/pdbsum/1yls PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 16:		Line 16:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
-
-	==See Also==
-	*[[Ribozyme\|Ribozyme]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Dauter, Z.]]	+	[[Category: Dauter, Z]]
-	[[Category: Hobartner, C.]]	+	[[Category: Hobartner, C]]
-	[[Category: Jaschke, A.]]	+	[[Category: Jaschke, A]]
-	[[Category: Keiper, S.]]	+	[[Category: Keiper, S]]
-	[[Category: Malinina, L.]]	+	[[Category: Malinina, L]]
-	[[Category: Micura, R.]]	+	[[Category: Micura, R]]
-	[[Category: Patel, D J.]]	+	[[Category: Patel, D J]]
-	[[Category: Phan, A T.]]	+	[[Category: Phan, A T]]
-	[[Category: Polonskaia, A.]]	+	[[Category: Polonskaia, A]]
-	[[Category: Serganov, A.]]	+	[[Category: Serganov, A]]
-	[[Category: Skripkin, E.]]	+	[[Category: Skripkin, E]]
-	[[Category: Tereshko, V.]]	+	[[Category: Tereshko, V]]
-	[[Category: Wombacher, R.]]	+	[[Category: Wombacher, R]]
	[[Category: Carbon-carbon bond formation]]		[[Category: Carbon-carbon bond formation]]
	[[Category: Catalytic mechanism]]		[[Category: Catalytic mechanism]]

OCA at 23:46, 28 September 2014

OCA — Sun, 28 Sep 2014 23:46:50 GMT

←Older revision		Revision as of 23:46, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1yls.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of selenium-modified Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene==
		+	<StructureSection load='1yls' size='340' side='right' caption='[[1yls]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1yls]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YLS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YLS FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSL:(D)-2-METHYLSELENYL-2-DEOXYCYTIDINE-5-PHOSPHATE'>CSL</scene>, <scene name='pdbligand=UMS:2-METHYLSELENYL-2-DEOXYURIDINE-5-PHOSPHATE'>UMS</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ykq\|1ykq]], [[1ykv\|1ykv]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yls FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yls OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yls RCSB], [http://www.ebi.ac.uk/pdbsum/1yls PDBsum]</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.

-	~~{{STRUCTURE_1yls\| PDB=1yls \| SCENE= }}~~	+	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>

-	~~===Crystal structure~~ of ~~selenium-modified Diels-Alder ribozyme complexed with~~ the ~~product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15723077}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1yls]] is a 4 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=1YLS OCA].~~	+

	==See Also==		==See Also==
	*[[Ribozyme\|Ribozyme]]		*[[Ribozyme\|Ribozyme]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015723077<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Dauter, Z.]]		[[Category: Dauter, Z.]]
	[[Category: Hobartner, C.]]		[[Category: Hobartner, C.]]

OCA at 17:56, 20 October 2012

OCA — Sat, 20 Oct 2012 17:56:29 GMT

←Older revision		Revision as of 17:56, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1yls]] is a 4 chain structure ~~of [[Ribozyme]]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YLS OCA].	+	[[1yls]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YLS OCA].

	==See Also==		==See Also==

OCA: Protected "1yls" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 02:28:45 GMT

Protected "1yls" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:28, 27 July 2012