1ykv
From Proteopedia
(New page: 200px<br /><applet load="1ykv" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ykv, resolution 3.30Å" /> '''Crystal structure of...) |
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| - | [[Image:1ykv.gif|left|200px]]<br /><applet load="1ykv" size=" | + | [[Image:1ykv.gif|left|200px]]<br /><applet load="1ykv" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1ykv, resolution 3.30Å" /> | caption="1ykv, resolution 3.30Å" /> | ||
'''Crystal structure of the Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene'''<br /> | '''Crystal structure of the Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The majority of structural efforts addressing RNA's catalytic function | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 1YKV is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with MG and DAI as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 1YKV is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=DAI:'>DAI</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YKV OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Malinina, L.]] | [[Category: Malinina, L.]] | ||
[[Category: Micura, R.]] | [[Category: Micura, R.]] | ||
| - | [[Category: Patel, D | + | [[Category: Patel, D J.]] |
| - | [[Category: Phan, A | + | [[Category: Phan, A T.]] |
[[Category: Polonskaia, A.]] | [[Category: Polonskaia, A.]] | ||
[[Category: Serganov, A.]] | [[Category: Serganov, A.]] | ||
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[[Category: ribozyme]] | [[Category: ribozyme]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:06:21 2008'' |
Revision as of 14:06, 21 February 2008
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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
Overview
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.
About this Structure
1YKV is a Protein complex structure of sequences from [1] with and as ligands. Full crystallographic information is available from OCA.
Reference
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
Page seeded by OCA on Thu Feb 21 16:06:21 2008
Categories: Protein complex | Dauter, Z. | Hobartner, C. | Jaschke, A. | Keiper, S. | Malinina, L. | Micura, R. | Patel, D J. | Phan, A T. | Polonskaia, A. | Serganov, A. | Skripkin, E. | Tereshko, V. | Wombacher, R. | DAI | MG | Carbon-carbon bond | Catalytic mechanism | Crystal structure | Diels-alder reaction | Ribozyme
