1ykv: Difference between revisions
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[[Image:1ykv.gif|left|200px]] | [[Image:1ykv.gif|left|200px]] | ||
'''Crystal structure of the Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene''' | {{Structure | ||
|PDB= 1ykv |SIZE=350|CAPTION= <scene name='initialview01'>1ykv</scene>, resolution 3.30Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <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> | |||
|ACTIVITY= | |||
|GENE= | |||
}} | |||
'''Crystal structure of the Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1YKV is a [ | 1YKV is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YKV OCA]. | ||
==Reference== | ==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:[http:// | 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: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Dauter, Z.]] | [[Category: Dauter, Z.]] | ||
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[[Category: ribozyme]] | [[Category: ribozyme]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:24:14 2008'' | ||
Revision as of 16:24, 20 March 2008
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| , resolution 3.30Å | |||||||
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| Ligands: | and | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of the Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene
OverviewOverview
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 StructureAbout this Structure
1YKV is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
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
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