1YKV

Crystal structure of the Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene

1YKV の概要

• エントリーDOI: 10.2210/pdb1ykv/pdb
• 関連するPDBエントリー: 1YKQ 1YLS
• 分子名称: Diels-Alder ribozyme, (3AS,9AS)-2-PENTYL-4-HYDROXYMETHYL-3A,4,9,9A-TETRAHYDRO-4,9[1',2']-BENZENO-1H-BENZ[F]ISOINDOLE-1,3(2H)-DIONE, MAGNESIUM ION, ... (4 entities in total)
• 機能のキーワード: carbon-carbon bond, catalytic mechanism, diels-alder reaction, ribozyme, rna
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 32440.01

構造登録者

Serganov, A.,Keiper, S.,Malinina, L.,Tereshko, V.,Skripkin, E.,Hobartner, C.,Polonskaia, A.,Phan, A.T.,Wombacher, R.,Micura, R.,Dauter, Z.,Jaschke, A.,Patel, D.J. (登録日: 2005-01-18, 公開日: 2005-02-22, 最終更新日: 2023-08-23)

主引用文献

Serganov, A.,Keiper, S.,Malinina, L.,Tereshko, V.,Skripkin, E.,Hobartner, C.,Polonskaia, A.,Phan, A.T.,Wombacher, R.,Micura, R.,Dauter, Z.,Jaschke, A.,Patel, D.J.
Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation.
Nat.Struct.Mol.Biol., 12:218-224, 2005

PubMed Abstract: 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.

PubMed: 15723077
DOI: 10.1038/nsmb906

実験手法

X-RAY DIFFRACTION (3.3 Å)