1YKQ

Crystal structure of Diels-Alder ribozyme

Summary for 1YKQ

• Entry DOI: 10.2210/pdb1ykq/pdb
• Related: 1ykv 1yls
• Descriptor: Diels-Alder ribozyme, CADMIUM ION, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: carbon-carbon bond, catalytic mechanism, rna crystal structure, diels-alder reaction, ribozyme, rna
• Total number of polymer chains: 4
• Total formula weight: 32251.15

Authors

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. (deposition date: 2005-01-18, release date: 2005-02-22, Last modification date: 2023-08-23)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (3.5 Å)