Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation Journal Article


Authors: Serganov, A.; Keiper, S.; Malinina, L.; Terechko, V.; Skripkin, E.; Höbartner, C.; Polonskaia, A.; Phan, A. T.; Wombacher, R.; Micura, R.; Dauter, Z.; Jäschke, A.; Patel, D. J.
Article Title: Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation
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 λ-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.
Keywords: comparative study; molecular genetics; structure activity relation; structure-activity relationship; chemistry; molecular sequence data; nucleotide sequence; base sequence; binding site; crystal structure; hydrogen bond; hydrogen bonding; crystallography, x-ray; binding sites; chemical structure; molecular structure; catalysis; conformation; nucleic acid conformation; rna structure; crystallization; structure analysis; x ray crystallography; enzyme structure; catalytic domain; diels alder reaction; stereochemistry; chemical bond; carbon; enzyme active site; enantioselectivity; ribozyme; rna, catalytic; betulaceae; carbon carbon bond; interactions with rna
Journal Title: Nature Structural & Molecular Biology
Volume: 12
Issue: 3
ISSN: 1545-9985
Publisher: Nature Publishing Group  
Date Published: 2005-03-01
Start Page: 218
End Page: 224
Language: English
DOI: 10.1038/nsmb906
PUBMED: 15723077
PROVIDER: scopus
PMCID: PMC4692364
DOI/URL:
Notes: --- - "Cited By (since 1996): 104" - "Export Date: 24 October 2012" - "CODEN: NSMBC" - "Source: Scopus"
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MSK Authors
  1. Anh Tuan Phan
    23 Phan
  2. Dinshaw J Patel
    392 Patel