1YKQ: Crystal Structure Of Diels-Alder Ribozyme

Citation:
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.
PDB ID: 1YKQDownload
MMDB ID: 52138
PDB Deposition Date: 2005/1/18
Updated in MMDB: 2007/10
Experimental Method:
x-ray diffraction
Resolution: 3.5  Å
Biological Unit for 1YKQ: dimeric; determined by author
Molecular Components in 1YKQ
Label Count Molecule
Nucleotides(2 molecules)
1
Diels-alder Ribozyme
Molecule annotation
1
Diels-alder Ribozyme
Molecule annotation
Chemicals (6 molecules)
1
3
2
3
* Click molecule labels to explore molecular sequence information.

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