1YKV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

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This is version 1.2 of the entry. See complete history


Literature

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, A.T.Wombacher, R.Micura, R.Dauter, Z.Jaschke, A.Patel, D.J.

(2005) Nat Struct Mol Biol 12: 218-224

  • DOI: 10.1038/nsmb906
  • Primary Citation of Related Structures:  
    1YKQ, 1YKV, 1YLS

  • 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 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.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    Diels-Alder ribozymeA, C11N/A
    Protein Feature View
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    • Reference Sequence
    Find similar nucleic acids by:  (by identity cutoff)  |  Structure
    Entity ID: 2
    MoleculeChainsLengthOrganismImage
    Diels-Alder ribozymeB, D38N/A
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Binding Affinity Annotations 
    IDSourceBinding Affinity
    DAI PDBBind:  1YKV Kd: 1.00e+4 (nM) from 1 assay(s)
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.30 Å
    • R-Value Free: 0.262 
    • R-Value Work: 0.228 
    • R-Value Observed: 0.230 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 78.288α = 90
    b = 44.039β = 106.87
    c = 79.998γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement
    HKL-2000data reduction
    SCALEPACKdata scaling
    AMoREphasing

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2005-02-22
      Type: Initial release
    • Version 1.1: 2008-04-30
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Advisory, Refinement description, Version format compliance