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: 3.3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


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:  

  • 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 rep ...

    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 proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
Diels-Alder ribozymeA,C11N/A
Entity ID: 2
MoleculeChainsLengthOrganism
Diels-Alder ribozymeB,D38N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
B, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
DAI
Query on DAI

Download SDF File 
Download CCD File 
A, C
(3AS,9AS)-2-PENTYL-4-HYDROXYMETHYL-3A,4,9,9A-TETRAHYDRO-4,9[1',2']-BENZENO-1H-BENZ[F]ISOINDOLE-1,3(2H)-DIONE
(11S,12S)-9-HYDROXYMETHYL-11,12-(2-PENTYL-1,3-DIOXO-2-AZAPROPANO)-9,10-DIHYDRO-9,10-ETHANOANTHRACENE
C24 H25 N O3
ZXWOIFZYPFUNNQ-VMIIQTFKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DAIKd: 10000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 78.288α = 90.00
b = 44.039β = 106.87
c = 79.998γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
AMoREphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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