2OEU

Full-length hammerhead ribozyme with Mn(II) bound

  • Classification: RNA
  • Mutation(s): No 

  • Deposited: 2007-01-01 Released: 2007-02-20 
  • Deposition Author(s): Martick, M., Scott, W.G.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Solvent structure and hammerhead ribozyme catalysis.

Martick, M.Lee, T.S.York, D.M.Scott, W.G.

(2008) Chem Biol 15: 332-342

  • DOI: 10.1016/j.chembiol.2008.03.010
  • Primary Citation of Related Structures:  
    2OEU

  • PubMed Abstract: 
  • Although the hammerhead ribozyme is regarded as a prototype for understanding RNA catalysis, the mechanistic roles of associated metal ions and water molecules in the cleavage reaction remain controversial. We have investigated the catalytic potential of observed divalent metal ions and water molecules bound to a 2 A structure of the full-length hammerhead ribozyme by using X-ray crystallography in combination with molecular dynamics simulations ...

    Although the hammerhead ribozyme is regarded as a prototype for understanding RNA catalysis, the mechanistic roles of associated metal ions and water molecules in the cleavage reaction remain controversial. We have investigated the catalytic potential of observed divalent metal ions and water molecules bound to a 2 A structure of the full-length hammerhead ribozyme by using X-ray crystallography in combination with molecular dynamics simulations. A single Mn(2+) is observed to bind directly to the A9 phosphate in the active site, accompanying a hydrogen-bond network involving a well-ordered water molecule spanning N1 of G12 (the general base) and 2'-O of G8 (previously implicated in general acid catalysis) that we propose, based on molecular dynamics calculations, facilitates proton transfer in the cleavage reaction. Phosphate-bridging metal interactions and other mechanistic hypotheses are also tested with this approach.


    Organizational Affiliation

    Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsLengthOrganismImage
Hammerhead RibozymeA 43N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-R(*GP*GP*CP*GP*UP*(OMC)P*CP*UP*GP*GP*(5BU)P*AP*UP*CP*CP*AP*AP*UP*CP*(DC))-3'B 20N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.171 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.312α = 90
b = 68.981β = 112.62
c = 60.443γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
CCP4data scaling
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance