6R47

The structure of pistol ribozyme bound to magnesium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Comparison of the Structures and Mechanisms of the Pistol and Hammerhead Ribozymes.

Wilson, T.J.Liu, Y.Li, N.S.Dai, Q.Piccirilli, J.A.Lilley, D.M.J.

(2019) J Am Chem Soc 141: 7865-7875

  • DOI: 10.1021/jacs.9b02141
  • Primary Citation of Related Structures:  
    6R47

  • PubMed Abstract: 
  • Comparison of the secondary and three-dimensional structures of the hammerhead and pistol ribozymes reveals many close similarities, so in this work we have asked if they are mechanistically identical. We have determined a new crystal structure of th ...

    Comparison of the secondary and three-dimensional structures of the hammerhead and pistol ribozymes reveals many close similarities, so in this work we have asked if they are mechanistically identical. We have determined a new crystal structure of the pistol ribozyme and have shown that G40 acts as general base in the cleavage reaction. The conformation in the active site ensures an in-line attack of the O2' nucleophile, and the conformation at the scissile phosphate and the position of the general base are closely similar to those in the hammerhead ribozyme. However, the two ribozymes differ in the nature of the general acid. 2'-Amino substitution experiments indicate that the general acid of the hammerhead ribozyme is the O2' of G8, while that of the pistol ribozyme is a hydrated metal ion. The two ribozymes are related but mechanistically distinct.


    Organizational Affiliation

    Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex , The University of Dundee , Dow Street , Dundee DD1 5EH , U.K.



Macromolecules
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (50-MER)A50Alistipes putredinis
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNAB15Alistipes putredinis
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    MG
    Query on MG

    Download CCD File 
    A
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.10 Å
    • R-Value Free: 0.180 
    • R-Value Work: 0.176 
    • R-Value Observed: 0.176 
    • Space Group: P 61
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 94.309α = 90
    b = 94.309β = 90
    c = 96.031γ = 120
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    PDB_EXTRACTdata extraction
    iMOSFLMdata reduction
    pointlessdata scaling
    PHENIXphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Cancer Research UKUnited KingdomA18604

    Revision History 

    • Version 1.0: 2019-07-03
      Type: Initial release
    • Version 1.1: 2019-08-21
      Changes: Data collection