6UEY

Pistol ribozyme transition-state analog vanadate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crucial Roles of Two Hydrated Mg2+Ions in Reaction Catalysis of the Pistol Ribozyme.

Teplova, M.Falschlunger, C.Krasheninina, O.Egger, M.Ren, A.Patel, D.J.Micura, R.

(2020) Angew Chem Int Ed Engl 59: 2837-2843

  • DOI: 10.1002/anie.201912522
  • Primary Citation of Related Structures:  
    6UEY, 6UF1, 6UFJ, 6UFK

  • PubMed Abstract: 
  • Pistol ribozymes constitute a new class of small self-cleaving RNAs. Crystal structures have been solved, providing three-dimensional snapshots along the reaction coordinate of pistol phosphodiester cleavage, corresponding to the pre-catalytic state, a v ...

    Pistol ribozymes constitute a new class of small self-cleaving RNAs. Crystal structures have been solved, providing three-dimensional snapshots along the reaction coordinate of pistol phosphodiester cleavage, corresponding to the pre-catalytic state, a vanadate mimic of the transition state, and the product. The results led to the proposed underlying chemical mechanism. Importantly, a hydrated Mg 2+ ion remains innersphere-coordinated to N7 of G33 in all three states, and is consistent with its likely role as acid in general acid base catalysis (δ and β catalysis). Strikingly, the new structures shed light on a second hydrated Mg 2+ ion that approaches the scissile phosphate from its binding site in the pre-cleavage state to reach out for water-mediated hydrogen bonding in the cyclophosphate product. The major role of the second Mg 2+ ion appears to be the stabilization of product conformation. This study delivers a mechanistic understanding of ribozyme-catalyzed backbone cleavage.


    Organizational Affiliation

    Institute of Organic Chemistry and Center for Molecular Biosciences, Leopold-Franzens University, Innrain 80-82, 6020, Innsbruck, Austria.



Macromolecules
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (50-MER)A, C50Escherichia coli
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*(GVA)*UP*CP*CP*AP*A)-3')B, D15Escherichia coli
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.80 Å
    • R-Value Free: 0.252 
    • R-Value Work: 0.212 
    • R-Value Observed: 0.216 
    • Space Group: P 42 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 91.829α = 90
    b = 91.829β = 90
    c = 123.444γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    PDB_EXTRACTdata extraction
    HKL-2000data reduction
    HKL-2000data scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)United States--

    Revision History 

    • Version 1.0: 2019-12-18
      Type: Initial release
    • Version 1.1: 2020-01-22
      Changes: Database references
    • Version 1.2: 2020-02-19
      Changes: Database references