4QJH

Crystal Structure of the Twister Ribozyme with the Nucleotide 5'- to the Cleavage Site Ordered at 4.1 A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.88 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme.

Eiler, D.Wang, J.Steitz, T.A.

(2014) Proc Natl Acad Sci U S A 111: 13028-13033

  • DOI: 10.1073/pnas.1414571111
  • Primary Citation of Related Structures:  
    4QJD, 4QJH

  • PubMed Abstract: 
  • Twister is a recently discovered RNA motif that is estimated to have one of the fastest known catalytic rates of any naturally occurring small self-cleaving ribozyme. We determined the 4.1-Å resolution crystal structure of a twister sequence from an organism that has not been cultured in isolation, and it shows an ordered scissile phosphate and nucleotide 5' to the cleavage site ...

    Twister is a recently discovered RNA motif that is estimated to have one of the fastest known catalytic rates of any naturally occurring small self-cleaving ribozyme. We determined the 4.1-Å resolution crystal structure of a twister sequence from an organism that has not been cultured in isolation, and it shows an ordered scissile phosphate and nucleotide 5' to the cleavage site. A second crystal structure of twister from Orzyza sativa determined at 3.1-Å resolution exhibits a disordered scissile phosphate and nucleotide 5' to the cleavage site. The core of twister is stabilized by base pairing, a large network of stacking interactions, and two pseudoknots. We observe three nucleotides that appear to mediate catalysis: a guanosine that we propose deprotonates the 2'-hydroxyl of the nucleotide 5' to the cleavage site and a conserved adenosine. We suggest the adenosine neutralizes the negative charge on a nonbridging phosphate oxygen atom at the cleavage site. The active site also positions the labile linkage for in-line nucleophilic attack, and thus twister appears to simultaneously use three strategies proposed for small self-cleaving ribozymes. The twister crystal structures (i) show its global structure, (ii) demonstrate the significance of the double pseudoknot fold, (iii) provide a possible hypothesis for enhanced catalysis, and (iv) illuminate the roles of all 10 highly conserved nucleotides of twister that participate in the formation of its small and stable catalytic pocket.


    Organizational Affiliation

    Department of Molecular Biochemistry and Biophysics and Howard Hughes Medical Institute, Yale University, New Haven, CT 06520 thomas.steitz@yale.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsLengthOrganismImage
Twister RibozymeA, C, E26N/A
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
Twister RibozymeB, D, F48N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.88 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 228.77α = 90
b = 228.77β = 90
c = 101.06γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
HKL2Mapmodel building
REFMACrefinement
XDSdata reduction
HKL2Mapphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2014-09-10
    Changes: Database references
  • Version 1.2: 2014-09-24
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Refinement description