1Y0Q

Crystal structure of an active group I ribozyme-product complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.277 

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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of a phage Twort group I ribozyme-product complex

Golden, B.L.Kim, H.Chase, E.

(2005) Nat Struct Mol Biol 12: 82-89

  • DOI: https://doi.org/10.1038/nsmb868
  • Primary Citation of Related Structures:  
    1Y0Q

  • PubMed Abstract: 

    Group I introns are catalytic RNAs capable of orchestrating two sequential phosphotransesterification reactions that result in self-splicing. To understand how the group I intron active site facilitates catalysis, we have solved the structure of an active ribozyme derived from the orf142-I2 intron from phage Twort bound to a four-nucleotide product RNA at a resolution of 3.6 A. In addition to the three conserved domains characteristic of all group I introns, the Twort ribozyme has peripheral insertions characteristic of phage introns. These elements form a ring that completely envelops the active site, where a snug pocket for guanosine is formed by a series of stacked base triples. The structure of the active site reveals three potential binding sites for catalytic metals, and invokes a role for the 2' hydroxyl of the guanosine substrate in organization of the active site for catalysis.


  • Organizational Affiliation

    Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, Indiana 47907, USA. barbgolden@purdue.edu


Macromolecules
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Entity ID: 1
MoleculeChains LengthOrganismImage
Group I ribozyme229Twortvirus twort
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-R(*GP*CP*UP*U)-3'4N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.277 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.57α = 90
b = 140.97β = 90
c = 210.85γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
DMphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations