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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: 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 ...

    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.


    Related Citations: 
    • Unexpected abundance of self-splicing introns in the genome of bacteriophage Twort: Introns in multiple genes, a single gene with three introns, and exon skipping by group I ribozymes
      Landthaler, M., Shub, D.A.
      (1999) Proc Natl Acad Sci U S A 96: 7005

    Organizational Affiliation

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



Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
Group I ribozymeA229Staphylococcus virus Twort
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-R(*GP*CP*UP*U)-3'B4N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SPK (Subject of Investigation/LOI)
    Query on SPK

    Download Ideal Coordinates CCD File 
    C [auth A]SPERMINE (FULLY PROTONATED FORM)
    C10 H30 N4
    PFNFFQXMRSDOHW-UHFFFAOYSA-R
     Ligand Interaction
    SO4
    Query on SO4

    Download Ideal Coordinates CCD File 
    H [auth A]SULFATE ION
    O4 S
    QAOWNCQODCNURD-UHFFFAOYSA-L
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    D [auth A], E [auth A], F [auth A], G [auth A]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    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

    View Full Validation Report



    Ligand Structure Quality Assessment  



    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