1Y0Q

Crystal structure of an active group I ribozyme-product complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.277 

wwPDB Validation 3D Report Full Report


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

  • 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 a ...

    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.USA 96: 7005


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
Group I ribozymeA229Staphylococcus virus Twort
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*GP*CP*UP*U)-3'B4N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
SPK
Query on SPK

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Download CCD File 
A
SPERMINE (FULLY PROTONATED FORM)
C10 H30 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-R
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.277 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 94.570α = 90.00
b = 140.970β = 90.00
c = 210.850γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CNSrefinement
DMphasing
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance