2EX5

Group I Intron-encoded Homing Endonuclease I-CeuI Complexed With DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.7 of the entry. See complete history


Literature

The structure of I-CeuI homing endonuclease: Evolving asymmetric DNA recognition from a symmetric protein scaffold.

Spiegel, P.C.Chevalier, B.Sussman, D.Turmel, M.Lemieux, C.Stoddard, B.L.

(2006) Structure 14: 869-880

  • DOI: https://doi.org/10.1016/j.str.2006.03.009
  • Primary Citation of Related Structures:  
    2EX5

  • PubMed Abstract: 

    Homing endonucleases are highly specific catalysts of DNA strand breaks, leading to the transfer of mobile intervening sequences containing the endonuclease ORF. We have determined the structure and DNA recognition behavior of I-CeuI, a homodimeric LAGLIDADG endonuclease from Chlamydomonas eugametos. This symmetric endonuclease displays unique structural elaborations on its core enzyme fold, and it preferentially cleaves a highly asymmetric target site. This latter property represents an early step, prior to gene fusion, in the generation of asymmetric DNA binding platforms from homodimeric ancestors. The divergence of the sequence, structure, and target recognition behavior of homing endonucleases, as illustrated by this study, leads to the invasion of novel genomic sites by mobile introns during evolution.


  • Organizational Affiliation

    Graduate Programs in Biomolecular Structure and Design and Molecular and Cellular Biology, University of Washington, Seattle, Washington 98195, USA.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA endonuclease I-CeuIC [auth A],
D [auth B]
207Chlamydomonas moewusiiMutation(s): 1 
Gene Names: I-CeuI
EC: 3.1
UniProt
Find proteins for P32761 (Chlamydomonas moewusii)
Explore P32761 
Go to UniProtKB:  P32761
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32761
Sequence Annotations
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  • Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
I-CeuI DNA target siteA [auth X]26synthetic construct
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
I-CeuI DNA target site, complementary strandB [auth Y]26synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.234α = 90
b = 69.176β = 90
c = 169.414γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-23
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2019-01-30
    Changes: Data collection, Source and taxonomy, Structure summary
  • Version 1.5: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.6: 2024-02-14
    Changes: Data collection
  • Version 1.7: 2024-04-03
    Changes: Refinement description