4AQU

Crystal structure of I-CreI complexed with its target methylated at position plus 2 (in the b strand) in the presence of calcium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

5'-Cytosine-Phosphoguanine (Cpg) Methylation Impacts the Activity of Natural and Engineered Meganucleases.

Valton, J.Daboussi, F.Leduc, S.Molina, R.Redondo, P.Macmaster, R.Montoya, G.Duchateau, P.

(2012) J Biol Chem 287: 30139

  • DOI: https://doi.org/10.1074/jbc.M112.379966
  • Primary Citation of Related Structures:  
    4AQU, 4AQX

  • PubMed Abstract: 

    In this study, we asked whether CpG methylation could influence the DNA binding affinity and activity of meganucleases used for genome engineering applications. A combination of biochemical and structural approaches enabled us to demonstrate that CpG methylation decreases I-CreI DNA binding affinity and inhibits its endonuclease activity in vitro. This inhibition depends on the position of the methylated cytosine within the DNA target and was almost total when it is located inside the central tetrabase. Crystal structures of I-CreI bound to methylated cognate target DNA suggested a molecular basis for such inhibition, although the precise mechanism still has to be specified. Finally, we demonstrated that the efficacy of engineered meganucleases can be diminished by CpG methylation of the targeted endogenous site, and we proposed a rational design of the meganuclease DNA binding domain to alleviate such an effect. We conclude that although activity and sequence specificity of engineered meganucleases are crucial parameters, target DNA epigenetic modifications need to be considered for successful gene editions.


  • Organizational Affiliation

    CELLECTIS S.A., 8 Rue de la Croix Jarry, 75013 Paris, France. julien.valton@cellectis.com


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA ENDONUCLEASE I-CREI
A, B
152Chlamydomonas reinhardtiiMutation(s): 0 
EC: 3.1
UniProt
Find proteins for P05725 (Chlamydomonas reinhardtii)
Explore P05725 
Go to UniProtKB:  P05725
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05725
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*DTP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*DAP *GP*AP*CP*AP*GP*TP*TP*TP*GP*G)-3'24synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*DCP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*5CMP *GP*AP*CP*GP*TP*TP*TP*TP*GP*A)-3'24synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.200 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.58α = 90
b = 45.355β = 90
c = 172.331γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-04
    Type: Initial release
  • Version 1.1: 2012-09-12
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description