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 1.1 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: 10.1074/jbc.M112.379966
  • Structures With Same Primary Citation

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA ENDONUCLEASE I-CREIA, B152Chlamydomonas reinhardtiiMutation(s): 0 
EC: 3.1
Find proteins for P05725 (Chlamydomonas reinhardtii)
Explore P05725 
Go to UniProtKB:  P05725
Protein Feature View
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  • Reference Sequence

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsLengthOrganism
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'D24synthetic construct

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsLengthOrganism
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'C24synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
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 

  • Version 1.0: 2012-07-04
    Type: Initial release
  • Version 1.1: 2012-09-12
    Changes: Database references