4AQX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.202 

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
  • Primary Citation of Related Structures:  

  • 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-CREI
A, B
152Chlamydomonas reinhardtiiMutation(s): 0 
EC: 3.1.-.-
Find proteins for P05725 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P05725
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP)-3'C14synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*GP*AP*CP*AP*GP*TP*TP*TP*GP*GP)-3'D10synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
5'-D(*CP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*5CM)-3'E14synthetic construct
Entity ID: 5
MoleculeChainsLengthOrganism
5'-D(*GP*AP*CP*GP*TP*TP*TP*TP*GP*AP)-3'F10synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
D, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
E
DNA LINKINGC10 H16 N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.202 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.839α = 90.00
b = 71.401β = 90.00
c = 179.054γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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