4AQU | pdb_00004aqu

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

• PDB DOI: https://doi.org/10.2210/pdb4AQU/pdb
• NAKB: 4AQU

• Classification: HYDROLASE
• Organism(s): Chlamydomonas reinhardtii, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-19 Released: 2012-07-04 
• Deposition Author(s): Valton, J., Daboussi, F., Leduc, S., Redondo, P., Macmaster, R., Molina, R., Montoya, G., Duchateau, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.249 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

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 Biological Chem 287: 30139

• PubMed: 22740697 
• DOI: https://doi.org/10.1074/jbc.M112.379966
• Primary Citation 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.

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Organizational Affiliation: 
• CELLECTIS S.A., 8 Rue de la Croix Jarry, 75013 Paris, France. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.05 kDa 
• Atom Count: 3,567 
• Modeled Residue Count: 352 
• Deposited Residue Count: 352 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA ENDONUCLEASE I-CREI	A, B	152	Chlamydomonas reinhardtii	Mutation(s): 0  EC: 3.1
UniProt
Find proteins for P05725 (Chlamydomonas reinhardtii) Explore P05725  Go to UniProtKB:  P05725

Entity ID: 2
Molecule	Chains	Length	Organism	Image
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'	C	24	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
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'	D	24	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	E [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.249 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.58	α = 90
b = 45.355	β = 90
c = 172.331	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-04 
Deposition Author(s): Valton, J., Daboussi, F., Leduc, S., Redondo, P., Macmaster, R., Molina, R., Montoya, G., Duchateau, P.

Revision History  

• 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