4AAB | pdb_00004aab

Crystal structure of the mutant D75N I-CreI in complex with its wild- type target (The four central bases, 2NN region, are composed by GTAC from 5' to 3')

• PDB DOI: https://doi.org/10.2210/pdb4AAB/pdb
• NAKB: 4AAB

• Classification: HYDROLASE/DNA
• Organism(s): Chlamydomonas reinhardtii, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-12-01 Released: 2012-05-02 
• Deposition Author(s): Molina, R., Redondo, P., Stella, S., Marenchino, M., D'Abramo, M., Gervasio, F.L., Epinat, J.C., Valton, J., Grizot, S., Duchateau, P., Prieto, J., Montoya, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.225 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Non-Specific Protein-DNA Interactions Control I-Crei Target Binding and Cleavage.

Molina, R., Redondo, P., Stella, S., Marenchino, M., D'Abramo, M., Gervasio, F.L., Charles Epinat, J., Valton, J., Grizot, S., Duchateau, P., Prieto, J., Montoya, G.

(2012) Nucleic Acids Res 40: 6936-6945

• PubMed: 22495931 
• DOI: https://doi.org/10.1093/nar/gks320
• Primary Citation Related Structures: 
  4AAB, 4AAD, 4AAE, 4AAF, 4AAG


• PubMed Abstract: 
  

  Homing endonucleases represent protein scaffolds that provide powerful tools for genome manipulation, as these enzymes possess a very low frequency of DNA cleavage in eukaryotic genomes due to their high specificity. The basis of protein-DNA recognition must be understood to generate tailored enzymes that target the DNA at sites of interest. Protein-DNA interaction engineering of homing endonucleases has demonstrated the potential of these approaches to create new specific instruments to target genes for inactivation or repair. Protein-DNA interface studies have been focused mostly on specific contacts between amino acid side chains and bases to redesign the binding interface. However, it has been shown that 4 bp in the central DNA sequence of the 22-bp substrate of a homing endonuclease (I-CreI), which do not show specific protein-DNA interactions, is not devoid of content information. Here, we analyze the mechanism of target discrimination in this substrate region by the I-CreI protein, determining how it can occur independently of the specific protein-DNA interactions. Our data suggest the important role of indirect readout in this substrate region, opening the possibility for a fully rational search of new target sequences, thus improving the development of redesigned enzymes for therapeutic and biotechnological applications.

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Organizational Affiliation: 
• Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group, Madrid, Spain.

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: 50.15 kDa 
• Atom Count: 3,603 
• 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): 1  EC: 3.1
UniProt
Find proteins for P05725 (Chlamydomonas reinhardtii) Explore P05725  Go to UniProtKB:  P05725

Entity ID: 2
Molecule	Chains	Length	Organism	Image
14MER DNA 5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*CP)-3'	C [auth D], E [auth F]	14	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
10MER DNA 5'-D(*GP*AP*CP*GP*TP*TP*TP*TP*GP*AP)-3'	D [auth E], F [auth G]	10	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGO	G [auth B], H [auth B], K [auth D], L [auth E], M [auth E]	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N
MG	I [auth B], J [auth B], N [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	O [auth G]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.225 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.97	α = 90
b = 71.1	β = 90
c = 46.92	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: 2012-05-02 
Deposition Author(s): Molina, R., Redondo, P., Stella, S., Marenchino, M., D'Abramo, M., Gervasio, F.L., Epinat, J.C., Valton, J., Grizot, S., Duchateau, P., Prieto, J., Montoya, G.

Revision History  

• Version 1.0: 2012-05-02
  Type: Initial release
  
• Version 1.1: 2012-08-22
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description