6FB5

Crystal Structure of a Tailored I-CreI Homing Endonuclease Protein (3115 variant) in complex with an altered version of its target DNA (Haemoglobin beta subunit gene) at 5NNN region in the presence of Magnesium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Understanding the indirect DNA read-out specificity of I-CreI Meganuclease.

Prieto, J.Redondo, P.Lopez-Mendez, B.D'Abramo, M.Merino, N.Blanco, F.J.Duchateau, P.Montoya, G.Molina, R.

(2018) Sci Rep 8: 10286-10286

  • DOI: https://doi.org/10.1038/s41598-018-28599-0
  • Primary Citation of Related Structures:  
    6FB0, 6FB1, 6FB2, 6FB5, 6FB6, 6FB7, 6FB8, 6FB9

  • PubMed Abstract: 

    The high DNA specificity of homing endonucleases makes them a powerful protein scaffold to engineer enzymes for genome manipulation. Understanding their molecular recognition of DNA is an important prerequisite to generate engineered enzymes able to cleave DNA in specific desired genome sites. Protein-DNA recognition studies have been mostly focused on specific direct contacts between amino acid side chains and bases to redesign the binding interface. However, the important role of indirect readout in the central region of the target DNA of the homing endonuclease I-CreI suggested that indirect readout may play a key role in the redesign of protein-DNA interactions. The sequences of the I-CreI central substrate region, 2NN, along with the adjacent 5NNN, are key for substrate cleavage. Here, we analyse the mechanism of target discrimination at the 5NNN region by the I-CreI protein, revealing its critical role in the location and occupancy of the catalytic metal ions, which is crucial for cleavage. Our data highlight the importance of indirect readout for target DNA cleavage, thus aiding I-CreI engineering when targeting new DNA sequences.


  • Organizational Affiliation

    Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group, c/Melchor Fdez. Almagro 3, 28029, Madrid, Spain.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
I-CreI monomer A153Chlamydomonas reinhardtiiMutation(s): 0 
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 Sequence LengthOrganismDetailsImage
I-CreI monomer B154Chlamydomonas reinhardtiiMutation(s): 0 
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: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*CP*AP*GP*AP*CP*TP*TP*GP*TP*CP*CP*AP*CP*AP*GP*GP*AP*GP*TP*CP*AP*GP*A)-3')C [auth D]24synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*CP*TP*GP*AP*CP*TP*CP*CP*TP*GP*TP*GP*GP*AP*CP*AP*AP*GP*TP*CP*TP*GP*A)-3')D [auth F]24synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.29α = 90
b = 68.005β = 96.55
c = 83.03γ = 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: 2018-07-18
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description