6FB7

Crystal Structure of the I-CreI Homing Endonuclease D75N variant in complex with its target DNA in the presence of Manganese


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.689 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1038/s41598-018-28599-0
  • Primary Citation of Related Structures:  

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA endonuclease I-CreI
A, B
152Chlamydomonas reinhardtiiMutation(s): 1 
EC: 3.1.-.-
Find proteins for P05725 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P05725
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*C)-3')D,F14synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*GP*A)-3')E,G10synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.689 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 71.504α = 90.00
b = 169.153β = 90.00
c = 49.015γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-12-18 
  • Released Date: 2018-07-18 
  • Deposition Author(s): Molina, R., Prieto, J.

Revision History 

  • Version 1.0: 2018-07-18
    Type: Initial release