5A74

Crystal structure of the homing endonuclease I-CvuI in complex with its target (Sro1.3) in the presence of 2 mM Mn


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of the Homing Endonuclease I-Cvui Provides a New Template for Genome Modification

Molina, R.Redondo, P.Lopez-Mendez, B.Villate, M.Merino, N.Blanco, F.J.Valton, J.Grizot, S.Duchateau, P.Prieto, J.Montoya, G.

(2015) J.Biol.Chem. 290: 28727

  • DOI: 10.1074/jbc.M115.678342
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Homing endonucleases recognize and generate a DNA double-strand break, which has been used to promote gene targeting. These enzymes recognize long DNA stretches; they are highly sequence-specific enzymes and display a very low frequency of cleavage e ...

    Homing endonucleases recognize and generate a DNA double-strand break, which has been used to promote gene targeting. These enzymes recognize long DNA stretches; they are highly sequence-specific enzymes and display a very low frequency of cleavage even in complete genomes. Although a large number of homing endonucleases have been identified, the landscape of possible target sequences is still very limited to cover the complexity of the whole eukaryotic genome. Therefore, the finding and molecular analysis of homing endonucleases identified but not yet characterized may widen the landscape of possible target sequences. The previous characterization of protein-DNA interaction before the engineering of new homing endonucleases is essential for further enzyme modification. Here we report the crystal structure of I-CvuI in complex with its target DNA and with the target DNA of I-CreI, a homologue enzyme widely used in genome engineering. To characterize the enzyme cleavage mechanism, we have solved the I-CvuI DNA structures in the presence of non-catalytic (Ca(2+)) and catalytic ions (Mg(2+)). We have also analyzed the metal dependence of DNA cleavage using Mg(2+) ions at different concentrations ranging from non-cleavable to cleavable concentrations obtained from in vitro cleavage experiments. The structure of I-CvuI homing endonuclease expands the current repertoire for engineering custom specificities, both by itself as a new scaffold alone and in hybrid constructs with other related homing endonucleases or other DNA-binding protein templates.


    Organizational Affiliation

    From the Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group, C/Melchor Fernández Almagro 3, 28029 Madrid, Spain, the Protein Structure & Function Programme, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark, guillermo.montoya@cpr.ku.dk.,the Protein Structure & Function Programme, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.,CELLECTIS S. A., 8 rue de la croix Jarry, 75013 Paris, France.,From the Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group, C/Melchor Fernández Almagro 3, 28029 Madrid, Spain.,From the Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group, C/Melchor Fernández Almagro 3, 28029 Madrid, Spain, jprieto@cnio.es.,the Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia 800, 48160 Derio, Spain, IKERBASQUE, Basque Foundation for Science, María Díaz de Haro 3, 48013 Bilbao, Spain, and.,the Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia 800, 48160 Derio, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA ENDONUCLEASE I-CVUI
A, B
172Chlorella vulgarisMutation(s): 0 
EC: 3.1.-.-
Find proteins for P56347 (Chlorella vulgaris)
Go to UniProtKB:  P56347
Entity ID: 2
MoleculeChainsLengthOrganism
14MER DNA, 5'-D(*TP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*AP*CP)-3'C,D14synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
10MER DNA, 5'-D(*GP*AP*CP*GP*TP*TP*CP*TP*GP*AP)-3'E,F10synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.730α = 90.00
b = 82.030β = 90.00
c = 94.490γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2015-12-09
    Type: Database references