2VS7

The crystal structure of I-DmoI in complex with DNA and Ca


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of I-Dmoi in Complex with its Target DNA Provides New Insights Into Meganuclease Engineering.

Marcaida, M.J.Prieto, J.Redondo, P.Nadra, A.D.Alibes, A.Serrano, L.Grizot, S.Duchateau, P.Paques, F.Blanco, F.J.Montoya, G.

(2008) Proc.Natl.Acad.Sci.USA 105: 16888

  • DOI: 10.1073/pnas.0804795105
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Homing endonucleases, also known as meganucleases, are sequence-specific enzymes with large DNA recognition sites. These enzymes can be used to induce efficient homologous gene targeting in cells and plants, opening perspectives for genome engineerin ...

    Homing endonucleases, also known as meganucleases, are sequence-specific enzymes with large DNA recognition sites. These enzymes can be used to induce efficient homologous gene targeting in cells and plants, opening perspectives for genome engineering with applications in a wide series of fields, ranging from biotechnology to gene therapy. Here, we report the crystal structures at 2.0 and 2.1 A resolution of the I-DmoI meganuclease in complex with its substrate DNA before and after cleavage, providing snapshots of the catalytic process. Our study suggests that I-DmoI requires only 2 cations instead of 3 for DNA cleavage. The structure sheds light onto the basis of DNA binding, indicating key residues responsible for nonpalindromic target DNA recognition. In silico and in vivo analysis of the I-DmoI DNA cleavage specificity suggests that despite the relatively few protein-base contacts, I-DmoI is highly specific when compared with other meganucleases. Our data open the door toward the generation of custom endonucleases for targeted genome engineering using the monomeric I-DmoI scaffold.


    Organizational Affiliation

    Macromolecular Crystallography and Nuclear Magnetic Resonance Groups, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, c/Melchor Fdez. Almagro 3, 28029 Madrid, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HOMING ENDONUCLEASE I-DMOI
A, D, G
199Desulfurococcus mobilisMutation(s): 0 
EC: 3.1.-.-
Find proteins for P21505 (Desulfurococcus mobilis)
Go to UniProtKB:  P21505
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP *GP*TP*AP*AP*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*G)-3'B,E,H25Desulfurococcus mucosus
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP *CP*TP*TP*AP*CP*CP*CP*GP*GP*CP*AP*AP*GP*GP*C)-3'C,F,I25Desulfurococcus mucosus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, D, G
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 106.988α = 90.00
b = 70.587β = 119.75
c = 106.848γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SHARPphasing
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-11
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance