5AKM

THE CRYSTAL STRUCTURE OF I-DMOI G20S IN COMPLEX WITH ITS TARGET DNA IN THE PRESENCE OF 2MM MG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Engineering a Nickase on the Homing Endonuclease I-Dmoi Scaffold.

Molina, R.Marcaida, M.J.Redondo, P.Marenchino, M.Duchateau, P.D'Abramo, M.Montoya, G.Prieto, J.

(2015) J.Biol.Chem. 290: 18534

  • DOI: 10.1074/jbc.M115.658666
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Homing endonucleases are useful tools for genome modification because of their capability to recognize and cleave specifically large DNA targets. These endonucleases generate a DNA double strand break that can be repaired by the DNA damage response m ...

    Homing endonucleases are useful tools for genome modification because of their capability to recognize and cleave specifically large DNA targets. These endonucleases generate a DNA double strand break that can be repaired by the DNA damage response machinery. The break can be repaired by homologous recombination, an error-free mechanism, or by non-homologous end joining, a process susceptible to introducing errors in the repaired sequence. The type of DNA cleavage might alter the balance between these two alternatives. The use of "nickases" producing a specific single strand break instead of a double strand break could be an approach to reduce the toxicity associated with non-homologous end joining by promoting the use of homologous recombination to repair the cleavage of a single DNA break. Taking advantage of the sequential DNA cleavage mechanism of I-DmoI LAGLIDADG homing endonuclease, we have developed a new variant that is able to cut preferentially the coding DNA strand, generating a nicked DNA target. Our structural and biochemical analysis shows that by decoupling the action of the catalytic residues acting on each strand we can inhibit one of them while keeping the other functional.


    Organizational Affiliation

    From the Macromolecular Crystallography Group and.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HOMING ENDONUCLEASE I-DMOI
A, F, K
199Desulfurococcus mobilisMutation(s): 1 
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)-3'B,G,L14synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3'C,H,M11synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3'D,I,N15synthetic construct
Entity ID: 5
MoleculeChainsLengthOrganism
5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'E,J,O10synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, F
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, F, K
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 107.390α = 90.00
b = 68.650β = 119.94
c = 107.340γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2015-08-05
    Type: Database references
  • Version 1.2: 2017-08-23
    Type: Data collection