Summary information and primary citation

PDB-id
5akf; DSSR-derived features in text and JSON formats
Class
hydrolase
Method
X-ray (2.45 Å)
Summary
The crystal structure of i-dmoi q42ak120m in complex with its target DNA nicked in the coding strand a and in the presence of 2mm mn
Reference
Molina R, Marcaida MJ, Redondo P, Marenchino M, Duchateau P, D'Abramo M, Montoya G, Prieto J (2015): "Engineering a Nickase on the Homing Endonuclease I-Dmoi Scaffold." J.Biol.Chem., 290, 18534. doi: 10.1074/JBC.M115.658666.
Abstract
Homing endonucleases are useful tools for genome modification due to 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 introduce 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 to 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.

Cartoon-block schematics in six views (download the tarball)

PyMOL session file Download PDB file View in 3Dmol.js