PMID: 17870091 , Related PDB ids: 2D3Y, 2DDG, 2DEM

Authors:

Kosaka H, Hoseki J, Nakagawa N, Kuramitsu S, Masui R

Title:

Crystal structure of family 5 uracil-DNA glycosylase bound to DNA.

Journal:

J Mol Biol. 2007 Nov 2;373(4):839-50. Epub 2007 Aug 21.

Abstract:

Uracil-DNA glycosylase (UDG) removes uracil generated by the deamination of cytosine or misincorporation of deoxyuridine monophosphate. Within the UDG superfamily, a fifth UDG family lacks a polar residue in the active-site motif, which mediates the hydrolysis of the glycosidic bond by activation of a water molecule in UDG families 1-4. We have determined the crystal structure of a novel family 5 UDG from Thermus thermophilus HB8 complexed with DNA containing an abasic site. The active-site structure suggests this enzyme uses both steric force and water activation for its excision reaction. A conserved asparagine residue acts as a ligand to the catalytic water molecule. The structure also implies that another water molecule acts as a barrier during substrate recognition. Based on no significant open-closed conformational change upon binding to DNA, we propose a "slide-in" mechanism for initial damage recognition.