2DDG: Crystal Structure Of Uracil-dna Glycosylase In Complex With Ap:g Containing Dna

Citation:
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.
PDB ID: 2DDGDownload
MMDB ID: 68904
PDB Deposition Date: 2006/1/28
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 2.1  Å
Source Organism:
Thermus thermophilus HB8
Similar Structures:
Biological Unit for 2DDG: trimeric; determined by author
Molecular Components in 2DDG
Label Count Molecule
Protein (1 molecule)
1
Uracil-dna Glycosylase(Gene symbol: TTHA1149)
Molecule annotation
Nucleotides(2 molecules)
1
5'-d(*ap*tp*gp*tp*tp*gp*cp*(d1p)p*tp*tp*ap*gp*tp*cp*c)-3'
Molecule annotation
1
5'-d(*gp*gp*ap*cp*tp*ap*ap*gp*gp*cp*ap*ap*cp*a)-3'
Molecule annotation
Chemicals (6 molecules)
1
2
2
2
3
1
4
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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