2DDG

Crystal structure of uracil-DNA glycosylase in complex with AP:G containing DNA

Summary for 2DDG

• Entry DOI: 10.2210/pdb2ddg/pdb
• Related: 2D3Y
• Descriptor: 5'-D(*AP*TP*GP*TP*TP*GP*CP*(D1P)P*TP*TP*AP*GP*TP*CP*C)-3', 5'-D(*GP*GP*AP*CP*TP*AP*AP*GP*GP*CP*AP*AP*CP*A)-3', uracil-DNA glycosylase, ... (9 entities in total)
• Functional Keywords: base excision repair, uracil-dna glycosylase, iron/sulfer cluster, dna complex, thermophile, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, hydrolase-dna complex, hydrolase/dna
• Biological source: Thermus thermophilus
• Total number of polymer chains: 3
• Total formula weight: 34044.92

Authors

Kosaka, H.,Nakagawa, N.,Masui, R.,Hoseki, J.,Kuramitsu, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2006-01-28, release date: 2007-02-13, Last modification date: 2024-03-13)

Primary citation

Kosaka, H.,Hoseki, J.,Nakagawa, N.,Kuramitsu, S.,Masui, R.
Crystal structure of family 5 uracil-DNA glycosylase bound to DNA.
J.Mol.Biol., 373:839-850, 2007

PubMed 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.

PubMed: 17870091
DOI: 10.1016/j.jmb.2007.08.022

Experimental method

X-RAY DIFFRACTION (2.1 Å)