2D3Y

Crystal structure of uracil-DNA glycosylase from Thermus Thermophilus HB8

2D3Y の概要

• エントリーDOI: 10.2210/pdb2d3y/pdb
• 分子名称: uracil-DNA glycosylase, ACETATE ION, IRON/SULFUR CLUSTER, ... (5 entities in total)
• 機能のキーワード: base excision repair, uracil-dna glycosylase, iron/sulfer cluster, thermophile, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, hydrolase
• 由来する生物種: Thermus thermophilus
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 25102.05

構造登録者

Kosaka, H.,Nakagawa, N.,Masui, R.,Kuramitsu, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (登録日: 2005-10-04, 公開日: 2006-10-17, 最終更新日: 2024-03-13)

主引用文献

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

実験手法

X-RAY DIFFRACTION (1.55 Å)