3N9D

Monoclinic Structure of P. aeruginosa LigD phosphoesterase domain

3N9D の概要

• エントリーDOI: 10.2210/pdb3n9d/pdb
• 関連するPDBエントリー: 3N9B
• 分子名称: Probable ATP-dependent DNA ligase, MANGANESE (II) ION, SULFATE ION, ... (5 entities in total)
• 機能のキーワード: phosphoesterase, metalloenzyme, ligase, nhej, manganese, beta barrel
• 由来する生物種: Pseudomonas aeruginosa
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 19899.84

構造登録者

Shuman, S.,Nair, P.,Smith, P. (登録日: 2010-05-28, 公開日: 2010-08-11, 最終更新日: 2023-09-06)

主引用文献

Nair, P.A.,Smith, P.,Shuman, S.
Structure of bacterial LigD 3'-phosphoesterase unveils a DNA repair superfamily
Proc.Natl.Acad.Sci.USA, 107:12822-12827, 2010

PubMed Abstract: The DNA ligase D (LigD) 3'-phosphoesterase (PE) module is a conserved component of the bacterial nonhomologous end-joining (NHEJ) apparatus that performs 3' end-healing reactions at DNA double-strand breaks. Here we report the 1.9 A crystal structure of Pseudomonas aeruginosa PE, which reveals that PE exemplifies a unique class of DNA repair enzyme. PE has a distinctive fold in which an eight stranded beta barrel with a hydrophobic interior supports a crescent-shaped hydrophilic active site on its outer surface. Six essential side chains coordinate manganese and a sulfate mimetic of the scissile phosphate. The PE active site and mechanism are unique vis à vis other end-healing enzymes. We find PE homologs in archaeal and eukaryal proteomes, signifying that PEs comprise a DNA repair superfamily.

PubMed: 20616014
DOI: 10.1073/pnas.1005830107

実験手法

X-RAY DIFFRACTION (2.3 Å)