Open AccessStructure of bacterial LigD 3′-phosphoesterase unveils a DNA repair superfamily
Author(s) -
Pravin A. Nair,
Paul Smith,
Stewart Shuman
Publication year - 2010
Publication title -
proceedings of the national academy of sciences of the united states of america
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.011
H-Index - 771
eISSN - 1091-6490
pISSN - 0027-8424
DOI - 10.1073/pnas.1005830107
Subject(s) - dna ligase , dna , dna repair , dna ligases , biology , superfamily , biochemistry , microbiology and biotechnology , gene
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 Å crystal structure ofPseudomonas aeruginosa PE, which reveals that PE exemplifies a unique class of DNA repair enzyme. PE has a distinctive fold in which an eight stranded β 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 uniquevis à vis other end-healing enzymes. We find PE homologs in archaeal and eukaryal proteomes, signifying that PEs comprise a DNA repair superfamily.