3N9B

Crystal Structure of the P. aeruginosa LigD phosphoesterase domain

Summary for 3N9B

• Entry DOI: 10.2210/pdb3n9b/pdb
• Related: 3N9D
• Descriptor: Probable ATP-dependent DNA ligase, SULFATE ION, CHLORIDE ION, ... (7 entities in total)
• Functional Keywords: phosphoesterase, metalloenzyme, ligase, nhej, manganese, beta barrel
• Biological source: Pseudomonas aeruginosa
• Total number of polymer chains: 2
• Total formula weight: 39941.25

Authors

Shuman, S.,Nair, P.,Smith, P. (deposition date: 2010-05-28, release date: 2010-08-11, Last modification date: 2024-02-21)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.92 Å)