3N9D: Monoclinic Structure Of P. Aeruginosa Ligd Phosphoesterase Domain

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 a vis other end-healing enzymes. We find PE homologs in archaeal and eukaryal proteomes, signifying that PEs comprise a DNA repair superfamily.
PDB ID: 3N9DDownload
MMDB ID: 84028
PDB Deposition Date: 2010/5/28
Updated in MMDB: 2010/09
Experimental Method:
x-ray diffraction
Resolution: 2.3  Å
Source Organism:
Similar Structures:
Biological Unit for 3N9D: monomeric; determined by author
Molecular Components in 3N9D
Label Count Molecule
Protein (1 molecule)
Probable Atp-dependent DNA Ligase(Gene symbol: PA2138)
Molecule annotation
Chemicals (5 molecules)
* Click molecule labels to explore molecular sequence information.

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