3N9D
Monoclinic Structure of P. aeruginosa LigD phosphoesterase domain
Summary for 3N9D
| Entry DOI | 10.2210/pdb3n9d/pdb |
| Related | 3N9B |
| Descriptor | Probable ATP-dependent DNA ligase, MANGANESE (II) ION, SULFATE ION, ... (5 entities in total) |
| Functional Keywords | phosphoesterase, metalloenzyme, ligase, nhej, manganese, beta barrel |
| Biological source | Pseudomonas aeruginosa |
| Total number of polymer chains | 1 |
| Total formula weight | 19899.84 |
| Authors | Shuman, S.,Nair, P.,Smith, P. (deposition date: 2010-05-28, release date: 2010-08-11, Last modification date: 2023-09-06) |
| 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 Cited by 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: 20616014DOI: 10.1073/pnas.1005830107 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.3 Å) |
Structure validation
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