› 3n9d

X-ray diffraction
2.3Å resolution

Monoclinic Structure of P. aeruginosa LigD phosphoesterase domain

Released:
DOI: 10.2210/pdb3n9d/pdb
PDB entry 3n9d coloured by chain, front view.
PDB entry 3n9d coloured by chain, side view.
PDB entry 3n9d coloured by chain, top view.
Source organism: Pseudomonas aeruginosa
Primary publication:
Structure of bacterial LigD 3'-phosphoesterase unveils a DNA repair superfamily.
Nair PA, Smith P, Shuman S
Proc Natl Acad Sci U S A 107 12822-7 (2010)
PMID: 20616014

Function and Biology Details

Reaction catalysed: 
(1a) ATP + [DNA ligase]-L-lysine = [DNA ligase]-N(6)-(5'-adenylyl)-L-lysine + diphosphate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-191279 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Multifunctional non-homologous end joining protein LigD Chain: A
Molecule details ›
Chain: A
Length: 171 amino acids
Theoretical weight: 19.47 KDa
Source organism: Pseudomonas aeruginosa
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9I1X7 (Residues: 17-187; Coverage: 20%)
Gene names: PA2138, ligD
Sequence domains: DNA polymerase Ligase (LigD)

Ligands and Environments

3 bound ligands:
Ligand MN 1 x MN
Ligand SO4 2 x SO4
Ligand YT3 2 x YT3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: C2
Unit cell:
a: 90.997Å b: 56.585Å c: 43.503Å
α: 90° β: 118.33° γ: 90°
R-values:
R R work R free
0.217 0.212 0.263
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Bacterial NHEJ: a never ending story.
Bertrand et al. (2019)
4 more

1 mention without citation

Structure of bacterial LigD 3'-phosphoesterase unveils a DNA repair superfamily.
Nair et al. (2010)