› 3n9b

X-ray diffraction
1.92Å resolution

Crystal Structure of the P. aeruginosa LigD phosphoesterase domain

Released:
DOI: 10.2210/pdb3n9b/pdb
PDB entry 3n9b coloured by chain, front view.
PDB entry 3n9b coloured by chain, side view.
PDB entry 3n9b 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 Chains: A, B
Molecule details ›
Chains: A, B
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

5 bound ligands:
Ligand SO4 4 x SO4
Ligand CL 1 x CL
Ligand PEG 1 x PEG
Ligand MN 2 x MN
Ligand YT3 4 x YT3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12C
Spacegroup: P1
Unit cell:
a: 41.583Å b: 45.55Å c: 53.384Å
α: 102.32° β: 109.43° γ: 104.59°
R-values:
R R work R free
0.153 0.148 0.199
Expression system: Escherichia coli

Quick links

Citations

3 review citations

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

6 mentions without citation

LigD: A Structural Guide to the Multi-Tool of Bacterial Non-Homologous End Joining.
Amare et al. (2021)
5 more