› 2fao

X-ray diffraction
1.5Å resolution

Crystal Structure of Pseudomonas aeruginosa LigD polymerase domain

Released:
DOI: 10.2210/pdb2fao/pdb
PDB entry 2fao coloured by chain, front view.
PDB entry 2fao coloured by chain, side view.
PDB entry 2fao coloured by chain, top view.
Source organism: Pseudomonas aeruginosa
Primary publication:
Atomic structure and nonhomologous end-joining function of the polymerase component of bacterial DNA ligase D.
Zhu H, Nandakumar J, Aniukwu J, Wang LK, Glickman MS, Lima CD, Shuman S
Proc Natl Acad Sci U S A 103 1711-6 (2006)
PMID: 16446439

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 domains:

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: 309 amino acids
Theoretical weight: 34.19 KDa
Source organism: Pseudomonas aeruginosa
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9I1X7 (Residues: 533-840; Coverage: 37%)
Gene names: PA2138, ligD
Sequence domains: LigD, primase-polymerase domain
Structure domains: DNA primase, PRIM domain

Ligands and Environments

1 bound ligand:
Ligand SO4 5 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P21212
Unit cell:
a: 71.745Å b: 203.577Å c: 44.2Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.206 0.214
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Bacterial DNA repair by non-homologous end joining.
Shuman et al. (2007)
4 more

3 mentions without citation

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