› 2owo

X-ray diffraction
2.3Å resolution

Last Stop on the Road to Repair: Structure of E.coli DNA Ligase Bound to Nicked DNA-Adenylate

Released:
DOI: 10.2210/pdb2owo/pdb
PDB entry 2owo coloured by chain, front view.
PDB entry 2owo coloured by chain, side view.
PDB entry 2owo coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Last stop on the road to repair: structure of E. coli DNA ligase bound to nicked DNA-adenylate.
Nandakumar J, Nair PA, Shuman S
Mol Cell 26 257-71 (2007)
PMID: 17466627

Function and Biology Details

Reaction catalysed: 
(1a) NAD(+) + [DNA ligase]-L-lysine = [DNA ligase]-N(6)-(5'-adenylyl)-L-lysine + beta-nicotinamide D-nucleotide
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115742 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA ligase Chain: A
Molecule details ›
Chain: A
Length: 671 amino acids
Theoretical weight: 73.7 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P15042 (Residues: 1-671; Coverage: 100%)
Gene names: JW2403, b2411, dnaL, lig, ligA, lop, pdeC
Sequence domains:
Structure domains:
26-MER Chain: B
Molecule details ›
Chain: B
Length: 26 nucleotides
Theoretical weight: 8.03 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided
5'-D(*AP*CP*AP*AP*TP*TP*GP*CP*GP*AP*CP*(OMC)P*C)-3' Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 3.95 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided
5'-D(*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*G)-3' Chain: D
Molecule details ›
Chain: D
Length: 13 nucleotides
Theoretical weight: 3.98 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand AMP 1 x AMP
Ligand ZN 1 x ZN
Ligand SO4 4 x SO4
1 modified residue:
Ligand OMC 1 x OMC

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: C2
Unit cell:
a: 110.441Å b: 99.273Å c: 86.245Å
α: 90° β: 105.33° γ: 90°
R-values:
R R work R free
0.217 0.217 0.254
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

6 review citations

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

26 mentions without citation

Eukaryotic DNA ligases: structural and functional insights.
Ellenberger et al. (2008)
25 more