› 1v9p

X-ray diffraction
2.9Å resolution

Crystal Structure Of Nad+-Dependent DNA Ligase

Released:
DOI: 10.2210/pdb1v9p/pdb
PDB entry 1v9p coloured by chain, front view.
PDB entry 1v9p coloured by chain, side view.
PDB entry 1v9p coloured by chain, top view.
Source organism: Thermus filiformis
Primary publication:
Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications.
Lee JY, Chang C, Song HK, Moon J, Yang JK, Kim HK, Kwon ST, Suh SW
EMBO J 19 1119-29 (2000)
PMID: 10698952

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:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195655 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA ligase Chains: A, B
Molecule details ›
Chains: A, B
Length: 584 amino acids
Theoretical weight: 67.32 KDa
Source organism: Thermus filiformis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9ZHI0 (Residues: 1-584; Coverage: 87%)
Gene name: ligA
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand AMP 2 x AMP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X8C
Spacegroup: P21
Unit cell:
a: 89.21Å b: 117.33Å c: 97.48Å
α: 90° β: 115.09° γ: 90°
R-values:
R R work R free
0.232 0.232 0.293
Expression system: Escherichia coli

Quick links

Citations

19 review citations

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

7 mentions without citation

Molecular mechanisms of the whole DNA repair system: a comparison of bacterial and eukaryotic systems.
Morita et al. (2010)
6 more