› 1vs0

X-ray diffraction
2.4Å resolution

Crystal Structure of the Ligase Domain from M. tuberculosis LigD at 2.4A

Released:
DOI: 10.2210/pdb1vs0/pdb
PDB entry 1vs0 coloured by chain, front view.
PDB entry 1vs0 coloured by chain, side view.
PDB entry 1vs0 coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Primary publication:
Crystal structure and nonhomologous end-joining function of the ligase component of Mycobacterium DNA ligase D.
Akey D, Martins A, Aniukwu J, Glickman MS, Shuman S, Berger JM
J. Biol. Chem. 281 13412-23 (2006)
PMID: 16476729

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161894 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Multifunctional non-homologous end joining DNA repair protein LigD Chains: A, B
Molecule details ›
Chains: A, B
Length: 310 amino acids
Theoretical weight: 34.74 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli
UniProt:
  • Canonical: P9WNV3 (Residues: 452-759; Coverage: 41%)
Gene names: MTCY08D9.01c, MTCY10D7.36c, Rv0938, ligD
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand ZN 4 x ZN
Ligand CL 4 x CL
Ligand MG 1 x MG
2 modified residues:
Ligand MSE 8 x MSE
Ligand APK 2 x APK

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: P3221
Unit cell:
a: 57.102Å b: 57.102Å c: 368.957Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.195 0.192 0.248
Expression system: Escherichia coli

Quick links

Citations

9 review citations

Eukaryotic DNA ligases: structural and functional insights.
Ellenberger et al. (2008)
8 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