› 2iry

X-ray diffraction
1.78Å resolution

Crystal Structure of the Polymerase Domain from Mycobacterium tuberculosis Ligase D with dGTP and Manganese.

Released:
DOI: 10.2210/pdb2iry/pdb
PDB entry 2iry coloured by chain, front view.
PDB entry 2iry coloured by chain, side view.
PDB entry 2iry coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Primary publication:
Structure and function of a mycobacterial NHEJ DNA repair polymerase.
Pitcher RS, Brissett NC, Picher AJ, Andrade P, Juarez R, Thompson D, Fox GC, Blanco L, Doherty AJ
J Mol Biol 366 391-405 (2007)
PMID: 17174332

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-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: 303 amino acids
Theoretical weight: 32.83 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P9WNV3 (Residues: 1-300; Coverage: 40%)
Gene names: MTCY08D9.01c, MTCY10D7.36c, Rv0938, ligD
Sequence domains: LigD, primase-polymerase domain
Structure domains: Alpha-Beta Plaits

Ligands and Environments

2 bound ligands:
Ligand MN 2 x MN
Ligand DGT 2 x DGT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P21
Unit cell:
a: 41.221Å b: 75.87Å c: 95.809Å
α: 90° β: 92.59° γ: 90°
R-values:
R R work R free
0.185 0.182 0.23
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

14 review citations

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

1 mention without citation

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