› 2r9l

X-ray diffraction
2.4Å resolution

Polymerase Domain from Mycobacterium tuberculosis Ligase D in complex with DNA

Released:
DOI: 10.2210/pdb2r9l/pdb
PDB entry 2r9l coloured by chain, front view.
PDB entry 2r9l coloured by chain, side view.
PDB entry 2r9l coloured by chain, top view.
Source organisms:
Primary publication:
Structure of a NHEJ polymerase-mediated DNA synaptic complex.
Brissett NC, Pitcher RS, Juarez R, Picher AJ, Green AJ, Dafforn TR, Fox GC, Blanco L, Doherty AJ
Science 318 456-9 (2007)
PMID: 17947582

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:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-218919 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
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
DNA (5'-D(P*DGP*DCP*DGP*DGP*DC)-3') Chains: C, E
Molecule details ›
Chains: C, E
Length: 5 nucleotides
Theoretical weight: 1.52 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DAP*DCP*DGP*DCP*DA)-3') Chain: D
Molecule details ›
Chain: D
Length: 11 nucleotides
Theoretical weight: 3.33 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DAP*DCP*DGP*DCP*DAP*DCP*DG)-3') Chain: F
Molecule details ›
Chain: F
Length: 13 nucleotides
Theoretical weight: 3.95 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand EDO 6 x EDO
Ligand PEG 1 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM16
Spacegroup: P212121
Unit cell:
a: 48.531Å b: 111.788Å c: 139.542Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.229 0.227 0.272
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

9 review citations

Microhomology-Mediated End Joining: A Back-up Survival Mechanism or Dedicated Pathway?
Sfeir et al. (2015)
8 more

4 mentions without citation

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