› 4gz1

X-ray diffraction
1.5Å resolution

Mus Musculus Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex at 1.5 Angstroms resolution

Released:
DOI: 10.2210/pdb4gz1/pdb
PDB entry 4gz1 coloured by chain, front view.
PDB entry 4gz1 coloured by chain, side view.
PDB entry 4gz1 coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Mechanism of repair of 5'-topoisomerase II-DNA adducts by mammalian tyrosyl-DNA phosphodiesterase 2.
Schellenberg MJ, Appel CD, Adhikari S, Robertson PD, Ramsden DA, Williams RS
Nat Struct Mol Biol 19 1363-71 (2012)
PMID: 23104055

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero dimer
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117568 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Tyrosyl-DNA phosphodiesterase 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 256 amino acids
Theoretical weight: 28.89 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9JJX7 (Residues: 118-370; Coverage: 68%)
Gene names: Tdp2, Ttrap
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase
DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3') Chains: C, D
Molecule details ›
Chains: C, D
Length: 9 nucleotides
Theoretical weight: 2.72 KDa
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand EPE 1 x EPE
Ligand MG 2 x MG
Ligand FMT 1 x FMT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 55.2Å b: 69.139Å c: 167.789Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.147 0.145 0.175
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

10 review citations

Tyrosyl-DNA-phosphodiesterases (TDP1 and TDP2).
Pommier et al. (2014)
9 more

14 mentions without citation

Tyrosyl-DNA phosphodiesterases: rescuing the genome from the risks of relaxation.
Kawale et al. (2018)
13 more