› 4puq

X-ray diffraction
1.6Å resolution

Mus Musculus Tdp2 reaction product complex with 5'-phosphorylated RNA/DNA, glycerol, and Mg2+

Released:
DOI: 10.2210/pdb4puq/pdb
PDB entry 4puq coloured by chain, front view.
PDB entry 4puq coloured by chain, side view.
PDB entry 4puq coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Proteolytic degradation of topoisomerase II (Top2) enables the processing of Top2·DNA and Top2·RNA covalent complexes by tyrosyl-DNA-phosphodiesterase 2 (TDP2).
Gao R, Schellenberg MJ, Huang SY, Abdelmalak M, Marchand C, Nitiss KC, Nitiss JL, Williams RS, Pommier Y
J Biol Chem 289 17960-9 (2014)
PMID: 24808172

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113163 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA/RNA hybrid 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/RNA hybrid Chains: C, D
Molecule details ›
Chains: C, D
Length: 9 nucleotides
Theoretical weight: 2.73 KDa
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand GOL 3 x GOL
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 54.828Å b: 69.258Å c: 167.107Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.131 0.129 0.171
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

27 review citations

Roles of eukaryotic topoisomerases in transcription, replication and genomic stability.
Pommier et al. (2016)
26 more

2 mentions without citation

Proteolytic degradation of topoisomerase II (Top2) enables the processing of Top2·DNA and Top2·RNA covalent complexes by tyrosyl-DNA-phosphodiesterase 2 (TDP2).
Gao et al. (2014)
1 more