› 4f1h

X-ray diffraction
1.66Å resolution

Crystal structure of TDP2 from Danio rerio complexed with a single strand DNA

Released:
DOI: 10.2210/pdb4f1h/pdb
PDB entry 4f1h coloured by chain, front view.
PDB entry 4f1h coloured by chain, side view.
PDB entry 4f1h coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.
Shi K, Kurahashi K, Gao R, Tsutakawa SE, Tainer JA, Pommier Y, Aihara H
Nat Struct Mol Biol 19 1372-7 (2012)
PMID: 23104058

Function and Biology Details

Biochemical function:
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-117443 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (3 distinct):
Tyrosyl-DNA phosphodiesterase 2 Chain: A
Molecule details ›
Chain: A
Length: 250 amino acids
Theoretical weight: 28.48 KDa
Source organism: Danio rerio
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5XJA0 (Residues: 120-369; Coverage: 68%)
Gene names: si:ch211-81e5.5, si:dkey-218n20.5, tdp2, ttrap, ttrapl
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase
Tyrosyl-DNA phosphodiesterase 2 Chain: B
Molecule details ›
Chain: B
Length: 251 amino acids
Theoretical weight: 28.61 KDa
Source organism: Danio rerio
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5XJA0 (Residues: 119-369; Coverage: 68%)
Gene names: si:ch211-81e5.5, si:dkey-218n20.5, tdp2, ttrap, ttrapl
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase
DNA (5'-D(P*TP*GP*CP*AP*G)-3') Chain: C
Molecule details ›
Chain: C
Length: 5 nucleotides
Theoretical weight: 1.52 KDa

Ligands and Environments

3 bound ligands:
Ligand PO4 1 x PO4
Ligand GOL 4 x GOL
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 57.918Å b: 95.1Å c: 104.732Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.164 0.164 0.192
Expression system: Escherichia coli

Quick links

Citations

10 review citations

Topoisomerase-mediated chromosomal break repair: an emerging player in many games.
Ashour et al. (2015)
9 more

5 mentions without citation

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