› 1q32

X-ray diffraction
2.03Å resolution

Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase

Released:
DOI: 10.2210/pdb1q32/pdb
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PDB entry 1q32 coloured by chain, front view.
PDB entry 1q32 coloured by chain, side view.
PDB entry 1q32 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Mutation of a conserved active site residue converts tyrosyl-DNA phosphodiesterase I into a DNA topoisomerase I-dependent poison.
He X, van Waardenburg RCAM, Babaoglu K, Price AC, Nitiss KC, Nitiss JL, Bjornsti MA, White SW
J Mol Biol 372 1070-1081 (2007)
PMID: 17707402

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domain:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153609 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Tyrosyl-DNA phosphodiesterase 1 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 544 amino acids
Theoretical weight: 62.41 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P38319 (Residues: 1-544; Coverage: 100%)
Gene names: TDP1, YBR1520, YBR223C
Sequence domains: Tyrosyl-DNA phosphodiesterase
Structure domains: Endonuclease Chain A

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12B, APS BEAMLINE 22-ID
Spacegroup: P1
Unit cell:
a: 64.163Å b: 82.207Å c: 98.442Å
α: 89.39° β: 85.81° γ: 67.12°
R-values:
R R work R free
0.214 0.214 0.241
Expression system: Escherichia coli

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Citations

7 review citations

Targeting DNA topoisomerase II in cancer chemotherapy.
Nitiss JL. (2009)
6 more

279 mentions without citation

Inflammatory bowel disease.
Abraham et al. (2009)
278 more

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