› 3sq5

X-ray diffraction
2.3Å resolution

Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase H432N Mutant

Released:
DOI: 10.2210/pdb3sq5/pdb
PDB entry 3sq5 coloured by chain, front view.
PDB entry 3sq5 coloured by chain, side view.
PDB entry 3sq5 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Analysis of the active-site mechanism of tyrosyl-DNA phosphodiesterase I: a member of the phospholipase D superfamily.
Gajewski S, Comeaux EQ, Jafari N, Bharatham N, Bashford D, White SW, van Waardenburg RC
J Mol Biol 415 741-58 (2012)
PMID: 22155078

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
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: 470 amino acids
Theoretical weight: 54.03 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P38319 (Residues: 79-539; Coverage: 85%)
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: APS BEAMLINE 22-BM
Spacegroup: P1
Unit cell:
a: 64.453Å b: 82.036Å c: 98.677Å
α: 89.8° β: 94.33° γ: 112.78°
R-values:
R R work R free
0.204 0.203 0.236
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

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

1 mention without citation

Analysis of the active-site mechanism of tyrosyl-DNA phosphodiesterase I: a member of the phospholipase D superfamily.
Gajewski et al. (2012)