› 3l4k

X-ray diffraction
2.98Å resolution

Topoisomerase II-DNA cleavage complex, metal-bound

Released:
DOI: 10.2210/pdb3l4k/pdb
PDB entry 3l4k coloured by chain, front view.
PDB entry 3l4k coloured by chain, side view.
PDB entry 3l4k coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases.
Schmidt BH, Burgin AB, Deweese JE, Osheroff N, Berger JM
Nature 465 641-4 (2010)
PMID: 20485342

Function and Biology Details

Reaction catalysed: 
ATP-dependent breakage, passage and rejoining of double-stranded DNA
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116522 (preferred)
Entry contents:
1 distinct polypeptide molecule
4 distinct DNA molecules
Macromolecules (5 distinct):
DNA topoisomerase 2 Chain: A
Molecule details ›
Chain: A
Length: 757 amino acids
Theoretical weight: 88.03 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P06786 (Residues: 421-1177; Coverage: 53%)
Gene names: N2244, TOP2, TOR3, YNL088W
Sequence domains:
Structure domains:
DNA (5'-D(P*CP*CP*TP*AP*CP*TP*GP*CP*TP*AP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 11 nucleotides
Theoretical weight: 3.27 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided
DNA (5'-D(*CP*GP*CP*GP*GP*TP*AP*GP*CP*AP*GP*TP*AP*GP*G)-3') Chain: C
Molecule details ›
Chain: C
Length: 15 nucleotides
Theoretical weight: 4.68 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided
DNA (5'-D(P*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*)-3') Chain: D
Molecule details ›
Chain: D
Length: 10 nucleotides
Theoretical weight: 3.11 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*CP*GP*TP*CP*AP*TP*CP*C)-3') Chain: E
Molecule details ›
Chain: E
Length: 15 nucleotides
Theoretical weight: 4.53 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 8 x ZN
Ligand TSP 1 x TSP
1 modified residue:
Ligand PTR 1 x PTR

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Unit cell:
a: 86.064Å b: 91.851Å c: 115.939Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.241 0.239 0.273
Expression systems:
  • Saccharomyces cerevisiae
  • Not provided

Quick links

Citations

23 review citations

Mechanism of quinolone action and resistance.
Aldred et al. (2014)
22 more

13 mentions without citation

DNA Topoisomerase Inhibitors: Trapping a DNA-Cleaving Machine in Motion.
Bax et al. (2019)
12 more