› 2o54

X-ray diffraction
2.5Å resolution

Structure of E. coli topoisomerase III in complex with an 8-base single stranded oligonucleotide. Frozen in glycerol at pH 7.0

Released:
DOI: 10.2210/pdb2o54/pdb
PDB entry 2o54 coloured by chain, front view.
PDB entry 2o54 coloured by chain, side view.
PDB entry 2o54 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structural studies of E. coli topoisomerase III-DNA complexes reveal a novel type IA topoisomerase-DNA conformational intermediate.
Changela A, DiGate RJ, Mondragón A
J Mol Biol 368 105-18 (2007)
PMID: 17331537

Function and Biology Details

Reaction catalysed: 
ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115702 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
DNA topoisomerase 3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 659 amino acids
Theoretical weight: 74.15 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P14294 (Residues: 1-653; Coverage: 100%)
Gene names: JW1752, b1763, topB
Sequence domains:
Structure domains:
5'-D(*CP*GP*CP*AP*AP*CP*TP*T)-3' Chains: C, D
Molecule details ›
Chains: C, D
Length: 8 nucleotides
Theoretical weight: 2.39 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CL 2 x CL
Ligand ACY 1 x ACY
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 5ID-B
Spacegroup: P43212
Unit cell:
a: 101.83Å b: 101.83Å c: 452.38Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.225 0.222 0.269
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

Drugging topoisomerases: lessons and challenges.
Pommier Y. (2013)
6 more

2 mentions without citation

DNA topoisomerases: Advances in understanding of cellular roles and multi-protein complexes via structure-function analysis.
McKie et al. (2021)
1 more