› 3m4a

X-ray diffraction
1.65Å resolution

Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site

Released:
DOI: 10.2210/pdb3m4a/pdb
PDB entry 3m4a coloured by chain, front view.
PDB entry 3m4a coloured by chain, side view.
PDB entry 3m4a coloured by chain, top view.
Source organism: Deinococcus radiodurans
Primary publication:
Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site.
Patel A, Yakovleva L, Shuman S, Mondragón A
Structure 18 725-33 (2010)
PMID: 20541510

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116547 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA topoisomerase Chain: A
Molecule details ›
Chain: A
Length: 346 amino acids
Theoretical weight: 39.08 KDa
Source organism: Deinococcus radiodurans
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9RWH8 (Residues: 1-346; Coverage: 100%)
Gene name: DR_0690
Sequence domains:
Structure domains:
DNA (5'-D(*GP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 12 nucleotides
Theoretical weight: 3.74 KDa
Source organism: Deinococcus radiodurans
Expression system: Not provided
DNA (5'-D(*GP*CP*GP*CP*CP*CP*TP*TP*AP*TP*TP*C)-3') Chain: E
Molecule details ›
Chain: E
Length: 12 nucleotides
Theoretical weight: 3.59 KDa
Source organism: Deinococcus radiodurans
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200, null
Spacegroup: C2
Unit cell:
a: 119.67Å b: 53.44Å c: 77.36Å
α: 90° β: 96.33° γ: 90°
R-values:
R R work R free
0.195 0.193 0.222
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

4 review citations

All tangled up: how cells direct, manage and exploit topoisomerase function.
Vos et al. (2011)
3 more

5 mentions without citation

Archaea: A Gold Mine for Topoisomerase Diversity.
Garnier et al. (2021)
4 more