Type IB DNA topoisomerases (TopIB) are monomeric enzymes that relax supercoils by cleaving and resealing one strand of duplex DNA within a protein clamp that embraces a ∼21 DNA segment. A longstanding conundrum concerns the capacity of TopIB enzymes to stabilize intramolecular duplex DNA crossovers and form protein-DNA synaptic filaments. Here we report a structure of Deinococcus radiodurans TopIB in complex with a 12 bp duplex DNA that demonstrates a secondary DNA binding site located on the surface of the C-terminal domain. It comprises a distinctive interface with one strand of the DNA duplex and is conserved in all TopIB enzymes. Modeling of a TopIB with both DNA sites suggests that the secondary site could account for DNA crossover binding, nucleation of DNA synapsis, and generation of a filamentous plectoneme. Mutations of the secondary site eliminate synaptic plectoneme formation without affecting DNA cleavage or supercoil relaxation.
ASJC Scopus subject areas
- Molecular Biology
- Structural Biology
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Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site
Patel, A. (Contributor), Yakovleva, L. (Contributor), Shuman, S. (Contributor) & Mondragon, A. (Contributor), Protein Data Bank (PDB), Jul 14 2010