Crystal Structure of a Bacterial Topoisomerase IB in Complex with DNA Reveals a Secondary DNA Binding Site

Journal Article · Fri Oct 22 04:00:00 EDT 2010 · Structure

DOI:https://doi.org/10.1016/j.str.2010.03.007· OSTI ID:1002532

Patel, Asmita; Yakovleva, Lyudmila; Shuman, Stewart; Mondragón, Alfonso ^[1]

---

1. NWU

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 {approx}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.

• Research Organization: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)
• Sponsoring Organization: USDOE
• OSTI ID: 1002532
• Journal Information: Structure, Journal Name: Structure Journal Issue: (6) ; 06, 2010 Vol. 18
• Country of Publication: United States
• Language: ENGLISH

Related Subjects

36 MATERIALS SCIENCE
CAPACITY
CLEAVAGE
CRYSTAL STRUCTURE
DNA
ENZYMES
MUTATIONS
NUCLEATION
PROTEINS
RELAXATION
SIMULATION