title: Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site.
abstract: 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 approximately 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.
authors.affiliation: Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA.
authors.forename: Asmita
authors.initials: A
authors.lastname: Patel
authors.forename: Lyudmila
authors.initials: L
authors.lastname: Yakovleva
authors.forename: Stewart
authors.initials: S
authors.lastname: Shuman
authors.forename: Alfonso
authors.initials: A
authors.lastname: Mondragón
mesh_terms: D001419:Bacteria / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites / Q000235:genetics; D055592:Biophysical Phenomena; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D034301:Deinococcus / Q000201:enzymology* / Q000235:genetics / Q000378:metabolism; D007535:Isomerases / Q000235:genetics / Q000378:metabolism
chemical_list: D004269:DNA, Bacterial; D007535:Isomerases