3M4A

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

Summary for 3M4A

• Entry DOI: 10.2210/pdb3m4a/pdb
• Descriptor: Putative Type I topoisomerase, DNA (5'-D(*GP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*C)-3'), DNA (5'-D(*GP*CP*GP*CP*CP*CP*TP*TP*AP*TP*TP*C)-3'), ... (6 entities in total)
• Functional Keywords: type ib, topib, protein-dna complex, isomerase-dna complex, isomerase/dna
• Biological source: Deinococcus radiodurans
• Total number of polymer chains: 3
• Total formula weight: 46547.60

Authors

Patel, A.,Yakovleva, L.,Shuman, S.,Mondragon, A. (deposition date: 2010-03-10, release date: 2010-07-14, Last modification date: 2023-09-06)

Primary citation

Patel, A.,Yakovleva, L.,Shuman, S.,Mondragon, A.
Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site.
Structure, 18:725-733, 2010

PubMed 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.

PubMed: 20541510
DOI: 10.1016/j.str.2010.03.007

Experimental method

X-RAY DIFFRACTION (1.65 Å)