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 ∼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.
Original language | English (US) |
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Pages (from-to) | 725-733 |
Number of pages | 9 |
Journal | Structure |
Volume | 18 |
Issue number | 6 |
DOIs | |
State | Published - Jun 2010 |
Funding
Support from the R.H. Lurie Comprehensive Cancer Center of Northwestern University to the Structural Biology Facility is acknowledged. This research was supported by National Institutes of Health grants GM51350 (to A.M.) and GM46330 (to S.S.). S.S. is an American Cancer Society Research Professor. Portions of this work were performed at the DuPont-Northwestern-Dow Collaborative Access Team (DND-CAT) Synchrotron Research Center at the Advanced Photon Source (APS). DND-CAT is supported by Dupont, DOW, and the National Science Foundation. Use of the APS is supported by the Department of Energy. We thank G. Van Duyne for providing the coordinates of the poxvirus TopIB-DNA vanadate transition state mimetic in advance of publication.
Keywords
- DNA
ASJC Scopus subject areas
- Structural Biology
- Molecular Biology
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Dive into the research topics of 'Crystal Structure of a Bacterial Topoisomerase IB in Complex with DNA Reveals a Secondary DNA Binding Site'. Together they form a unique fingerprint.Datasets
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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) & Mondragón, A. (Contributor), Protein Data Bank (PDB), Jul 14 2010
DOI: 10.2210/pdb3M4A/pdb, https://www.wwpdb.org/pdb?id=pdb_00003m4a
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