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

Asmita Patel; Lyudmila Yakovleva; Stewart Shuman; Alfonso Mondragón

doi:10.1016/j.str.2010.03.007

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

Asmita Patel, Lyudmila Yakovleva, Stewart Shuman, Alfonso Mondragón^*

^*Corresponding author for this work

Molecular Biosciences

Research output: Contribution to journal › Article › peer-review

25 Scopus citations

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)
Pages (from-to)	725-733
Number of pages	9
Journal	Structure
Volume	18
Issue number	6
DOIs	https://doi.org/10.1016/j.str.2010.03.007
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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10.1016/j.str.2010.03.007

Cite this

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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 ∼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.",

keywords = "DNA",

author = "Asmita Patel and Lyudmila Yakovleva and Stewart Shuman and Alfonso Mondrag{\'o}n",

note = "Funding Information: 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. ",

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AU - Mondragón, Alfonso

N1 - Funding Information: 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.

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N2 - 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.

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

Abstract

Funding

Keywords

ASJC Scopus subject areas

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