The recombination-associated protein RdgC adopts a novel toroidal architecture for DNA binding

Jun Yong Ha; Hye Kyong Kim; Do Jin Kim; Kyoung Hoon Kim; Sung Jin Oh; Hyung Ho Lee; Hye Jin Yoon; Hyun Kyu Song; Se Won Suh

doi:10.1093/nar/gkm144

The recombination-associated protein RdgC adopts a novel toroidal architecture for DNA binding

Jun Yong Ha
, Hye Kyong Kim
, Do Jin Kim
, Kyoung Hoon Kim
, Sung Jin Oh
, Hyung Ho Lee
, Hye Jin Yoon
, Hyun Kyu Song
, Se Won Suh^*

^*Corresponding author for this work

Department of Life Sciences

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

8 Citations (Scopus)

Abstract

RecA plays a central role in the nonmutagenic repair of stalled replication forks in bacteria. RdgC, a recombination-associated DNA-binding protein, is a potential negative regulator of RecA function. Here, we have determined the crystal structure of RdgC from Pseudomonas aeruginosa. The J-shaped monomer has a unique fold and can be divided into three structural domains: Tip domain, center domain and base domain. Two such monomers dimerize to form a ring-shaped molecule of approximate 2-fold symmetry. Of the two inter-subunit interfaces within the dimer, one interface ('interface A') between tip/center domains is more nonpolar than the other ('interface B') between base domains. The structure allows us to propose that the RdgC dimer binds dsDNA through the central hole of ∼30° diameter. The proposed model is supported by our DNA-binding assays coupled with mutagenesis, which indicate that the conserved positively charged residues on the protein surface around the central hole play important roles in DNA binding. The novel ring-shaped architecture of the RdgC dimer has significant implications for its role in homologous recombination.

Original language	English
Pages (from-to)	2671-2681
Number of pages	11
Journal	Nucleic acids research
Volume	35
Issue number	8
DOIs	https://doi.org/10.1093/nar/gkm144
Publication status	Published - 2007 Apr

Bibliographical note

Funding Information:
We thank the staff at beamlines BL-5A, BL-6A and NW-12A of Photon Factory, Tsukuba, Japan, and beamlines BL-4A and BL-6B of Pohang Light Source, Pohang, Korea, for assistance during X-ray diffraction experiments. This work was supported by grants from the Korean Ministry of Science and Technology (NRL-2001) and Korea Sanhak Foundation. J.Y.H., D.J.K., K.H.K., S.J.O. and H.H.L. are recipients of BK21 fellowships from the Korean Ministry of Education & Human Resources Development. Funding to pay the open Access publication charge was provided by Seoul National University.

ASJC Scopus subject areas

Genetics

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10.1093/nar/gkm144

Cite this

@article{41ae659aedaa4ef78798494b97d82b64,

title = "The recombination-associated protein RdgC adopts a novel toroidal architecture for DNA binding",

abstract = "RecA plays a central role in the nonmutagenic repair of stalled replication forks in bacteria. RdgC, a recombination-associated DNA-binding protein, is a potential negative regulator of RecA function. Here, we have determined the crystal structure of RdgC from Pseudomonas aeruginosa. The J-shaped monomer has a unique fold and can be divided into three structural domains: Tip domain, center domain and base domain. Two such monomers dimerize to form a ring-shaped molecule of approximate 2-fold symmetry. Of the two inter-subunit interfaces within the dimer, one interface ('interface A') between tip/center domains is more nonpolar than the other ('interface B') between base domains. The structure allows us to propose that the RdgC dimer binds dsDNA through the central hole of ∼30° diameter. The proposed model is supported by our DNA-binding assays coupled with mutagenesis, which indicate that the conserved positively charged residues on the protein surface around the central hole play important roles in DNA binding. The novel ring-shaped architecture of the RdgC dimer has significant implications for its role in homologous recombination.",

author = "Ha, \{Jun Yong\} and Kim, \{Hye Kyong\} and Kim, \{Do Jin\} and Kim, \{Kyoung Hoon\} and Oh, \{Sung Jin\} and Lee, \{Hyung Ho\} and Yoon, \{Hye Jin\} and Song, \{Hyun Kyu\} and Suh, \{Se Won\}",

note = "Funding Information: We thank the staff at beamlines BL-5A, BL-6A and NW-12A of Photon Factory, Tsukuba, Japan, and beamlines BL-4A and BL-6B of Pohang Light Source, Pohang, Korea, for assistance during X-ray diffraction experiments. This work was supported by grants from the Korean Ministry of Science and Technology (NRL-2001) and Korea Sanhak Foundation. J.Y.H., D.J.K., K.H.K., S.J.O. and H.H.L. are recipients of BK21 fellowships from the Korean Ministry of Education \& Human Resources Development. Funding to pay the open Access publication charge was provided by Seoul National University.",

year = "2007",

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doi = "10.1093/nar/gkm144",

language = "English",

volume = "35",

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journal = "Nucleic acids research",

issn = "0305-1048",

publisher = "Oxford University Press",

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AU - Ha, Jun Yong

AU - Kim, Hye Kyong

AU - Kim, Do Jin

AU - Kim, Kyoung Hoon

AU - Oh, Sung Jin

AU - Lee, Hyung Ho

AU - Yoon, Hye Jin

AU - Song, Hyun Kyu

AU - Suh, Se Won

N1 - Funding Information: We thank the staff at beamlines BL-5A, BL-6A and NW-12A of Photon Factory, Tsukuba, Japan, and beamlines BL-4A and BL-6B of Pohang Light Source, Pohang, Korea, for assistance during X-ray diffraction experiments. This work was supported by grants from the Korean Ministry of Science and Technology (NRL-2001) and Korea Sanhak Foundation. J.Y.H., D.J.K., K.H.K., S.J.O. and H.H.L. are recipients of BK21 fellowships from the Korean Ministry of Education & Human Resources Development. Funding to pay the open Access publication charge was provided by Seoul National University.

PY - 2007/4

Y1 - 2007/4

N2 - RecA plays a central role in the nonmutagenic repair of stalled replication forks in bacteria. RdgC, a recombination-associated DNA-binding protein, is a potential negative regulator of RecA function. Here, we have determined the crystal structure of RdgC from Pseudomonas aeruginosa. The J-shaped monomer has a unique fold and can be divided into three structural domains: Tip domain, center domain and base domain. Two such monomers dimerize to form a ring-shaped molecule of approximate 2-fold symmetry. Of the two inter-subunit interfaces within the dimer, one interface ('interface A') between tip/center domains is more nonpolar than the other ('interface B') between base domains. The structure allows us to propose that the RdgC dimer binds dsDNA through the central hole of ∼30° diameter. The proposed model is supported by our DNA-binding assays coupled with mutagenesis, which indicate that the conserved positively charged residues on the protein surface around the central hole play important roles in DNA binding. The novel ring-shaped architecture of the RdgC dimer has significant implications for its role in homologous recombination.

AB - RecA plays a central role in the nonmutagenic repair of stalled replication forks in bacteria. RdgC, a recombination-associated DNA-binding protein, is a potential negative regulator of RecA function. Here, we have determined the crystal structure of RdgC from Pseudomonas aeruginosa. The J-shaped monomer has a unique fold and can be divided into three structural domains: Tip domain, center domain and base domain. Two such monomers dimerize to form a ring-shaped molecule of approximate 2-fold symmetry. Of the two inter-subunit interfaces within the dimer, one interface ('interface A') between tip/center domains is more nonpolar than the other ('interface B') between base domains. The structure allows us to propose that the RdgC dimer binds dsDNA through the central hole of ∼30° diameter. The proposed model is supported by our DNA-binding assays coupled with mutagenesis, which indicate that the conserved positively charged residues on the protein surface around the central hole play important roles in DNA binding. The novel ring-shaped architecture of the RdgC dimer has significant implications for its role in homologous recombination.

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JO - Nucleic acids research

JF - Nucleic acids research

IS - 8

ER -

The recombination-associated protein RdgC adopts a novel toroidal architecture for DNA binding

Abstract

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