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Nucleic Acids Research Advance Access originally published online on April 10, 2007
Nucleic Acids Research 2007 35(8):2671-2681; doi:10.1093/nar/gkm144
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Nucleic Acids Research, 2007, Vol. 35, No. 8 2671-2681
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structural Biology

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

Jun Yong Ha1, Hye Kyong Kim1, Do Jin Kim1, Kyoung Hoon Kim1, Sung Jin Oh1, Hyung Ho Lee1, Hye Jin Yoon1, Hyun Kyu Song2 and Se Won Suh1,*

1Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea and 2Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea

*To whom correspondence should be addressed. Tel: +82-2-880-6653; Fax: +82-2-889-1568; E-mail: sewonsuh{at}snu.ac.kr

Received January 14, 2007. Revised February 24, 2007. Accepted February 25, 2007.

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 Å 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.

Present address: Jun Yong Ha, Drug Discovery, AmorePacific R&D Center, Yongin-si, Gyeonggi-do 449-729, Korea


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