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J. Biol. Chem., Vol. 279, Issue 51, 53175-53185, December 17, 2004

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Cooperation of the N-terminal Helicase and C-terminal Endonuclease Activities of Archaeal Hef Protein in Processing Stalled Replication Forks^*

Kayoko Komori, Masumi Hidaka, Takashi Horiuchi, Ryosuke Fujikane¶||, Hideo Shinagawa¶, and Yoshizumi Ishino||**

From the Department of Molecular Biology, Biomolecular Engineering Research Institute, Suita, Osaka 565-0874, Japan, National Institute for Basic Biology, Myodaijicho, Okazaki 444-8585, Japan, ^¶Department of Molecular Microbiology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan, and ^||Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Fukuoka-shi, Fukuoka 812-8581, Japan

Blockage of replication fork progression often occurs during DNA replication, and repairing and restarting stalled replication forks are essential events in all organisms for the maintenance of genome integrity. The repair system employs processing enzymes to restore the stalled fork. In Archaea Hef is a well conserved protein that specifically cleaves nicked, flapped, and fork-structured DNAs. This enzyme contains two distinct domains that are similar to the DEAH helicase family and XPF nuclease superfamily proteins. Analyses of truncated mutant proteins consisting of each domain revealed that the C-terminal nuclease domain independently recognized and incised fork-structured DNA. The N-terminal helicase domain also specifically unwound fork-structured DNA and Holliday junction DNA in the presence of ATP. Moreover, the endonuclease activity of the whole Hef protein was clearly stimulated by ATP hydrolysis catalyzed by the N-terminal domain. These enzymatic properties suggest that Hef efficiently resolves stalled replication forks by two steps, which are branch point transfer to the 5'-end of the nascent lagging strand by the N-terminal helicase followed by template strand incision for leading strand synthesis by the C-terminal endonuclease.

Received for publication, August 12, 2004 , and in revised form, October 8, 2004.

^* This work was supported in part by the Japan New Energy and Industrial Technology Development Organization and by a grant-in-aid from the Ministry of Education, Science, and Sports of Japan (to Y. I. and H. S.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

^** Supported by the Human Frontier Science Program. To whom correspondence should be addressed: Dept. of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka-shi, Fukuoka 812-8581, Japan. Tel.: 81-92-642-4217; Fax: 81-92-642-3051; E-mail: ishino{at}agr.kyushu-u.ac.jp.

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