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J. Biol. Chem., Vol. 279, Issue 39, 41067-41076, September 24, 2004

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Crystal Structure of the Endonuclease Domain Encoded by the Telomere-specific Long Interspersed Nuclear Element, TRAS1^*

Nobuo Maita¶, Tomohiro Anzai||, Hideyuki Aoyagi||, Hiroshi Mizuno, and Haruhiko Fujiwara||**

From the Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan and the ^||Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Bioscience Bldg. 501, Kashiwa, 277-8562, Japan

The telomere-specific long interspersed nuclear element, TRAS1, encodes an endonuclease domain, TRAS1-EN, which specifically cleaves the telomeric repeat targets (TTAGG)_n of insects and (TTAGGG)_n of vertebrates. To elucidate the sequence-specific recognition properties of TRAS1-EN, we determined the crystal structure at 2.4-Å resolution. TRAS1-EN has a four-layered / sandwich structure; its topology is similar to apurinic/apyrimidinic endonucleases, but the -hairpin (₁₀-₁₁) at the edge of the DNA-binding surface makes an extra loop that distinguishes TRAS1-EN from cellular apurinic/apyrimidinic endonucleases. A protein-DNA complex model suggests that the ₁₀-₁₁ hairpin fits into the minor groove, enabling interaction with the telomeric repeats. Mutational studies of TRAS1-EN also indicated that the Asp-130 and ₁₀-₁₁ hairpin structure are involved in specific recognition of telomeric repeats.

Received for publication, June 11, 2004

The atomic coordinates and structure factors (code 1WDU) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

^* This work was supported by grants from the Ministry of Education, Science, and Culture of Japan and by a grant-in-aid from the Research for the Future Program of the Japan Society for the Promotion Science. 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.

The on-line version of this article (available at http://www.jbc.org) contains an additional figure and references.

These authors contributed equally to this work.

^¶ Present address: Division of Molecular Biophysics, Science of Biological Supramolecular Systems, Yokohama City University, Yokohama, 230-0045, Japan.

^** To whom correspondence should be addressed. Tel.: 81-4-7136-3659; Fax: 81-4-7136-3660; E-mail: haruh{at}k.u-tokyo.ac.jp.

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