Plant Cell Advance Online Publication
Published on February 10, 2005; 10.1105/tpc.104.026435
Received July 28, 2004
Accepted December 4, 2004
Solution Structure of an Arabidopsis WRKY DNA Binding Domain
Kazuhiko Yamasaki 1*, Takanori Kigawa 2, Makoto Inoue 2, Masaru Tateno 3, Tomoko Yamasaki 4, Takashi Yabuki 2, Masaaki Aoki 2, Eiko Seki 2, Takayoshi Matsuda 2, Yasuko Tomo 2, Nobuhiro Hayami 2, Takaho Terada 5, Mikako Shirouzu 5, Akiko Tanaka 2, Motoaki Seki 6, Kazuo Shinozaki 7, and Shigeyuki Yokoyama 8
1 Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan; Protein Research Group, RIKEN Genomic Sciences Center, Yokohama 230-0045, Japan
2 Protein Research Group, RIKEN Genomic Sciences Center, Yokohama 230-0045, Japan
3 Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan; Center for Biological Resources and Informatics, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
4 Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
5 Protein Research Group, RIKEN Genomic Sciences Center, Yokohama 230-0045, Japan; RIKEN Harima Institute at SPring-8, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan
6 Laboratory of Plant Molecular Biology, RIKEN Tsukuba Institute, Tsukuba 305-0074, Japan; Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center, Yokohama 230-0045, Japan
7 Laboratory of Plant Molecular Biology, RIKEN Tsukuba Institute, Tsukuba 305-0074, Japan; Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center, Yokohama 230-0045, Japan; Institute of Biological Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
8 Protein Research Group, RIKEN Genomic Sciences Center, Yokohama 230-0045, Japan; RIKEN Harima Institute at SPring-8, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan; Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
* To whom correspondence should be addressed. E-mail: k-yamasaki{at}aist.go.jp.
The WRKY proteins comprise a major family of transcription factors that are essential in pathogen and salicylic acid responses of higher plants as well as a variety of plant-specific reactions. They share a DNA binding domain, designated as the WRKY domain, which contains an invariant WRKYGQK sequence and a CX4-5CX22-23HXH zinc binding motif. Herein, we report the NMR solution structure of the C-terminal WRKY domain of the Arabidopsis thaliana WRKY4 protein. The structure consists of a four-stranded  -sheet, with a zinc binding pocket formed by the conserved Cys/His residues located at one end of the -sheet, revealing a novel zinc and DNA binding structure. The WRKYGQK residues correspond to the most N-terminal -strand, kinked in the middle of the sequence by the Gly residue, which enables extensive hydrophobic interactions involving the Trp residue and contributes to the structural stability of the -sheet. Based on a profile of NMR chemical shift perturbations, we propose that the same strand enters the DNA groove and forms contacts with the DNA bases.
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