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Solution Structure of an Arabidopsis WRKY DNA Binding Domain

^a Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
^b Protein Research Group, RIKEN Genomic Sciences Center, Yokohama 230-0045, Japan
^c Center for Biological Resources and Informatics, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
^d RIKEN Harima Institute at SPring-8, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan
^e Laboratory of Plant Molecular Biology, RIKEN Tsukuba Institute, Tsukuba 305-0074, Japan
^f Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center, Yokohama 230-0045, Japan
^g Institute of Biological Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
^h Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan

¹ To whom correspondence should be addressed. E-mail k-yamasaki{at}aist.go.jp; fax 81-29-8612706.

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 CX_4–5CX_22–23HXH 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 ß-sheet, with a zinc binding pocket formed by the conserved Cys/His residues located at one end of the ß-sheet, revealing a novel zinc and DNA binding structure. The WRKYGQK residues correspond to the most N-terminal ß-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 ß-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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