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  • The EMBO Journal (1998) 17, 5484 - 5496
  • doi:10.1093/emboj/17.18.5484

A novel mode of DNA recognition by a bold beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA

Mark D. Allen2,6, Kazuhiko Yamasaki2,3,6, Masaru Ohme-Takagi1, Masaru Tateno2 and Masashi Suzuki2,4,5

  1. AIST-NIBHT Plant Molecular Biology Laboratory, Higashi 1-1, Tsukuba 305-0046, Japan
  2. AIST-NIBHT CREST Centre of Structural Biology, Higashi 1-1, Tsukuba 305-0046, Japan
  3. NMR spectroscopy
  4. Graduate School of Human and Environmental Sciences, University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-0041, Japan
  5. AIST-NIBHT
  6. M.D.Allen and K.Yamasaki contributed equally to this work

Received 9 March 1998; Accepted 22 July 1998; Revised 22 June 1998

The 3D solution structure of the GCC-box binding domain of a protein from Arabidopsis thaliana in complex with its target DNA fragment has been determined by heteronuclear multidimensional NMR in combination with simulated annealing and restrained molecular dynamic calculation. The domain consists of a three-stranded anti-parallel beta-sheet and an alpha-helix packed approximately parallel to the beta-sheet. Arginine and tryptophan residues in the beta-sheet are identified to contact eight of the nine consecutive base pairs in the major groove, and at the same time bind to the sugar phosphate backbones. The target DNA bends slightly at the central CG step, thereby allowing the DNA to follow the curvature of the beta-sheet.

  • Keywords:

    • Arabidopsis thaliana,
    • DNA–protein interaction,
    • DNA recognition,
    • NMR,
    • restrained molecular dynamic calculation