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  • The EMBO Journal (2001) 20, 6612 - 6618
  • doi:10.1093/emboj/20.23.6612

Crystal structure of the CENP-B protein–DNA complex: the DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA

Yoshinori Tanaka1,2,5, Osamu Nureki2,5, Hitoshi Kurumizaka1,3,5, Shuya Fukai2, Shinichi Kawaguchi3, Mari Ikuta2,3, Junji Iwahara2,3, Tsuneko Okazaki4 and Shigeyuki Yokoyama1,2,3

  1. RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
  2. Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
  3. Cellular Signaling Laboratory, RIKEN Harima Institute at SPring8, 1-1-1 Kohto, Mikazuki-cho, Sayo, Hyogo 679-5143, Japan
  4. Institute for Comprehensive Medical Science, Fujita Health University and CREST of JST, Toyoake-shi, Aichi 470-1192, Japan
  5. Y.Tanaka, O.Nureki and H.Kurumizaka contributed equally to this work

Correspondence to:

Shigeyuki Yokoyama, E-mail: yokoyama@biochem.s.u-tokyo.ac.jp

Received 16 July 2001; Accepted 4 October 2001; Revised 4 October 2001

The human centromere protein B (CENP-B), one of the centromere components, specifically binds a 17 bp sequence (the CENP-B box), which appears in every other alpha-satellite repeat. In the present study, the crystal structure of the complex of the DNA-binding region (129 residues) of CENP-B and the CENP-B box DNA has been determined at 2.5 Å resolution. The DNA-binding region forms two helix–turn–helix domains, which are bound to adjacent major grooves of the DNA. The DNA is kinked at the two recognition helix contact sites, and the DNA region between the kinks is straight. Among the major groove protein-bound DNAs, this 'kink–straight–kink' bend contrasts with ordinary 'round bends' (gradual bending between two protein contact sites). The larger kink (43°) is induced by a novel mechanism, 'phosphate bridging by an arginine-rich helix': the recognition helix with an arginine cluster is inserted perpendicularly into the major groove and bridges the groove through direct interactions with the phosphate groups. The overall bending angle is 59°, which may be important for the centromere-specific chromatin structure.

  • Keywords:

    • CENP-B,
    • centromere,
    • DNA bending,
    • helix–turn–helix,
    • protein–DNA complex