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 Tanaka, Osamu Nureki, Hitoshi Kurumizaka, Shuya Fukai, Shinichi Kawaguchi, Mari Ikuta, Junji Iwahara, Tsuneko Okazaki, Shigeyuki Yokoyama

Research output: Contribution to journalArticle

55 Citations (Scopus)

Abstract

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 α-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.

Original languageEnglish (US)
Pages (from-to)6612-6618
Number of pages7
JournalEMBO Journal
Volume20
Issue number23
DOIs
StatePublished - Dec 3 2001
Externally publishedYes

Fingerprint

Centromere Protein B
Crystal structure
DNA
Proteins
Arginine
Phosphates
Centromere
Chromatin
Satellites

Keywords

  • CENP-B
  • Centromere
  • DNA bending
  • Helix-turn-helix
  • Protein-DNA complex

ASJC Scopus subject areas

  • Genetics
  • Cell Biology

Cite this

Tanaka, Y., Nureki, O., Kurumizaka, H., Fukai, S., Kawaguchi, S., Ikuta, M., ... Yokoyama, S. (2001). Crystal structure of the CENP-B protein-DNA complex: The DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA. EMBO Journal, 20(23), 6612-6618. https://doi.org/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. / Tanaka, Yoshinori; Nureki, Osamu; Kurumizaka, Hitoshi; Fukai, Shuya; Kawaguchi, Shinichi; Ikuta, Mari; Iwahara, Junji; Okazaki, Tsuneko; Yokoyama, Shigeyuki.

In: EMBO Journal, Vol. 20, No. 23, 03.12.2001, p. 6612-6618.

Research output: Contribution to journalArticle

Tanaka, Y, Nureki, O, Kurumizaka, H, Fukai, S, Kawaguchi, S, Ikuta, M, Iwahara, J, Okazaki, T & Yokoyama, S 2001, 'Crystal structure of the CENP-B protein-DNA complex: The DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA', EMBO Journal, vol. 20, no. 23, pp. 6612-6618. https://doi.org/10.1093/emboj/20.23.6612
Tanaka, Yoshinori ; Nureki, Osamu ; Kurumizaka, Hitoshi ; Fukai, Shuya ; Kawaguchi, Shinichi ; Ikuta, Mari ; Iwahara, Junji ; Okazaki, Tsuneko ; Yokoyama, Shigeyuki. / Crystal structure of the CENP-B protein-DNA complex : The DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA. In: EMBO Journal. 2001 ; Vol. 20, No. 23. pp. 6612-6618.
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