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

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 ever y other alpha -satellite repeat. In the present study, the crystal structur e 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 Angstrom resolution. The DNA-bin ding 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 c ontact sites, and the DNA region between the kinks is straight. Among the m ajor groove protein-bound DNAs, this 'kink-straight-kink' bend contrasts wi th ordinary 'round bends' (gradual bending between two protein contact site s). The larger kink (43 degrees) is induced by a novel mechanism, 'phosphat e bridging by an arginine-rich helix': the recognition helix with an argini ne cluster is inserted perpendicularly into the major groove and bridges th e groove through direct interactions with the phosphate groups. The overall bending angle is 59 degrees, which may be important for the centromere-spe cific chromatin structure.