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Crystal structure of the CENP‐B protein–DNA complex: the DNA‐binding domains of CENP‐B induce kinks in the CENP‐B box DNA
Author(s) -
Tanaka Yoshinori,
Nureki Osamu,
Kurumizaka Hitoshi,
Fukai Shuya,
Kawaguchi Shinichi,
Ikuta Mari,
Iwahara Junji,
Okazaki Tsuneko,
Yokoyama Shigeyuki
Publication year - 2001
Publication title -
the embo journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.484
H-Index - 392
eISSN - 1460-2075
pISSN - 0261-4189
DOI - 10.1093/emboj/20.23.6612
Subject(s) - biology , dna , hmg box , chromatin , helix (gastropod) , biophysics , centromere , dna binding protein , binding site , crystallography , microbiology and biotechnology , genetics , transcription factor , chromosome , chemistry , gene , ecology , snail
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.