A helix-turn-helix structure unit in human centromere protein B (CENP-B)

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Abstract
CENP‐B has been suggested to organize arrays of centromere satellite DNA into a higher order structure which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The N‐terminal portion of CENP‐B is a 15 kDa DNA binding domain (DBD) consisting of two repeating units, RP1 and RP2. The DBD specifically binds to the CENP‐B box sequence (17 bp) in centromere DNA. We determined the solution structure of human CENP‐B DBD RP1 by multi‐dimensional 1H, 13C and 15N NMR methods. The CENP‐B DBD RP1 structure consists of four helices and has a helix–turn–helix structure. The overall folding is similar to those of some other eukaryotic DBDs, although significant sequence homology with these proteins was not found. The DBD of yeast RAP1, a telomere binding protein, is most similar to CENP‐B DBD RP1. We studied the interaction between CENP‐B DBD RP1 and the CENP‐B box by the use of NMR chemical shift perturbation. The results suggest that CENP‐B DBD RP1 interacts with one of the essential regions of the CENP‐B box DNA, mainly at the N‐terminal basic region, the N‐terminal portion of helix 2 and helix 3.