A Helix-Turn-Helix Structure Unit in Human Centromere Protein B (CENP-B)

EMBO J. 1998 Feb 2;17(3):827-37. doi: 10.1093/emboj/17.3.827.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Autoantigens*
  • Base Composition
  • Binding Sites
  • Centromere Protein B
  • Chromosomal Proteins, Non-Histone / chemistry*
  • DNA-Binding Proteins / chemistry
  • Helix-Turn-Helix Motifs
  • Humans
  • Macromolecular Substances
  • Magnetic Resonance Spectroscopy
  • Models, Biological
  • Molecular Sequence Data
  • Protein Structure, Tertiary
  • Sequence Homology, Amino Acid
  • Solutions


  • Autoantigens
  • CENPB protein, human
  • Centromere Protein B
  • Chromosomal Proteins, Non-Histone
  • DNA-Binding Proteins
  • Macromolecular Substances
  • Solutions