PROSITE documentation PDOC51253
CENPB-type HTH domain profile


The CENPB-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 70-75 amino acids, present in eukaryotic centromere proteins and transposases. The domain is named after the mammalian major centromere autoantigen B or centromere protein B (CENP-B), which is a fundamental centromere component of chromosomes. The N-terminus of CENP-B contains two DNA-binding HTH domains, which bind to adjacent major grooves of DNA. The N-terminus of CENP-B is formed by a psq-type HTH domain (see <PDOC50960>) and C-terminal to this domain lies the CENPB-type HTH domain. These two HTH domains together bind specifically to a 17-base-pair sequence, the CENP-B box, which occurs in α-satellite DNA in human centromeres [1].

The structure of the CENPB-type HTH domain is composed of three α-helices (see <PDB:1HLV>). The second and third helices connected via a turn comprise the helix-turn-helix motif. Helix 3 is termed the recognition helix as it binds the DNA major groove, like in other HTHs. In CENP-B this domain recognizes site 3 of the CENP-B box, while the preceding psq-type HTH (see <PDOC50960>) binds site 1 of the CENP-B box, and a connecting linker loop binds in the minor groove of DNA and recognizes site 2 [2].

Some proteins known to contain a CENPB-type HTH domain:

  • Mammalian centromere protein B (CENP-B), associated with the centromere and specifically binding DNA to the CENP-B box.
  • Mammalian jerky protein, involved in epileptic seizures in mice.
  • Mammalian Pogo transposases.
  • Fission yeast ARS-binding protein 1 (abp1) and CENP-B homolog proteins (CBHP-1 and 2), which are centromere proteins.
  • Candida albicans protein PDC2.
  • Fungal transposases.

The profile we developed covers the entire CENPB-type HTH domain, including the N-terminal linker loop.

Last update:

September 2006 / First entry.


Technical section

PROSITE method (with tools and information) covered by this documentation:

HTH_CENPB, PS51253; CENPB-type HTH domain profile  (MATRIX)


1AuthorsTanaka Y. Tachiwana H. Yoda K. Masumoto H. Okazaki T. Kurumizaka H. Yokoyama S.
TitleHuman centromere protein B induces translational positioning of nucleosomes on alpha-satellite sequences.
SourceJ. Biol. Chem. 280:41609-41618(2005).
PubMed ID16183641

2AuthorsTanaka Y. Nureki O. Kurumizaka H. Fukai S. Kawaguchi S. Ikuta M. Iwahara J. Okazaki T. Yokoyama S.
TitleCrystal structure of the CENP-B protein-DNA complex: the DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA.
SourceEMBO J. 20:6612-6618(2001).
PubMed ID11726497

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