HTH CenpB-type DNA-binding domain (IPR006600)

Short name: HTH_CenpB_DNA-bd_dom

Overlapping homologous superfamilies


Domain relationships



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 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 alpha-satellite DNA in human centromeres [PMID: 16183641].

The structure of the CENPB-type HTH domain is composed of three alpha-helices. 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 recognises site 3 of the CENP-B box, while the preceding psq-type HTH binds site 1 of the CENP-B box, and a connecting linker loop binds in the minor groove of DNA and recognises site 2 [PMID: 11726497].

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 [PMID: 15487591].
  • Mammalian Pogo transposases [PMID: 9862965] and tigger transposable elements [PMID: 9097724].
  • Fission yeast ARS-binding protein 1 (abp1) [PMID: 17112379] and CENP-B homologue proteins (CBHP-1 and 2), which are centromere proteins [PMID: 9237993, PMID: 11238404].
  • Candida albicans protein PDC2 (Pyruvate DeCarboxylase 2) [PMID: 8264540, PMID: 19013460].
  • Fungal transposases.

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.
PROSITE profiles