InterPro domain: IPR006600

The CENPB-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain ofabout 70-75 amino acids, present in eukaryotic centromere proteins andtransposases. The domain is named after the mammalian major centromereautoantigen B or centromere protein B (CENP-B), which is a fundamentalcentromere component of chromosomes. The N terminus of CENP-B contains twoDNA-binding HTH domains, which bind to adjacent major grooves of DNA. TheN terminus of CENP-B is formed by a psq-type HTH domain andC-terminal to this domain lies the CENPB-type HTH domain. These two HTHdomains together bind specifically to a 17-base-pair sequence, the CENP-B box,which occurs in alpha-satellite DNA in human centromeres [ 1 ].

The structure of the CENPB-type HTH domain is composed of three alpha-helices. The second and third helices connected via a turn comprisethe helix-turn-helix motif. Helix 3 is termed the recognition helix as itbinds the DNA major groove, like in other HTHs. In CENP-B this domainrecognises 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 loopbinds in the minor groove of DNA and recognises 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 [ 3 ].
• Mammalian Pogo transposases [ 4 ] and tigger transposable elements [ 5 ].
• Fission yeast ARS-binding protein 1 (abp1) [ 6 ] and CENP-B homologue proteins (CBHP-1 and 2), which are centromere proteins [ 7 , 8 ].
• Candida albicans protein PDC2 (Pyruvate DeCarboxylase 2) [ 9 , 10 ].
• Fungal transposases.

1. Human centromere protein B induces translational positioning of nucleosomes on alpha-satellite sequences. J. Biol. Chem. 280, 41609-18
2. Crystal structure of the CENP-B protein-DNA complex: the DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA. EMBO J. 20, 6612-8
3. Isolation and characterization of a Jerky and JRK/JH8 like gene, tigger transposable element derived 7, TIGD7. Biochem. Genet. 42, 279-85
4. Pogo transposase contains a putative helix-turn-helix DNA binding domain that recognises a 12 bp sequence within the terminal inverted repeats. Nucleic Acids Res. 27, 455-61
5. Centromeres, CENP-B and Tigger too. Trends Genet. 13, 141-5
6. The CENP-B homolog, Abp1, interacts with the initiation protein Cdc23 (MCM10) and is required for efficient DNA replication in fission yeast. Cell Div 1, 27
7. Purification and characterization of a CENP-B homologue protein that binds to the centromeric K-type repeat DNA of Schizosaccharomyces pombe. Proc. Natl. Acad. Sci. U.S.A. 94, 8427-32
8. Functional redundancies, distinct localizations and interactions among three fission yeast homologs of centromere protein-B. Genetics 157, 1191-203
9. Characterisation of PDC2, a gene necessary for high level expression of pyruvate decarboxylase structural genes in Saccharomyces cerevisiae. Mol. Gen. Genet. 241, 657-66
10. Thiamin-dependent transactivation activity of PDC2 in Saccharomyces cerevisiae. FEBS Lett. 582, 3991-6