PROSITE documentation PDOC00578

NF-Y/HAP subunits signatures and profile

Diverse DNA binding proteins are known to bind the CCAAT box, a common cis-acting element found in the promoter and enhancer regions of a large number of genes in eukaryotes. Amongst these proteins is one known as the CCAAT-binding factor (CBF) or NF-Y [1]. CBF is a heteromeric transcription factor that consists of two different components both needed for DNA-binding.

The HAP protein complex of yeast binds to the upstream activation site of cytochrome C iso-1 gene (CYC1) as well as other genes involved in mitochondrial electron transport and activates their expression. It also recognizes the sequence CCAAT and is structurally and evolutionary related to CBF.

The first subunit of CBF, known as CBF-A or NF-YB in vertebrates and HAP3 in budding yeast, is a protein of 116 to 210 amino- acid residues which contains a highly conserved central domain of about 90 residues. This domain displays some sequence similarity to histones H2B (see <PDOC00308>) and seems to be involved in DNA-binding; we have developed a signature pattern from its central part.

The second subunit of CBF, known as CBF-B or NF-YA in vertebrates and HAP2 in budding yeast, is a protein of 265 to 350 amino-acid residues which contains a highly conserved region of about 60 residues. This region, called the 'essential core' [2], seems to consist of two subdomains: an N-terminal subunit-association domain and a C-terminal DNA recognition domain. We have developed a signature pattern from a section of the subunit-association domain (SAD) and a profile that covers both subdomains.