InterPro domain: IPR039997

Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit ( IPR002853 ) and the small beta ( IPR003166 ). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE [ 1 ].

The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow [ 2 ].

Archaea contain a TFIIE homologue, called TFE, which corresponds to the N-terminal half of TFIIEalpha. It appears that archaeal TFE corresponds to the minimal essential region of eukaryotic TFIIEalpha. In archaea TFE contains an N-terminal, weakly conserved, helix-turn-helix (HTH) motif within a leucine-rich region and a C-terminal zinc ribbon [ 2 , 3 , 4 ]. It has been proposed that the TFE/IIEalpha-type HTH domain acts as a bridging factor or adapter between the TATA box-binding protein, the polymerase, and possibly promoter DNA [ 5 ].

The TFE/IIEalpha-type HTH domain adopts a winged HTH (winged helix) fold, comprising three alpha-helices and three beta-strands in the canonical order alpha1-beta1-alpha2-alpha3-beta2-beta3. Conserved residues within helices alpha1-alpha3 form the tightly packed hydrophobic core of the winged helix domain. A specific feature of the structure is the extension of the canonical winged helix fold at the N and C termini by the additional helices alpha0 and alpha4, respectively. Hydrophobic residues from the additional helix alpha0 extend the hydrophobic core of the winged helix domain, and helix alpha0 is tightly packed against the canonical winged helix fold. Helix alpha4 comprises only one turn [ 6 ].

1. Structure of the central core domain of TFIIEbeta with a novel double-stranded DNA-binding surface. EMBO J. 19, 1346-56
2. Genetic analysis of the large subunit of yeast transcription factor IIE reveals two regions with distinct functions. Mol. Cell. Biol. 17, 5288-98
3. The archaeal TFIIEalpha homologue facilitates transcription initiation by enhancing TATA-box recognition. EMBO Rep. 2, 133-8
4. TFE, an archaeal transcription factor in Methanobacterium thermoautotrophicum related to eucaryal transcription factor TFIIEalpha. J. Bacteriol. 183, 1813-8
5. Effect of butylated hydroxyanisole on the metabolism of N-nitrosodi-n-butylamine and N-nitrosobutyl(4-hydroxybutyl)amine by rat hepatic S9 preparations in vitro. IARC Sci. Publ. , 183-4
6. An extended winged helix domain in general transcription factor E/IIE alpha. J. Biol. Chem. 278, 48267-74