Model for binding of transcription factor TFIIB to the TBP-DNA complex

Transcription factor TFIIB is essential for the formation of RNA polymerase II initiation complexes where it binds to the TATA-binding protein (TBP) complex with DNA and recruits RNA polymerase II. TFIIB is probably a target for various activators. Several models have been proposed for the position of TFIIB in the TFIIB-TBP-DNA complex. Here we examine the structure of this complex using gel mobility-shift assays and hydroxyl-radical footprinting. TFIIB requires at least seven base pairs of DNA on either side of the TATA box to form a stable TFIIB-TBP-DNA complex. The sugar residues protected from hydroxyl-radical cleavage by the TFIIB-TBP complex were mapped on the crystal-structure model of the TBP-DNA complex. This analysis suggests that TFIIB binds beneath the concave surface of TBP, contacting DNA both upstream and downstream of the TATA box. Our model predicts that TFIIB binds close to the C-terminal stirrup of TBP and provides one explanation for why TBP needs to bend DNA.