Mot1 is an essential, conserved TATA-binding protein (TBP)-associated factor in Saccharomyces cerevisiae and a member of the Snf2/Swi2 ATPase family. Mot1 uses ATP hydrolysis to displace TBP from DNA, an activity that can be readily reconciled with its global role in gene repression. Less well understood is how Mot1 directly activates gene expression. It has been suggested that Mot1-mediated activation can occur by displacement of inactive TBP-containing complexes from promoters, thereby permitting assembly of functional transcription complexes. Mot1 may also activate transcription by other mechanisms that have not yet been defined. A gap in our understanding has been the absence of biochemical information related to the activity of Mot1 on natural target genes. Using URA1 as a model Mot1-activated promoter, we show striking differences in the way that both TBP and Mot1 interact with DNA compared with other model DNA substrates analyzed previously. These differences are due at least in part to the propensity of TBP alone to bind to the URA1 promoter in the wrong orientation to direct appropriate assembly of the URA1 preinitiation complex. The results suggest that Mot1-mediated activation of URA1 transcription involves at least two steps, one of which is the removal of TBP bound to the promoter in the opposite orientation required for URA1 transcription.The TATA-binding protein (TBP) 2 is a central component of the RNA polymerase II (pol II) preinitiation complex (PIC) (1-3). Transcription can be regulated during many different steps in PIC assembly, but the regulation of TBP binding to promoters is a fundamentally important step exploited for regulation of a large number of genes (4, 5). TBP is a saddle-shaped protein that interacts with DNA as a monomer (6, 7). Because TBP can straddle DNA in either of two directions, its binding polarity determines the orientation of the assembled PIC and hence the direction in which transcription initiates (8). TBP recruitment to promoters is regulated by chromatin, activators, and co-activators that contact TBP directly, and general factors that modulate TBP binding and activity (1, 2, 4, 9 -11).NC2 and Mot1 are essential, conserved regulators of TBP function that cooperate to regulate gene expression on a global scale (12)(13)(14). NC2, a heterodimer of the Bur6 and Ydr1 subunits in yeast (15), interacts with the TBP-DNA complex and can block subsequent steps in PIC assembly (16). NC2 is also a direct activator of gene expression (17) that is found at promoters in vivo in proportion to the level of transcription (14). How this apparent negative regulator of transcription functions as an activator is likely related to the recent observation that NC2 binding can allow TBP to relocalize along the DNA contour (18). Such mobilization of TBP may be critical for clearance of TBP from inactive but high affinity sites, and may facilitate selection of appropriate TATA sequences among a collection of binding sites along accessible promoter DNA. Mot1 is a member of the Snf2/Swi2 ATPa...