Structural basis of core promoter recognition in a primitive eukaryote

Transcription start site selection in eukaryotes is mediated through combinations of the TATA, initiator (lnr), and downstream promoter elements (DPE). In Trichomonas vaginalis, a parabasalian flagellate thought to represent an ancient eukaryote lineage, the lnr appears to be solely responsible for start site selection and is recognized by the initiator binding protein 39 kDa (IBP39). IBP39 contains an N-terminal lnr binding domain (IBD) connected via a flexible linker to a C-terminal domain (C domain). Here we present crystal structures of the apoIBD and IBD-lnr complexes and the C domain. The 11313 structures reveal a winged-helix motif with prokaryotic and eukaryotic features and a scaffold similar to that of ETS-family proteins. The C domain structure and biochemical studies indicate that it interacts with the T. vaginalis RNAP 11 large subunit C-terminal domain. These data suggest that binding of IBP39 to the lnr directly recruits RNAP 11 and in this way initiates transcription.