title: The positions of TFIIF and TFIIE in the RNA polymerase II transcription preinitiation complex.
abstract: We incorporated the non-natural photoreactive amino acid p-benzoyl-L-phenylalanine (Bpa) into the RNA polymerase II (Pol II) surface surrounding the central cleft formed by the Rpb1 and Rpb2 subunits. Photo-cross-linking of preinitiation complexes (PICs) with these Pol II derivatives and hydroxyl-radical cleavage assays revealed that the TFIIF dimerization domain interacts with the Rpb2 lobe and protrusion domains adjacent to Rpb9, while TFIIE cross-links to the Rpb1 clamp domain on the opposite side of the Pol II central cleft. Mutations in the Rpb2 lobe and protrusion domains alter both Pol II-TFIIF binding and the transcription start site, a phenotype associated with mutations in TFIIF, Rpb9 and TFIIB. Together with previous biochemical and structural studies, these findings illuminate the structural organization of the PIC and the network of protein-protein interactions involved in transcription start site selection.
authors.affiliation: Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Mailstop A1-162, Seattle, Washington 98109, USA.
authors.forename: Hung-Ta
authors.initials: HT
authors.lastname: Chen
authors.forename: Linda
authors.initials: L
authors.lastname: Warfield
authors.forename: Steven
authors.initials: S
authors.lastname: Hahn
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D001665:Binding Sites; D003198:Computer Simulation; D019281:Dimerization; D008958:Models, Molecular; D009154:Mutation; D010449:Peptide Mapping; D017434:Protein Structure, Tertiary; D012319:RNA Polymerase II / Q000737:chemistry*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D013379:Substrate Specificity; D019473:Transcription Factors, TFII / Q000737:chemistry*; D024363:Transcription Initiation Site
chemical_list: D000596:Amino Acids; D019473:Transcription Factors, TFII; C066644:transcription factor TFIIE; D012319:RNA Polymerase II; C056604:transcription factor TFIIF