title: TFIIB is only ∼9 Å away from the 5'-end of a trimeric RNA primer in a functional RNA polymerase II preinitiation complex.
abstract: Recent X-ray crystallographic studies of Pol II in complex with the general transcription factor (GTF) IIB have begun to provide insights into the mechanism of transcription initiation. These structures have also shed light on the architecture of the transcription preinitiation complex (PIC). However, structural characterization of a functional PIC is still lacking, and even the topological arrangement of the GTFs in the Pol II complex is a matter of contention. We have extended our activity-based affinity crosslinking studies, initially developed to investigate the interaction of bacterial RNA polymerase with σ, to the eukaryotic transcription machinery. Towards that end, we sought to identify GTFs that are within the Pol II active site in a functioning PIC. We provide biochemical evidence that TFIIB is located within ∼9 Å of the -2 site of promoter DNA, where it is positioned to play a role in de novo transcription initiation.
authors.affiliation: Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, United States of America.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Bick
authors.affiliation: Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, United States of America.
authors.forename: Sohail
authors.initials: S
authors.lastname: Malik
authors.affiliation: Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, University Heights, Newark, NJ, United States of America.
authors.forename: Arkady
authors.initials: A
authors.lastname: Mustaev
authors.affiliation: Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, United States of America.
authors.forename: Seth A
authors.initials: SA
authors.lastname: Darst
mesh_terms: D001419:Bacteria / Q000378:metabolism*; D020134:Catalytic Domain; D005057:Eukaryotic Cells / Q000378:metabolism*; D008958:Models, Molecular; D011401:Promoter Regions, Genetic; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D012319:RNA Polymerase II / Q000737:chemistry / Q000378:metabolism*; D012808:Sigma Factor / Q000737:chemistry / Q000378:metabolism; D035581:Transcription Factor TFIIB / Q000737:chemistry / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: C034477:RNA primers; D012808:Sigma Factor; D035581:Transcription Factor TFIIB; D012313:RNA; D012319:RNA Polymerase II