title: Domain organization of RNA polymerase alpha subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding.
abstract: Using limited proteolysis, we show that the Escherichia coli RNA polymerase alpha subunit consists of an N-terminal domain comprised of amino acids 8-241, a C-terminal domain comprised of amino acids 249-329, and an unstructured and/or flexible interdomain linker. We have carried out a detailed structural and functional analysis of an 85 amino acid proteolytic fragment corresponding to the C-terminal domain (alpha CTD-2). Our results establish that alpha CTD-2 has a defined secondary structure (approximately 40% alpha helix, approximately 0% beta sheet). Our results further establish that alpha CTD-2 is a dimer and that alpha CTD-2 exhibits sequence-specific DNA binding activity. Our results suggest a model for the mechanism of involvement of alpha in transcription activation by promoter upstream elements and upstream-binding activator proteins.
authors.affiliation: Department of Chemistry, Rutgers University, New Brunswick, New Jersey 08855.
authors.forename: E E
authors.initials: EE
authors.lastname: Blatter
authors.forename: W
authors.initials: W
authors.lastname: Ross
authors.forename: H
authors.initials: H
authors.lastname: Tang
authors.forename: R L
authors.initials: RL
authors.lastname: Gourse
authors.forename: R H
authors.initials: RH
authors.lastname: Ebright
mesh_terms: D000595:Amino Acid Sequence; D004268:DNA-Binding Proteins / Q000378:metabolism*; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000378:metabolism*; D004926:Escherichia coli / Q000201:enzymology*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry; D011401:Promoter Regions, Genetic; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D012697:Serine Endopeptidases / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D004268:DNA-Binding Proteins; D010446:Peptide Fragments; D012321:DNA-Directed RNA Polymerases; D012697:Serine Endopeptidases; C028344:glutamyl endopeptidase