title: Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex.
abstract: We have used systematic fluorescence resonance energy transfer and distance-constrained docking to define the three-dimensional structures of bacterial RNA polymerase holoenzyme and the bacterial RNA polymerase-promoter open complex in solution. The structures provide a framework for understanding sigma(70)-(RNA polymerase core), sigma(70)-DNA, and sigma(70)-RNA interactions. The positions of sigma(70) regions 1.2, 2, 3, and 4 are similar in holoenzyme and open complex. In contrast, the position of sigma(70) region 1.1 differs dramatically in holoenzyme and open complex. In holoenzyme, region 1.1 is located within the active-center cleft, apparently serving as a "molecular mimic" of DNA, but, in open complex, region 1.1 is located outside the active center cleft. The approach described here should be applicable to the analysis of other nanometer-scale complexes.
authors.affiliation: Howard Hughes Medical Institute, Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Mekler
authors.forename: Ekaterine
authors.initials: E
authors.lastname: Kortkhonjia
authors.forename: Jayanta
authors.initials: J
authors.lastname: Mukhopadhyay
authors.forename: Jennifer
authors.initials: J
authors.lastname: Knight
authors.forename: Andrei
authors.initials: A
authors.lastname: Revyakin
authors.forename: Achillefs N
authors.initials: AN
authors.lastname: Kapanidis
authors.forename: Wei
authors.initials: W
authors.lastname: Niu
authors.forename: Yon W
authors.initials: YW
authors.lastname: Ebright
authors.forename: Ronald
authors.initials: R
authors.lastname: Levy
authors.forename: Richard H
authors.initials: RH
authors.lastname: Ebright
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D001483:Base Sequence; D004247:DNA / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry* / Q000378:metabolism; D004735:Energy Transfer; D019793:Fluorescein / Q000378:metabolism; D005456:Fluorescent Dyes / Q000378:metabolism; D008433:Mathematics; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D020836:Protein Structure, Quaternary; D012235:Rhodamines / Q000378:metabolism; D012808:Sigma Factor / Q000737:chemistry / Q000378:metabolism; D014158:Transcription, Genetic / Q000502:physiology*
chemical_list: D001426:Bacterial Proteins; D005456:Fluorescent Dyes; D012235:Rhodamines; D012808:Sigma Factor; C005358:tetramethylrhodamine; D004247:DNA; D012321:DNA-Directed RNA Polymerases; D019793:Fluorescein