title: Structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription.
abstract: RapA, as abundant as sigma70 in the cell, is an RNA polymerase (RNAP)-associated Swi2/Snf2 protein with ATPase activity. It stimulates RNAP recycling during transcription. We report a structure of RapA that is also a full-length structure for the entire Swi2/Snf2 family. RapA contains seven domains, two of which exhibit novel protein folds. Our model of RapA in complex with ATP and double-stranded DNA (dsDNA) suggests that RapA may bind to and translocate on dsDNA. Our kinetic template-switching assay shows that RapA facilitates the release of sequestered RNAP from a posttranscrption/posttermination complex for transcription reinitiation. Our in vitro competition experiment indicates that RapA binds to core RNAP only but is readily displaceable by sigma70. RapA is likely another general transcription factor, the structure of which provides a framework for future studies of this bacterial Swi2/Snf2 protein and its important roles in RNAP recycling during transcription.
authors.affiliation: Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
authors.forename: Gary
authors.initials: G
authors.lastname: Shaw
authors.forename: Jianhua
authors.initials: J
authors.lastname: Gan
authors.forename: Yan Ning
authors.initials: YN
authors.lastname: Zhou
authors.forename: Huijun
authors.initials: H
authors.lastname: Zhi
authors.forename: Priadarsini
authors.initials: P
authors.lastname: Subburaman
authors.forename: Rongguang
authors.initials: R
authors.lastname: Zhang
authors.forename: Andrzej
authors.initials: A
authors.lastname: Joachimiak
authors.forename: Ding Jun
authors.initials: DJ
authors.lastname: Jin
authors.forename: Xinhua
authors.initials: X
authors.lastname: Ji
mesh_terms: D000251:Adenosine Triphosphatases / Q000737:chemistry / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000378:metabolism; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001667:Binding, Competitive; D020134:Catalytic Domain / Q000502:physiology; D004247:DNA / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism* / Q000502:physiology; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism / Q000502:physiology*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011485:Protein Binding; D020836:Protein Structure, Quaternary; D017433:Protein Structure, Secondary; D012808:Sigma Factor / Q000378:metabolism; D014158:Transcription, Genetic / Q000502:physiology*
chemical_list: D029968:Escherichia coli Proteins; C074434:RapA protein, E coli; D012808:Sigma Factor; D000255:Adenosine Triphosphate; D004247:DNA; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases; D000251:Adenosine Triphosphatases
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