title: Functional roles of the pre-sensor I insertion sequence in an AAA+ bacterial enhancer binding protein.
abstract: Molecular machines belonging to the AAA+ superfamily of ATPases use NTP hydrolysis to remodel their versatile substrates. The presence of an insertion sequence defines the major phylogenetic pre-sensor I insertion (pre-SIi) AAA+ superclade. In the bacterial sigma(54)-dependent enhancer binding protein phage shock protein F (PspF) the pre-SIi loop adopts different conformations depending on the nucleotide-bound state. Single amino acid substitutions within the dynamic pre-SIi loop of PspF drastically change the ATP hydrolysis parameters, indicating a structural link to the distant hydrolysis site. We used a site-specific protein-DNA proximity assay to measure the contribution of the pre-SIi loop in sigma(54)-dependent transcription and demonstrate that the pre-SIi loop is a major structural feature mediating nucleotide state-dependent differential engagement with Esigma(54). We suggest that much, if not all, of the action of the pre-SIi loop is mediated through the L1 loop and relies on a conserved molecular switch, identified in a crystal structure of one pre-SIi variant and in accordance with the high covariance between some pre-SIi residues and distinct residues outside the pre-SIi sequence.
authors.affiliation: Department of Life Sciences, Division of Biology, Imperial College London, London, UK.
authors.forename: Patricia C
authors.initials: PC
authors.lastname: Burrows
authors.forename: Jörg
authors.initials: J
authors.lastname: Schumacher
authors.forename: Samuel
authors.initials: S
authors.lastname: Amartey
authors.forename: Tamaswati
authors.initials: T
authors.lastname: Ghosh
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Burgis
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Zhang
authors.forename: B Tracy
authors.initials: BT
authors.lastname: Nixon
authors.forename: Martin
authors.initials: M
authors.lastname: Buck
mesh_terms: D000251:Adenosine Triphosphatases / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000378:metabolism; D019943:Amino Acid Substitution; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D006868:Hydrolysis; D016254:Mutagenesis, Insertional; D017434:Protein Structure, Tertiary; D051877:RNA Polymerase Sigma 54 / Q000378:metabolism; D015534:Trans-Activators / Q000235:genetics / Q000378:metabolism*; D015533:Transcriptional Activation
chemical_list: D029968:Escherichia coli Proteins; C098954:PspF protein, E coli; D015534:Trans-Activators; C497751:rpoN protein, E coli; D000255:Adenosine Triphosphate; D051877:RNA Polymerase Sigma 54; D000251:Adenosine Triphosphatases