title: Structural insights into the activity of enhancer-binding proteins.
abstract: Activators of bacterial sigma54-RNA polymerase holoenzyme are mechanochemical proteins that use adenosine triphosphate (ATP) hydrolysis to activate transcription. We have determined by cryogenic electron microscopy (cryo-EM) a 20 angstrom resolution structure of an activator, phage shock protein F [PspF(1-275)], which is bound to an ATP transition state analog in complex with its basal factor, sigma54. By fitting the crystal structure of PspF(1-275) at 1.75 angstroms into the EM map, we identified two loops involved in binding sigma54. Comparing enhancer-binding structures in different nucleotide states and mutational analysis led us to propose nucleotide-dependent conformational changes that free the loops for association with sigma54.
authors.affiliation: Department of Biological Sciences, Imperial College London, London, SW7 2AZ, UK.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Rappas
authors.forename: Jorg
authors.initials: J
authors.lastname: Schumacher
authors.forename: Fabienne
authors.initials: F
authors.lastname: Beuron
authors.forename: Hajime
authors.initials: H
authors.lastname: Niwa
authors.forename: Patricia
authors.initials: P
authors.lastname: Bordes
authors.forename: Sivaramesh
authors.initials: S
authors.lastname: Wigneshweraraj
authors.forename: Catherine A
authors.initials: CA
authors.lastname: Keetch
authors.forename: Carol V
authors.initials: CV
authors.lastname: Robinson
authors.forename: Martin
authors.initials: M
authors.lastname: Buck
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Zhang
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D020285:Cryoelectron Microscopy; D018360:Crystallography, X-Ray; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism*; D006868:Hydrolysis; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D051922:PII Nitrogen Regulatory Proteins; D011487:Protein Conformation; D017510:Protein Folding; D020836:Protein Structure, Quaternary; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D051877:RNA Polymerase Sigma 54; D012808:Sigma Factor / Q000737:chemistry / Q000378:metabolism; D015534:Trans-Activators / Q000737:chemistry* / Q000378:metabolism*; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D051922:PII Nitrogen Regulatory Proteins; C098954:PspF protein, E coli; D012808:Sigma Factor; D015534:Trans-Activators; D014157:Transcription Factors; C497751:rpoN protein, E coli; D000255:Adenosine Triphosphate; D012321:DNA-Directed RNA Polymerases; D051877:RNA Polymerase Sigma 54