title: CopR binds and bends its target DNA: a footprinting and fluorescence resonance energy transfer study.
abstract: Plasmid pIP501 encoded transcriptional repressor CopR is one of the two regulators of plasmid copy number. Previous data suggested that CopR is a HTH protein belonging to a family of 578 HTH proteins (termed HTH 3-family). Only a very limited number of proteins in this family, among them lambda c1 repressor, 434 c1 repressor and P22 c2 repressor, have been characterized in detail so far. Previously, a CopR structural model was built based on structural homologies to the 434 c1 and P22 c2 repressor and used to identify amino acids involved in DNA binding and dimerization. Site-directed mutagenesis in combination with electrophoretic mobility shift assay (EMSA), dimerization studies and circular dichroism (CD) measurements verified the model predictions. In this study we used hydroxyl radical footprinting and fluorescence resonance energy transfer (FRET) measurements to obtain detailed information about the structure of the DNA in the CopR-DNA complex. Our results show that the DNA is bent gently around the protein, comparable to the bending angle of 20-25 degrees observed in the 434 c1 repressor-DNA complex and the lambda c1 repressor-DNA complex. The shape of CopR dimers as determined by sedimentation velocity experiments is extended and accounts for the relatively large area of protection observed with hydroxyl radical footprinting.
authors.affiliation: Institut für Molekularbiologie, Friedrich-Schiller-Universität Jena, Winzerlaer Strasse 10, D-07745 Jena, Germany. katrin@quantifoil.com
authors.forename: Katrin
authors.initials: K
authors.lastname: Steinmetzer
authors.forename: Joachim
authors.initials: J
authors.lastname: Behlke
authors.forename: Sabine
authors.initials: S
authors.lastname: Brantl
authors.forename: Mike
authors.initials: M
authors.lastname: Lorenz
mesh_terms: D001426:Bacterial Proteins; D001483:Base Sequence; D001665:Binding Sites; D001667:Binding, Competitive; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D018983:DNA Footprinting; D004268:DNA-Binding Proteins / Q000378:metabolism*; D019281:Dimerization; D005456:Fluorescent Dyes / Q000737:chemistry; D017665:Hydroxyl Radical / Q000737:chemistry; D009690:Nucleic Acid Conformation; D012097:Repressor Proteins / Q000378:metabolism; D013050:Spectrometry, Fluorescence; D015534:Trans-Activators / Q000378:metabolism*; D014461:Ultracentrifugation; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D005456:Fluorescent Dyes; D012097:Repressor Proteins; D015534:Trans-Activators; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins; D017665:Hydroxyl Radical; D004247:DNA