title: DNA structural deformations in the interaction of the controller protein C.AhdI with its operator sequence.
abstract: Controller proteins such as C.AhdI regulate the expression of bacterial restriction-modification genes, and ensure that methylation of the host DNA precedes restriction by delaying transcription of the endonuclease. The operator DNA sequence to which C.AhdI binds consists of two adjacent binding sites, O(L) and O(R). Binding of C.AhdI to O(L) and to O(L) + O(R) has been investigated by circular permutation DNA-bending assays and by circular dichroism (CD) spectroscopy. CD indicates considerable distortion to the DNA when bound by C.AhdI. Binding to one or two sites to form dimeric and tetrameric complexes increases the CD signal at 278 nm by 40 and 80% respectively, showing identical local distortion at both sites. In contrast, DNA-bending assays gave similar bend angles for both dimeric and tetrameric complexes (47 and 38 degrees, respectively). The relative orientation of C.AhdI dimers in the tetrameric complex and the structural role of the conserved Py-A-T sequences found at the centre of C-protein-binding sites are discussed.
authors.affiliation: Biophysics Laboratories, Institute of Biomedical and Biomolecular Science, St Michael's Building, University of Portsmouth, PO1 2DT, UK.
authors.forename: I
authors.initials: I
authors.lastname: Papapanagiotou
authors.forename: S D
authors.initials: SD
authors.lastname: Streeter
authors.forename: P D
authors.initials: PD
authors.lastname: Cary
authors.forename: G G
authors.initials: GG
authors.lastname: Kneale
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D001665:Binding Sites; D002942:Circular Dichroism; D015280:DNA Restriction-Modification Enzymes / Q000378:metabolism; D004269:DNA, Bacterial / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009875:Operator Regions, Genetic
chemical_list: D001426:Bacterial Proteins; D015280:DNA Restriction-Modification Enzymes; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins