title: Structural analysis of DNA-protein complexes regulating the restriction-modification system Esp1396I.
abstract: The controller protein of the type II restriction-modification (RM) system Esp1396I binds to three distinct DNA operator sequences upstream of the methyltransferase and endonuclease genes in order to regulate their expression. Previous biophysical and crystallographic studies have shown molecular details of how the controller protein binds to the operator sites with very different affinities. Here, two protein-DNA co-crystal structures containing portions of unbound DNA from native operator sites are reported. The DNA in both complexes shows significant distortion in the region between the conserved symmetric sequences, similar to that of a DNA duplex when bound by the controller protein (C-protein), indicating that the naked DNA has an intrinsic tendency to bend when not bound to the C-protein. Moreover, the width of the major groove of the DNA adjacent to a bound C-protein dimer is observed to be significantly increased, supporting the idea that this DNA distortion contributes to the substantial cooperativity found when a second C-protein dimer binds to the operator to form the tetrameric repression complex.
authors.affiliation: Institute of Biomedical and Biomolecular Science, University of Portsmouth, King Henry I Street, Portsmouth, Hampshire PO1 2DY, England.
authors.forename: Richard N A
authors.initials: RN
authors.lastname: Martin
authors.forename: John E
authors.initials: JE
authors.lastname: McGeehan
authors.forename: Neil J
authors.initials: NJ
authors.lastname: Ball
authors.forename: Simon D
authors.initials: SD
authors.lastname: Streeter
authors.forename: Sarah-Jane
authors.initials: SJ
authors.lastname: Thresh
authors.forename: G G
authors.initials: GG
authors.lastname: Kneale
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites; D018360:Crystallography, X-Ray; D015280:DNA Restriction-Modification Enzymes / Q000737:chemistry* / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics; D004926:Escherichia coli / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009875:Operator Regions, Genetic / Q000235:genetics; D011487:Protein Conformation; D055503:Protein Multimerization; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D015280:DNA Restriction-Modification Enzymes; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D011994:Recombinant Proteins
keywords: DNA distortion; DNA-binding proteins; helix–turn–helix motif; transcriptional regulation