title: Model-building of Fnr and FixK DNA-binding domains suggests a basis for specific DNA recognition.
abstract: The DNA-binding C-terminal domains of the regulatory proteins Fnr from Escherichia coli and FixK from Rhizobium meliloti have been modelled on the basis of their homologies to the CAP protein from E. coli. Residues Glu181, Thr182 and Arg185 of CAP, which are exposed residues of the DNA-recognition helix alpha F, are conserved in Fnr and FixK. However, Arg180 and Gly184 are substituted by Val and Ser respectively in Fnr. We propose that this valine makes a Van der Waals' contact with the first thymine in the Fnr consensus TTGA-N6-TCAA, and that the serine contributes to the binding by displacing a thymine-bound water molecule. The corresponding residues in FixK, Ile and Ser allow the same interactions with a thymine. Therefore we predict that FixK may recognize the same sites as Fnr. This is supported experimentally by showing that Fnr can substitute for FixK in activating the fixN gene in E. coli.
authors.affiliation: Laboratoire de Biologie Physicochimique, INRA, Université Paris-Sud, Orsay, France.
authors.forename: J
authors.initials: J
authors.lastname: Cherfils
authors.forename: J F
authors.initials: JF
authors.lastname: Gibrat
authors.forename: J
authors.initials: J
authors.lastname: Levin
authors.forename: J
authors.initials: J
authors.lastname: Batut
authors.forename: D
authors.initials: D
authors.lastname: Kahn
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites; D003196:Computer Graphics; D002373:Cyclic AMP Receptor Protein / Q000235:genetics; D004269:DNA, Bacterial / Q000378:metabolism / Q000502:physiology*; D004268:DNA-Binding Proteins; D004926:Escherichia coli / Q000235:genetics*; D005798:Genes, Bacterial; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009586:Nitrogen Fixation / Q000235:genetics; D009690:Nucleic Acid Conformation; D012231:Rhizobium / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid
chemical_list: D002373:Cyclic AMP Receptor Protein; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins