title: DNA binding by an amino acid residue in the C-terminal half of the Rel homology region.
abstract: BACKGROUND
  Members of the Rel family of transcription factors are important in regulating the inflammatory, acute phase, and immune responses in mammals. The structural basis for sequence-specific binding by Rel proteins is poorly understood, however. In the studies reported here, a new photoaffinity labeling procedure has been used to probe DNA contacts established by a Rel protein, the p50 homodimer of NF-kappa B.
  
  
  RESULTS
  Using a novel post-synthetic modification method, 8-azido-2'-deoxyadenosine (N3dA), a photoactive analog of 2'-deoxyadenosine, was introduced at a specific site within a consensus DNA binding site for the NF-kappa B p50 homodimer. Upon irradiation with ultraviolet light, the N3dA-substituted DNA was efficiently photocrosslinked to p50. The crosslinked amino acid of p50 was identified as K244, which lies in the carboxy-terminal half of the Rel homology region (RHR). Mutation of K244 exerts strong effects on DNA binding, confirming the importance of this residue for p50-DNA interactions.
  
  
  CONCLUSIONS
  We have used N3dA-containing DNA to identify a residue of NF-kappa B p50 that contacts DNA illustrating the value of this approach in studies of protein-DNA interactions. K244 appears not to contact a DNA base, but rather a phosphate moiety that lies nearby. The segment of protein sequence in which K244 resides has been implicated in dimerization. The results presented here suggest that the DNA-binding domain extends farther toward the carboxy-terminus than previously thought.
authors.affiliation: Department of Chemistry, Harvard University, Cambridge, MA 02138, USA.
authors.forename: J
authors.initials: J
authors.lastname: Liu
authors.forename: Q R
authors.initials: QR
authors.lastname: Fan
authors.forename: M
authors.initials: M
authors.lastname: Sodeoka
authors.forename: W S
authors.initials: WS
authors.lastname: Lane
authors.forename: G L
authors.initials: GL
authors.lastname: Verdine
mesh_terms: D000596:Amino Acids / Q000378:metabolism*; D003432:Cross-Linking Reagents; D004247:DNA / Q000235:genetics*; D009154:Mutation; D016328:NF-kappa B / Q000235:genetics; D019920:Photoaffinity Labels; D012689:Sequence Homology, Nucleic Acid
chemical_list: D000596:Amino Acids; D003432:Cross-Linking Reagents; D016328:NF-kappa B; D019920:Photoaffinity Labels; D004247:DNA