Interaction of Cd2+ with Zn finger 3 of transcription factor IIIA:: Structures and binding to cognate DNA

Finger 3 of transcription factor IIIA of Xenopus laevis was synthesized and constituted with Zn2+ or Cd2+. The C-block element of the internal control region of the promoter of the 5S rRNA gene binds to the Zn-F3 and Cd-F3 with dissociation constants of 2.6 x 10(-5) and 1.5 x 10(-4) M, respectively. According to NMR spectroscopy, Zn-F3, as well as Cd-F3, exists as a conformational equilibrium that is not susceptible to structural analysis by NMR methods. To restrict the observed conformational flexibility, a mutant F3 (mF3), which differs from F3 in the number and type of amino acids between the cysteine and the histidine ligands, was synthesized. The affinity of Zn-mF3 for the C-block DNA was greatly reduced relative to Zn-F3. Nevertheless, the metal ion dissociation constants of the Zn- and Cd-mF3 complexes remain similar to those of the native structures at 4.5 x 10(-9) and 3.2 x 10(-8) M, respectively. Zn-mF3 is more thermally stable than Cd-mF3, but both adopt similar conformations according to two-dimensional H-1 NMR spectroscopy. Each peptide displays a betabetaalpha fold for its backbone that is typical of this class of zinc finger domains. The Cd-113 ion in Cd-113-mF3 is coupled to the protons of two cysteine and two histidine residues and characterized by a chemical shift of 567 ppm.