Paramagnetic Cobalt as a Probe of the Orientation of an Accessory DNA-Binding Region of the Yeast ADR1 Zinc-Finger Protein

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Abstract
The minimal DNA-binding domain of the yeast ADR1 transcription factor consists of two Cys2−His2 zinc fingers and an additional 20 residues N-terminal and proximal to the fingers. The accessory sequence likely plays a role in contacting DNA. Paramagnetic cobalt was incorporated into the fingers of an ADR1 DNA-binding construct (ADR1z) to serve as a probe of the proximity of the accessory sequence to the zinc fingers. NMR signals from the accessory region are not perturbed by cobalt incorporation. Previous studies showed that this region is random coil in the ADR1z construct in the absence of DNA; it does not adopt a fixed orientation with respect to the cobalt sites. In contrast, many residues of the accessory region are perturbed by cobalt in the DNA-bound form of the protein, suggesting this region becomes constrained. This observation agrees with previous results showing a disorder-to-order transition for the accessory region upon DNA binding. Furthermore, these results indicate that the accessory region lies close to the fingers in the protein−DNA complex. This region thus does not extend along the DNA away from the zinc fingers; it more likely binds the same stretch of DNA contacted by the zinc fingers. Comparison to the behavior of other zinc-finger proteins that utilize an accessory DNA-binding sequence suggested that the region of ADR1 proximal to the zinc fingers might form an α-helix. Analysis of sequential NOEs in the accessory region of DNA-bound ADR1z reveals no helical structure.