Structure-function analysis of the Z-DNA-binding domain Zalpha of dsRNA adenosine deaminase type I reveals similarity to the (alpha +beta ) family of helix-turn-helix proteins

RNA editing alters pre-mRNA through site-selective adenosine deamination, which results in codon changes that lead to the production of novel proteins. An enzyme that catalyzes this reaction, double-stranded RNA adenosine deaminase (ADAR1), contains two N-terminal Z-DNA-binding motifs, Zα and Zβ, the function of which is as yet unknown. In this study, multidimensional NMR spectroscopy was used to show that the topology of Zα is α1β1α2α3β2β3. Long-range NOEs indicate that β1 and β3 interact with each other. Site-directed mutagenesis was used to identify residues in α3, β3 and the loop connecting β2 to β3 that affect Z-DNA binding. Also identified were 11 hydrophobic residues that are essential for protein stability. Comparison with known structures reveals some similarity between Zα and (α + β) helix–turn–helix proteins, such as histone 5 and the family of hepatocyte nuclear factor-3 winged-helix–turn–helix transcription factors. Taken together, the structural and functional data suggest that recognition of Z-DNA by Zα involves residues in both the α3 helix and the C-terminal β-sheet.