We present genetic and biochemical evidence that the amino-terminal region of ACE1, the activator of yeast Cu-metallothionein gene transcription, is composed of a single domain in which the DNA- and Cu-binding residues are interdigitated. Analysis of truncation mutants showed that both the DNA and Cu interactions functions of ACE1 are contained within an amino-terminal 101 amino acid peptide that can fold into a protease-resistant domain structure. Studies of point mutants revealed that two basic residues within this domain are required for efficient DNA binding although not for productive interaction with Cu. Mutations at these sites alter the specificity of ACE1 for two binding sites in the upstream activation region, both of which are shown to be necessary for efficient transcription in vivo. Systematic mutagenesis of the 12 cysteine residues in ACE1 showed that all 11 cysteines within the minimal DNA-binding domain are required for ACE1 to undergo a Cu-induced conformational switch into an active DNA-binding protein. A twelfth cysteine, located outside the DNA-binding domain, is not required for proper folding. The critical basic and cysteine residues of ACE1 are interdigitated, thereby providing an unusual example of overlapping small molecule and DNA binding functions within a directly regulated transcription factor. In contrast, the carboxyl-terminal region of ACE1 is shown to contain a constitutive trans-activation domain that is spatially distinct and functionally dissociable from the DNA- and Cu-binding domain.