WOPR-domain proteins are found throughout the fungal kingdom where they function as master regulators of cell morphology and pathogenesis. Genetic and biochemical experiments previously demonstrated that these proteins bind to specific DNA sequences and thereby regulate transcription. However, their primary sequence showed no relationship to any known DNA-binding domain, and the basis for their ability to recognize DNA sequences remained unknown. Here, we describe the 2.6-Å crystal structure of a WOPR domain in complex with its preferred DNA sequence. The structure reveals that two highly conserved regions, separated by an unconserved linker, form an interdigitated β-sheet that is tilted into the major groove of DNA. Although the main interaction surface is in the major groove, the highest-affinity interactions occur in the minor groove, primarily through a deeply penetrating arginine residue. The structure reveals a new, unanticipated mechanism by which proteins can recognize specific sequences of DNA.fungal pathogenesis | transcription factor | transcriptional regulation | protein-DNA interaction | Candida albicans T he WOPR family of transcriptional regulators [named for the members Wor1 (white-opaque regulator 1), Pac2 (pat1 compensator 2), and Ryp1 (required for yeast phase growth 1)] controls morphological changes and pathogenesis in a diverse group of fungal species (Fig. 1A), including the human pathogens Candida albicans (1-3), Histoplasma capsulatum (4), and Cryptococcus neoformans (5) and several plant pathogens (6-9). In C. albicans, Wor1 controls the process of white-opaque switching and mating (1-3), and it has a key role in promoting commensalism (10). In H. capsulatum, it controls the transition from the mycelia form (found in soil) and the yeast form (found in infected human hosts) (4). Recently, a series of in vitro and in vivo experiments demonstrated that the WOPR domain of Wor1 binds DNA in a sequence-specific fashion and defined the DNA sequence recognized by it (Fig. 1B) (11,12). Muc1 expressed independent of TEC1 1 (Mit1) from Saccharomyces cerevisiae, a fourth WOPR-domain protein, and Ryp1 from H. capsulatum have since been shown to recognize this same DNA sequence, representing conservation of the WOPR domain-DNA sequence interactions over a period of 600 million to 1.2 billion years (13).Biochemical experiments indicated that the WOPR domain binds DNA in an unusual way. The WOPR domain consists of two regions conserved across many fungal species (referred to here as "R1" and "R2"), separated by a poorly conserved "linker" region of variable length (Fig. 1C). R1 is 80 aa in length, R2 is 50 aa, and the linker ranges from less than 25 to more than 100 aa, depending on the species. The WOPR domain alone can bind DNA tightly (∼5 nM) and specifically (11). Additional experiments demonstrated that neither R1 nor R2 alone could bind to DNA individually, but binding was observed-albeit at lower affinity-when the two regions were expressed as separate peptides and mixed in the presence of DNA. ...