Cooperative DNA base and shape recognition by the CCAAT-binding complex and its bZIP transcription factor HapX

The heterotrimeric CCAAT-binding complex (CBC) is a master regulator of transcription. It specifically recognizes the CCAAT-box, a fundamental eukaryotic promoter element. Certain fungi, like Aspergilli, encode a fourth CBC-subunit, HapX, to fine-tune expression of genes involved in iron metabolism. Although being a basic region leucine zipper with its own DNA recognition motif, HapX function strictly relies on the CBC. We here report two crystal structures of the CBC-HapX complex bound to DNA duplexes with distinct sequence and position of HapX sites. In either structure, a HapX dimer targets the nucleic acid downstream of the CCAAT-box and the leash like N-terminus of the distal HapX subunit interacts with CBC and DNA. In vitro and in vivo analyses of HapX mutants support the structures, highlight the complex as an exceptional major and minor groove DNA binder, and enrich our understanding of the functional as well as structural plasticity of related complexes across species.