Cross-Kingdom Structural Conservation and Diversification of Homeodomains Across Major Eukaryotic Lineages

Homeodomain transcription factors share an ancient helix-turn-helix DNA-binding core yet regulate diverse developmental and reproductive programs across eukaryotes. We curated 355 nonredundant homeodomain structures spanning fungi, animals, and plants, including 118 experimental PDB entries and 237 high-confidence AlphaFold2 models, and performed large-scale structural comparisons using DaliLite5. Structural distances were summarized as a clustering tree visualized in iTOL and interpreted through topology-guided PyMOL superpositions and sequence-logo mapping of conserved positions. Across kingdoms, the canonical three-helix HTH geometry and the recognition-helix framework were strongly conserved, whereas structural diversification was concentrated in interhelical loops, terminal regions, linker segments, and lineage-specific auxiliary modules. Fungal mating-type homeodomains and major animal classes retained conserved recognition-helix architecture despite sequence divergence, while plant WOX, ZF-HD, PHD-associated, and SAWADEE-associated architectures illustrated modular expansion for developmental and chromatin-context integration.