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

Abstract

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.