Homeobox genes encode a typical DNA-binding domain of 60 amino acids, known as homeodomain. Typically, homeodomain folds into characteristic 3D structure containing three alpha-helices, of which the second and third form a helix-turn-helix motif. The HD-ZIP superclass is characterized by presence of a leucine-zipper adjacent to the C-terminus of the homeodomain. This super class is further subdivided into four individual classes, HD-ZIP I, HD-ZIP II, HD-ZIP III, and HD-ZIP IV. In HD-ZIP III and HD-ZIP IV classes additionally it have START (STeroidogenic Acute Regulatory protein–related lipid Transfer) and HD-SAD (START associated conserved domain). Presence of this associated START or START associated domain make to a significant new family with predicted new functional characteristics.
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