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.

Reference:

1. K. Mukherjee, T. R. Burglin, Comprehensive analysis of animal TALE homeobox genes: new conserved motifs and cases of accelerated evolution. J Mol Evol 65, 137 (2007).

2. Mukherjee, K., Brocchieri, L., and Burglin, T.R. (2009). A comprehensive classification and evolutionary analysis of plant homeobox genes. Mol Biol Evol 26, 2775-2794.

The family is the subfamily family of HB in PlnTFDB.