Plant homeobox genes can be classified into 14 classes based on sequence differentiation and fusion with characteristic codomain sequences. 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. Three-Amino acid-Loop Extension, or TALE, superclass is characterized by 63 aa, with three extra residues inserted between helix 1 and 2. KNOX and BEL are to subclass of TALE superclass. These two classes of TALE HD proteins found in plants, KNOX and BEL, are characterized by a conserved codomain structure. KNOX families conserve a diagnostic KNOX domain (~100 amino acid) upstream of the homeodomain, composed of two blocks (KNOX A and KNOX B) separated by a variable regionas well as a shorter motif adjacent to the homeodomain, named ELK.
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