DNA-binding specificity of the homeodomain-leucine zipper domain

Homeodomain-leucine zipper (HD-Zip) proteins are putative transcription factors identified only in plants. The study of the DNA-binding properties of the ATHB-1 and -2 HD-Zip (HD-Zip-1 and -2) domains showed that they interact with DNA as homodimers and recognize two distinct 9 bp pseudopalindromic sequences, CAAT(A/T)ATTG (BS-1) and CAAT(G/C)ATTG (BS-2), respectively, as determined by selecting high-affinity binding sites from random-sequence DNA. Here, we report a mutational analysis of the HD-Zip-2 domain. We determined that conserved amino acid residues of helix 3, Val47 and Asn51, and Arg55 are essential for the DNA-binding activity of the HD-Zip-2 domain. We demonstrated that the preferential recognition of a G/C base-pair at the central position by the HD-Zip-2 domain is abolished either by the replacement of Arg55 with lysine or by the substitution of Glu46 and Thr56 with the corresponding residues of the HD-Zip-1 domain (alanine and tryptophan, respectively). In contrast, substitution of Arg55 with lysine in the HD-Zip-1 domain significantly reduced DNA-binding activity without changing the specificity of recognition. Finally, we determined that differences in residues outside helix 3 further contribute to the DNA-binding specificity of the HD-Zip domain. Taken together, the data strongly suggest that the preferential recognition of BS-2 and -1 by the HD-Zip-2 and -1 domains, respectively, may be attributable to a distinct orientation of the side-chain of Arg55 in these two domains.