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Crystal structure of the MYB domain of the RAD transcription factor from Antirrhinum majus

Introduction. The RAD gene of Antirrhinum majus encodes a single-repeat MYB transcription factor that is implicated in the control of floral asymmetry. Herein we present the crystal structure of the MYB domain of the RAD protein determined using the anomalous signal of iodide and refined to a resolution of 1.9 Å. This constitutes the first X-ray structure of a single-repeat MYB protein. The structure conforms to the three-helix bundle fold of the canonical MYB domain, although the third helix is notably longer. Several developmental genes have been identified in Antirrhinum majus (garden snapdragon) that are implicated in the control of asymmetric floral architecture. Sequence analysis suggests that two of these genes, RADIALIS (RAD) and DIVARICATA (DIV), encode putative MYB transcription factors, this being consistent with their proposed signaling roles. MYB transcription factors are ubiquitous in eukaryotes, most notably in plants, and contain one or more copies of the so-called MYB DNAbinding domain. MYB domains are approximately 50 residues in length, highly variable in sequence, but are often characterized by three regularly spaced Trp residues. MYB proteins can be split into three subfamilies depending on whether they have one, two or three imperfect repeats of the MYB domain. Most MYB proteins from vertebrates consist of three imperfect repeats (R1, R2, and R3), but plants contain large numbers of two repeat (R2 and R3) MYBs. In some cases, however, only one MYB-like domain is present. The DIV protein contains two MYB-like domains, whilst the RAD protein contains only one. The latter is closely related in sequence to the N-terminal MYB domain of DIV, suggesting that RAD may have evolved through a C-terminal deletion of a DIV-like ancestral protein. RAD promotes dorsal identity of the flower, whereas DIV promotes ventral identity. It is thought that RAD is activated in the dorsal region of the developing flower, which then inhibits the activity of DIV, by either competitively binding to DIV’s target DNA sequences or to proteins that interact with DIV. So far, DNA binding functions for both RAD and DIV have yet to be demonstrated experimentally, and the possibility exists that they only bind to DNA as complexes with other proteins. To date, there are relatively few structures of MYB proteins in the Protein Data Bank (PDB), despite their prevalence in nature, possibly reflecting inherent problems in over expressing and crystallizing this family of proteins. Moreover, the majority of known structures have been determined using NMR rather than X-ray crystallography. In this article, we report the crystal structure determination of an 8 kDa fragment of the 10.8 kDa RAD protein from Antirrhinum majus that encompasses the entire MYB domain and was determined using the anomalous signal of iodide from X-ray data collected in-house.