Each WRKY protein has at least one WRKY domain of approximately 60 amino acids containing
the conserved amino acid sequence WRKYGQK at its N-terminus (from which the factors take
their name) and a novel zinc finger motif at its C-terminus [2-4].
The WRKY domain consists of four beta-strands. The first beta-strand contains the WRKYGQK
amino acid sequence and this appears to directly contact the W box binding site on the
promoters of target genes. The other three beta-strands form a novel zinc finger
For most WRKY transcription factors, the binding site is the W box (C/T)TGAC(T/C), an
element found in the promoters of many stress-related plant genes. W boxes are often
over-represented and clustered in the promoters of stress inducible genes as shown by
many transcriptome studies, starting with Maleck et al. (2000) .
Although WRKYs bind W boxes, some specificity is dependent on sequences flanking the W box
sequence (Ciolkowski et al., 2008) .