9M0K

Crystal structure of the WRKY DNA-binding domain in complex with the W-box DNA motif

Summary for 9M0K

• Entry DOI: 10.2210/pdb9m0k/pdb
• Descriptor: WRKY17 transcription factor, DNA (5'-D(P*TP*CP*TP*AP*GP*TP*CP*AP*AP*TP*CP*A)-3'), DNA (5'-D(P*TP*GP*AP*TP*TP*GP*AP*CP*TP*AP*GP*A)-3'), ... (5 entities in total)
• Functional Keywords: dna recognition mechanism, complex, gene regulation, binding specificity, dna binding protein/dna, dna binding protein-dna complex
• Biological source: Gossypium hirsutum (cotton); More
• Total number of polymer chains: 4
• Total formula weight: 22838.96

Authors

Liu, Y.L.,Xiao, Q.,Shang, X.C. (deposition date: 2025-02-25, release date: 2026-02-11)

Primary citation

Xiao, Q.,Wang, Y.,Shang, X.,Chen, Y.,Zhang, M.,Zhou, Y.,Huang, X.,Qin, S.,Min, J.,Xu, G.,Liu, Y.
Structural basis for sequence-specific DNA recognition by a group IId WRKY transcription factor GhWRKY17 in cotton.
Biochem.J., 483:-, 2026

PubMed Abstract: WRKY transcription factors, a plant-specific family of transcriptional regulators, are classified into four groups (I-IV) and play pivotal roles in plant defense, development, and stress responses. These proteins are characterized by conserved WRKY domains that preferentially bind to the W-box cis-element C/TTGACC/T in target gene promoters. In Gossypium hirsutum (Gh; upland cotton), the group IId member GhWRKY17 regulates cotton fiber development by activating downstream target genes such as GhHOX3 through promoter W-box binding. However, the structural basis for its DNA recognition specificity remains elusive. Here, we present the 1.8 Å resolution crystal structure of the GhWRKY17 WRKY domain in complex with the GhHOX3 promoter DNA-the first structural characterization of a group IId WRKY protein. Structural analysis reveals that it consists of four antiparallel β-strands, with the β2-strand (harboring the conserved 249WRKYGQK255 motif) and β3-strand co-operatively engaging the DNA major groove. Key residues (R250, K251, Y252, Q254, K255, R264, Y266, Y267) form an intricate hydrogen-bonding network essential for recognizing the extended G/TTTGACC motif. Comparative structural analyses with group I/IIa/III WRKY-DNA complexes reveal that GhWRKY17's dual-strand engagement and extensively hydrogen bond-mediated specific interaction represent novel mechanistic features distinguishing group IId members from other WRKY subgroups, emphasizing the necessity for subgroup-specific investigations. These findings not only establish a structural paradigm for group IId WRKY function but also provide molecular insights for engineering cotton fiber traits through transcriptional regulation.

PubMed: 41569870
DOI: 10.1042/BCJ20250191

Experimental method

X-RAY DIFFRACTION (1.8 Å)