9LPE

ATPDF2 HDZIP domain complexed with DNA

Summary for 9LPE

• Entry DOI: 10.2210/pdb9lpe/pdb
• Descriptor: Homeobox-leucine zipper protein PROTODERMAL FACTOR 2, DNA (5'-D(*CP*TP*AP*AP*AP*TP*GP*CP*AP*GP*TP*GP*CP*AP*TP*TP*TP*A)-3'), DNA (5'-D(*GP*TP*AP*AP*AP*TP*GP*CP*AP*CP*TP*GP*CP*AP*TP*TP*TP*A)-3') (3 entities in total)
• Functional Keywords: hd-zip transcription factors, dna, dna binding protein/dna, dna binding protein-dna complex
• Biological source: Arabidopsis thaliana (thale cress); More
• Total number of polymer chains: 4
• Total formula weight: 37948.96

Authors

Chen, W.,Huang, H.D. (deposition date: 2025-01-24, release date: 2025-12-03)

Primary citation

Chen, W.,Yan, W.,Jiang, K.,Huang, H.
Molecular insights into DNA recognition by HD-Zip transcription factors.
Plant Physiol., 198:-, 2025

PubMed Abstract: Homeodomain-leucine zipper (HD-Zip) genes encode a large family of plant-specific transcription factors (TFs) that are integral to plant development, growth, regulation, and responses to environmental and hormonal signals. While the roles and mechanisms of HD-Zip TFs have been extensively studied, the structural basis for their DNA recognition remains unclear. In this study, we analyzed DAP-seq data and identified consensus DNA motifs, 5'-AAT[W]AT-3' and 5'-[N]AAA[N][N]-3', preferentially bound by HD-Zip TFs. Both motifs feature a 5'-AA(T/A)-3' core, which is shared across previously identified HD-Zip target sequences, suggesting a common recognition feature within the HD-Zip family. Focusing on the well-characterized HD-Zip IV TF PROTEIN PRODUCTION FACTOR 2 (PDF2) from Arabidopsis (Arabidopsis thaliana) and its interaction with the L1 box DNA sequence, our structural and biochemical analyses revealed that the PDF2 HD-ZA module forms a dimer to specifically recognize the 5'-AATG-3' core through an asymmetric binding mode. In this mode, only the primary recognition helix of 1 protomer and the N-arm of the other protomer in the PDF2 HD-ZA dimer are involved in specific DNA interactions. Our study offers insights into the molecular mechanisms of HD-Zip TFs and provides a structural template for engineering applications in agricultural research.

PubMed: 40583771
DOI: 10.1093/plphys/kiaf292

Experimental method

X-RAY DIFFRACTION (3.11 Å)