9lpe | pdb_00009lpe
ATPDF2 HDZIP domain complexed with DNA
Structural highlights
FunctionPDF2_ARATH Probable transcription factor that binds to the L1 box DNA sequence 5'-TAAATG[CT]A-3'. Plays a role in maintaining the identity of L1 cells, possibly by interacting with their L1 box or other target-gene promoters; binds to the LIP1 gene promoter and stimulates its expression upon imbibition (PubMed:24989044). Acts as a positive regulator of gibberellins (GAs)-regulated epidermal gene expression (e.g. LIP1, LIP2, LTP1, FDH and PDF1) (PubMed:24989044). Functionally redundant to ATML1 (PubMed:24989044). Involved, together with HDG proteins (e.g. HDG1, HDG2, HDG5 and HDG12), in the regulation of flower organs development by promoting the expression of APETALA 3 (AP3) in the epidermis and internal cell layers of developing flowers (PubMed:23590515). Seems to promote cell differentiation (PubMed:25564655).[1] [2] [3] [4] Publication Abstract from PubMedHomeodomain-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. Molecular insights into DNA recognition by HD-Zip transcription factors.,Chen W, Yan W, Jiang K, Huang H Plant Physiol. 2025 Jul 3;198(3):kiaf292. doi: 10.1093/plphys/kiaf292. PMID:40583771[5] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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