9lpe
From Proteopedia
(Difference between revisions)
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| - | '''Unreleased structure''' | ||
| - | + | ==ATPDF2 HDZIP domain complexed with DNA== | |
| + | <StructureSection load='9lpe' size='340' side='right'caption='[[9lpe]], [[Resolution|resolution]] 3.11Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[9lpe]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9LPE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9LPE FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.11Å</td></tr> | ||
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9lpe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9lpe OCA], [https://pdbe.org/9lpe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9lpe RCSB], [https://www.ebi.ac.uk/pdbsum/9lpe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9lpe ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/PDF2_ARATH PDF2_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).<ref>PMID:12505995</ref> <ref>PMID:23590515</ref> <ref>PMID:24989044</ref> <ref>PMID:25564655</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | 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. | ||
| - | + | 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<ref>PMID:40583771</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| - | [[Category: Chen | + | <div class="pdbe-citations 9lpe" style="background-color:#fffaf0;"></div> |
| - | [[Category: Huang | + | == References == |
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Arabidopsis thaliana]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Chen W]] | ||
| + | [[Category: Huang HD]] | ||
Current revision
ATPDF2 HDZIP domain complexed with DNA
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