9lpe: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 9lpe is ~~ON HOLD until Paper~~ Publication

==ATPDF2 HDZIP domain complexed with DNA==

== 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>

== 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.

~~Authors:~~ Chen, W., Huang, H.D.

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>

~~Description~~: ~~ATPDF2 HDZIP domain complexed with DNA~~

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased~~ Structures]]

</div>

[[Category: Chen, W]]

[[Category: Huang~~, H.D~~]]

== References ==

__TOC__

</StructureSection>

[[Category: Arabidopsis thaliana]]

[[Category: Large Structures]]

[[Category: Chen W]]

[[Category: Huang HD]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9lpe is ON HOLD  until Paper Publication
+==ATPDF2 HDZIP domain complexed with DNA==
+<StructureSection load='9lpe' size='340' side='right'caption='[[9lpe]], [[Resolution|resolution]] 3.11&Aring;' 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]] 3.11&#8491;</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.
-Authors: Chen, W., Huang, H.D.
+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>
-Description: ATPDF2 HDZIP domain complexed with DNA
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Chen, W]]
+<div class="pdbe-citations 9lpe" style="background-color:#fffaf0;"></div>
-[[Category: Huang, H.D]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Arabidopsis thaliana]]
+[[Category: Large Structures]]
+[[Category: Chen W]]
+[[Category: Huang HD]]