5nqv: Difference between revisions

Latest revision as of 12:02, 22 November 2023

Structure of the Arabidopsis Thaliana TOPLESS N-terminal domain

Structural highlights

5nqv is a 8 chain structure with sequence from Arabidopsis thaliana and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.95Å
Ligands:	GOL, TLA
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TPL_ARATH Transcriptional corepressor. May repress the expression of root-promoting genes in the top half of the embryo to allow proper differentiation of the shoot pole during the transition stage of embryogenesis. Regulates the expression of PLT1 and PLT2. Negative regulator of jasmonate responses. Negative regulator of auxin responses. Negative regulator of multiple floral organ identity genes (PubMed:23034631). Required for ovule development (PubMed:25378179).^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

Publication Abstract from PubMed

Transcriptional repression involves a class of proteins called corepressors that link transcription factors to chromatin remodeling complexes. In plants such as Arabidopsis thaliana, the most prominent corepressor is TOPLESS (TPL), which plays a key role in hormone signaling and development. Here we present the crystallographic structure of the Arabidopsis TPL N-terminal region comprising the LisH and CTLH (C-terminal to LisH) domains and a newly identified third region, which corresponds to a CRA domain. Comparing the structure of TPL with the mammalian TBL1, which shares a similar domain structure and performs a parallel corepressor function, revealed that the plant TPLs have evolved a new tetramerization interface and unique and highly conserved surface for interaction with repressors. Using site-directed mutagenesis, we validated those surfaces in vitro and in vivo and showed that TPL tetramerization and repressor binding are interdependent. Our results illustrate how evolution used a common set of protein domains to create a diversity of corepressors, achieving similar properties with different molecular solutions.

Structure of the Arabidopsis TOPLESS corepressor provides insight into the evolution of transcriptional repression.,Martin-Arevalillo R, Nanao MH, Larrieu A, Vinos-Poyo T, Mast D, Galvan-Ampudia C, Brunoud G, Vernoux T, Dumas R, Parcy F Proc Natl Acad Sci U S A. 2017 Jul 25;114(30):8107-8112. doi:, 10.1073/pnas.1703054114. Epub 2017 Jul 11. PMID:28698367^[7]

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

References

↑ Long JA, Ohno C, Smith ZR, Meyerowitz EM. TOPLESS regulates apical embryonic fate in Arabidopsis. Science. 2006 Jun 9;312(5779):1520-3. PMID:16763149 doi:https://dx.doi.org/10.1126/science.1123841
↑ Szemenyei H, Hannon M, Long JA. TOPLESS mediates auxin-dependent transcriptional repression during Arabidopsis embryogenesis. Science. 2008 Mar 7;319(5868):1384-6. doi: 10.1126/science.1151461. Epub 2008 Feb, 7. PMID:18258861 doi:https://dx.doi.org/10.1126/science.1151461
↑ Smith ZR, Long JA. Control of Arabidopsis apical-basal embryo polarity by antagonistic transcription factors. Nature. 2010 Mar 18;464(7287):423-6. doi: 10.1038/nature08843. Epub 2010 Feb 28. PMID:20190735 doi:https://dx.doi.org/10.1038/nature08843
↑ Pauwels L, Barbero GF, Geerinck J, Tilleman S, Grunewald W, Perez AC, Chico JM, Bossche RV, Sewell J, Gil E, Garcia-Casado G, Witters E, Inze D, Long JA, De Jaeger G, Solano R, Goossens A. NINJA connects the co-repressor TOPLESS to jasmonate signalling. Nature. 2010 Apr 1;464(7289):788-91. doi: 10.1038/nature08854. PMID:20360743 doi:https://dx.doi.org/10.1038/nature08854
↑ Krogan NT, Hogan K, Long JA. APETALA2 negatively regulates multiple floral organ identity genes in Arabidopsis by recruiting the co-repressor TOPLESS and the histone deacetylase HDA19. Development. 2012 Nov;139(22):4180-90. doi: 10.1242/dev.085407. Epub 2012 Oct 3. PMID:23034631 doi:https://dx.doi.org/10.1242/dev.085407
↑ Wei B, Zhang J, Pang C, Yu H, Guo D, Jiang H, Ding M, Chen Z, Tao Q, Gu H, Qu LJ, Qin G. The molecular mechanism of sporocyteless/nozzle in controlling Arabidopsis ovule development. Cell Res. 2015 Jan;25(1):121-34. doi: 10.1038/cr.2014.145. Epub 2014 Nov 7. PMID:25378179 doi:https://dx.doi.org/10.1038/cr.2014.145
↑ Martin-Arevalillo R, Nanao MH, Larrieu A, Vinos-Poyo T, Mast D, Galvan-Ampudia C, Brunoud G, Vernoux T, Dumas R, Parcy F. Structure of the Arabidopsis TOPLESS corepressor provides insight into the evolution of transcriptional repression. Proc Natl Acad Sci U S A. 2017 Jul 25;114(30):8107-8112. doi:, 10.1073/pnas.1703054114. Epub 2017 Jul 11. PMID:28698367 doi:https://dx.doi.org/10.1073/pnas.1703054114

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OCA

[1] Long JA, Ohno C, Smith ZR, Meyerowitz EM. TOPLESS regulates apical embryonic fate in Arabidopsis. Science. 2006 Jun 9;312(5779):1520-3. PMID:16763149 doi:https://dx.doi.org/10.1126/science.1123841

[2] Szemenyei H, Hannon M, Long JA. TOPLESS mediates auxin-dependent transcriptional repression during Arabidopsis embryogenesis. Science. 2008 Mar 7;319(5868):1384-6. doi: 10.1126/science.1151461. Epub 2008 Feb, 7. PMID:18258861 doi:https://dx.doi.org/10.1126/science.1151461

[3] Smith ZR, Long JA. Control of Arabidopsis apical-basal embryo polarity by antagonistic transcription factors. Nature. 2010 Mar 18;464(7287):423-6. doi: 10.1038/nature08843. Epub 2010 Feb 28. PMID:20190735 doi:https://dx.doi.org/10.1038/nature08843

[4] Pauwels L, Barbero GF, Geerinck J, Tilleman S, Grunewald W, Perez AC, Chico JM, Bossche RV, Sewell J, Gil E, Garcia-Casado G, Witters E, Inze D, Long JA, De Jaeger G, Solano R, Goossens A. NINJA connects the co-repressor TOPLESS to jasmonate signalling. Nature. 2010 Apr 1;464(7289):788-91. doi: 10.1038/nature08854. PMID:20360743 doi:https://dx.doi.org/10.1038/nature08854

[5] Krogan NT, Hogan K, Long JA. APETALA2 negatively regulates multiple floral organ identity genes in Arabidopsis by recruiting the co-repressor TOPLESS and the histone deacetylase HDA19. Development. 2012 Nov;139(22):4180-90. doi: 10.1242/dev.085407. Epub 2012 Oct 3. PMID:23034631 doi:https://dx.doi.org/10.1242/dev.085407

[6] Wei B, Zhang J, Pang C, Yu H, Guo D, Jiang H, Ding M, Chen Z, Tao Q, Gu H, Qu LJ, Qin G. The molecular mechanism of sporocyteless/nozzle in controlling Arabidopsis ovule development. Cell Res. 2015 Jan;25(1):121-34. doi: 10.1038/cr.2014.145. Epub 2014 Nov 7. PMID:25378179 doi:https://dx.doi.org/10.1038/cr.2014.145

[7] Martin-Arevalillo R, Nanao MH, Larrieu A, Vinos-Poyo T, Mast D, Galvan-Ampudia C, Brunoud G, Vernoux T, Dumas R, Parcy F. Structure of the Arabidopsis TOPLESS corepressor provides insight into the evolution of transcriptional repression. Proc Natl Acad Sci U S A. 2017 Jul 25;114(30):8107-8112. doi:, 10.1073/pnas.1703054114. Epub 2017 Jul 11. PMID:28698367 doi:https://dx.doi.org/10.1073/pnas.1703054114

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@@ Line 3: / Line 3: @@
 <StructureSection load='5nqv' size='340' side='right'caption='[[5nqv]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5nqv]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NQV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5NQV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5nqv]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NQV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NQV FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5nqv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nqv OCA], [http://pdbe.org/5nqv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nqv RCSB], [http://www.ebi.ac.uk/pdbsum/5nqv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nqv ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></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=5nqv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nqv OCA], [https://pdbe.org/5nqv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nqv RCSB], [https://www.ebi.ac.uk/pdbsum/5nqv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nqv ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TPL_ARATH TPL_ARATH]] Transcriptional corepressor. May repress the expression of root-promoting genes in the top half of the embryo to allow proper differentiation of the shoot pole during the transition stage of embryogenesis. Regulates the expression of PLT1 and PLT2. Negative regulator of jasmonate responses. Negative regulator of auxin responses. Negative regulator of multiple floral organ identity genes (PubMed:23034631). Required for ovule development (PubMed:25378179).<ref>PMID:16763149</ref> <ref>PMID:18258861</ref> <ref>PMID:20190735</ref> <ref>PMID:20360743</ref> <ref>PMID:23034631</ref> <ref>PMID:25378179</ref>
+[https://www.uniprot.org/uniprot/TPL_ARATH TPL_ARATH] Transcriptional corepressor. May repress the expression of root-promoting genes in the top half of the embryo to allow proper differentiation of the shoot pole during the transition stage of embryogenesis. Regulates the expression of PLT1 and PLT2. Negative regulator of jasmonate responses. Negative regulator of auxin responses. Negative regulator of multiple floral organ identity genes (PubMed:23034631). Required for ovule development (PubMed:25378179).<ref>PMID:16763149</ref> <ref>PMID:18258861</ref> <ref>PMID:20190735</ref> <ref>PMID:20360743</ref> <ref>PMID:23034631</ref> <ref>PMID:25378179</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
+[[Category: Arabidopsis thaliana]]
 [[Category: Large Structures]]
-[[Category: Arevalillo, M R]]
+[[Category: Synthetic construct]]
-[[Category: Dumas, R]]
+[[Category: Arevalillo MR]]
-[[Category: Nanao, M H]]
+[[Category: Dumas R]]
-[[Category: Parcy, F]]
+[[Category: Nanao MH]]
-[[Category: Vinos-Poyo, T]]
+[[Category: Parcy F]]
-[[Category: Auxin]]
+[[Category: Vinos-Poyo T]]
-[[Category: Plant]]
-[[Category: Topless]]
-[[Category: Transcription]]
-[[Category: Transcription factor]]

5nqv: Difference between revisions

Latest revision as of 12:02, 22 November 2023

Structure of the Arabidopsis Thaliana TOPLESS N-terminal domain

Structural highlights

Function

Publication Abstract from PubMed

References

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