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| | ==Crystal Structure of VRN1 (Residues 208-341)== | | ==Crystal Structure of VRN1 (Residues 208-341)== |
| - | <StructureSection load='4i1k' size='340' side='right' caption='[[4i1k]], [[Resolution|resolution]] 1.60Å' scene=''> | + | <StructureSection load='4i1k' size='340' side='right'caption='[[4i1k]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4i1k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I1K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I1K FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4i1k]] is a 2 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=4I1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4I1K FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 1.6Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1wid|1wid]], [[1yel|1yel]], [[3hqf|3hqf]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VRN1, At3g18990, K13E13.10 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=4i1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i1k OCA], [https://pdbe.org/4i1k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4i1k RCSB], [https://www.ebi.ac.uk/pdbsum/4i1k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4i1k ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4i1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i1k OCA], [http://pdbe.org/4i1k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4i1k RCSB], [http://www.ebi.ac.uk/pdbsum/4i1k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4i1k ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/VRN1_ARATH VRN1_ARATH]] Involved in the regulation of vernalization. Acts as transcriptional repressor of FLC, a major target of the vernalization pathway. Binds DNA in vitro in a non-sequence-specific manner.<ref>PMID:12114624</ref> | + | [https://www.uniprot.org/uniprot/VRN1_ARATH VRN1_ARATH] Involved in the regulation of vernalization. Acts as transcriptional repressor of FLC, a major target of the vernalization pathway. Binds DNA in vitro in a non-sequence-specific manner.<ref>PMID:12114624</ref> |
| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed ==
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| - | The B3 DNA binding domain is a plant-specific domain, found throughout the plant kingdom from the alga Chlamydomonas to grasses and flowering plants. Over 100 B3 domain-containing proteins are found in the model plant Arabidopsis thaliana and one of these is critical for accelerating flowering in response to prolonged cold treatment; an epigenetic process called vernalization. Despite the specific phenotype of genetic vrn1 mutants, the VERNALIZATION1 (VRN1) protein localizes throughout the nucleus and in vitro shows sequence non-specific binding. In this work we used a dominant repressor tag that overcomes genetic redundancy to show that VRN1 is involved in processes beyond vernalization that are essential for Arabidopsis development. To understand its sequence non-specific binding we crystallized VRN1208-341 and solved its crystal structure to 1.6 A resolution using Se-SAD methods. The crystallized construct comprises the second VRN1 B3 domain and a preceding region conserved among VRN1 orthologs, but absent in other B3 domains. We established the DNA binding face using NMR then mutated positively charged residues on this surface with a series of 16 Ala and Glu substitutions ensuring the protein fold was not disturbed using HSQC NMR spectra. A triple mutant R249E R289E R296E was almost completely incapable of DNA binding in vitro. Thus, we have revealed that although VRN1 is sequence non-specific in DNA binding, it has a defined DNA binding surface.
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| - | The Arabidopsis B3 domain protein VERNALIZATION1 is involved in processes essential for development with structural and mutational studies revealing its DNA binding surface.,King G, Chanson AH, McCallum EJ, Ohme-Takagi M, Byriel K, Hill JM, Martin JL, Mylne JS J Biol Chem. 2012 Dec 19. PMID:23255593<ref>PMID:23255593</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 4i1k" style="background-color:#fffaf0;"></div>
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| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Arath]] | + | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Byriel, K]] | + | [[Category: Large Structures]] |
| - | [[Category: Chanson, A H]] | + | [[Category: Byriel K]] |
| - | [[Category: Hill, J M]] | + | [[Category: Chanson AH]] |
| - | [[Category: King, G]] | + | [[Category: Hill JM]] |
| - | [[Category: Martin, J L]] | + | [[Category: King G]] |
| - | [[Category: McCallum, E J]] | + | [[Category: Martin JL]] |
| - | [[Category: Mylne, J S]] | + | [[Category: McCallum EJ]] |
| - | [[Category: Ohme-Takagi, M]] | + | [[Category: Mylne JS]] |
| - | [[Category: B3 domain beta-barrel]]
| + | [[Category: Ohme-Takagi M]] |
| - | [[Category: Dna binding protein]]
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