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| | ==Crystal structure of VAL1 B3 domain in complex with cognate DNA== | | ==Crystal structure of VAL1 B3 domain in complex with cognate DNA== |
| - | <StructureSection load='6fas' size='340' side='right' caption='[[6fas]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='6fas' size='340' side='right'caption='[[6fas]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6fas]] is a 6 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=6FAS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FAS FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6fas]] is a 6 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=6FAS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6FAS FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</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]] 1.9Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VAL1, HSI2, At2g30470, T6B20.17 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene></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=6fas FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fas OCA], [http://pdbe.org/6fas PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6fas RCSB], [http://www.ebi.ac.uk/pdbsum/6fas PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6fas ProSAT]</span></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=6fas FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fas OCA], [https://pdbe.org/6fas PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6fas RCSB], [https://www.ebi.ac.uk/pdbsum/6fas PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6fas ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/VAL1_ARATH VAL1_ARATH]] Transcriptional repressor of gene expression involved in embryonic pathways, such as LEC1, ABI3, and FUS3. Repressor of the sugar-inducible genes involved in the seed maturation program in seedlings. Plays an essential role in regulating the transition from seed maturation to seedling growth. Functionally redundant with VAL2/HSL1.<ref>PMID:15894743</ref> <ref>PMID:17158584</ref> <ref>PMID:17267611</ref> | + | [https://www.uniprot.org/uniprot/VAL1_ARATH VAL1_ARATH] Transcriptional repressor of gene expression involved in embryonic pathways, such as LEC1, ABI3, and FUS3. Repressor of the sugar-inducible genes involved in the seed maturation program in seedlings. Plays an essential role in regulating the transition from seed maturation to seedling growth. Functionally redundant with VAL2/HSL1.<ref>PMID:15894743</ref> <ref>PMID:17158584</ref> <ref>PMID:17267611</ref> |
| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed ==
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| - | Arabidopsis thaliana requires a prolonged period of cold exposure during winter to initiate flowering in a process termed vernalization. Exposure to cold induces epigenetic silencing of the FLOWERING LOCUS C (FLC) gene by Polycomb group (PcG) proteins. A key role in this epigenetic switch is played by transcriptional repressors VAL1 and VAL2, which specifically recognize Sph/RY DNA sequences within FLC via B3 DNA binding domains, and mediate recruitment of PcG silencing machinery. To understand the structural mechanism of site-specific DNA recognition by VAL1, we have solved the crystal structure of VAL1 B3 domain (VAL1-B3) bound to a 12 bp oligoduplex containing the canonical Sph/RY DNA sequence 5'-CATGCA-3'/5'-TGCATG-3'. We find that VAL1-B3 makes H-bonds and van der Waals contacts to DNA bases of all six positions of the canonical Sph/RY element. In agreement with the structure, in vitro DNA binding studies show that VAL1-B3 does not tolerate substitutions at any position of the 5'-TGCATG-3' sequence. The VAL1-B3-DNA structure presented here provides a structural model for understanding the specificity of plant B3 domains interacting with the Sph/RY and other DNA sequences.
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| - | Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1.,Sasnauskas G, Kauneckaite K, Siksnys V Nucleic Acids Res. 2018 Apr 6. pii: 4962483. doi: 10.1093/nar/gky256. PMID:29660015<ref>PMID:29660015</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 6fas" style="background-color:#fffaf0;"></div>
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| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Arath]] | + | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Sasnauskas, G]] | + | [[Category: Large Structures]] |
| - | [[Category: B3 dna binding domain]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Complex]] | + | [[Category: Sasnauskas G]] |
| - | [[Category: Dna binding protein]]
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| - | [[Category: Epigenome reader]]
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| - | [[Category: Specific dna recognition]]
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| - | [[Category: Sph/ry sequence]]
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| - | [[Category: Val1 transcriptional regulator]]
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