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| | ==Crystal structure of Arabidopsis thaliana SUVH6 in complex with methylated DNA== | | ==Crystal structure of Arabidopsis thaliana SUVH6 in complex with methylated DNA== |
| - | <StructureSection load='6a5n' size='340' side='right' caption='[[6a5n]], [[Resolution|resolution]] 2.40Å' scene=''> | + | <StructureSection load='6a5n' size='340' side='right'caption='[[6a5n]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6a5n]] is a 3 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=6A5N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A5N FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6a5n]] is a 3 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=6A5N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A5N FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.4Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SUVH6, SDG23, SET23, At2g22740, T9I22.18 ([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=6a5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a5n OCA], [https://pdbe.org/6a5n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a5n RCSB], [https://www.ebi.ac.uk/pdbsum/6a5n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a5n ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone-lysine_N-methyltransferase Histone-lysine N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.43 2.1.1.43] </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=6a5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a5n OCA], [http://pdbe.org/6a5n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a5n RCSB], [http://www.ebi.ac.uk/pdbsum/6a5n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a5n ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/SUVH6_ARATH SUVH6_ARATH]] Histone methyltransferase. Methylates 'Lys-9' of histone H3. H3 'Lys-9' methylation represents a specific tag for epigenetic transcriptional repression. Seems to act preferentially on dsMRNA.<ref>PMID:15014946</ref> <ref>PMID:16287862</ref> | + | [https://www.uniprot.org/uniprot/SUVH6_ARATH SUVH6_ARATH] Histone methyltransferase. Methylates 'Lys-9' of histone H3. H3 'Lys-9' methylation represents a specific tag for epigenetic transcriptional repression. Seems to act preferentially on dsMRNA.<ref>PMID:15014946</ref> <ref>PMID:16287862</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6a5n" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6a5n" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Histone methyltransferase 3D structures|Histone methyltransferase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Arath]] | + | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Histone-lysine N-methyltransferase]] | + | [[Category: Large Structures]] |
| - | [[Category: Du, J]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Li, X]] | + | [[Category: Du J]] |
| - | [[Category: Dna methylation]] | + | [[Category: Li X]] |
| - | [[Category: Gene regulation]]
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| - | [[Category: Gene regulation-dna complex]]
| + | |
| - | [[Category: Histone methyltransferase]]
| + | |
| - | [[Category: Set]]
| + | |
| - | [[Category: Sra]]
| + | |
| Structural highlights
Function
SUVH6_ARATH Histone methyltransferase. Methylates 'Lys-9' of histone H3. H3 'Lys-9' methylation represents a specific tag for epigenetic transcriptional repression. Seems to act preferentially on dsMRNA.[1] [2]
Publication Abstract from PubMed
DNA methylation functions in gene silencing and the maintenance of genome integrity. In plants, non-CG DNA methylation is linked through a self-reinforcing loop with histone 3 lysine 9 dimethylation (H3K9me2). The plant-specific SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG (SUVH) family H3K9 methyltransferases (MTases) bind to DNA methylation marks and catalyze H3K9 methylation. Here, we analyzed the structure and function of Arabidopsis thaliana SUVH6 to understand how this class of enzyme maintains methylation patterns in the genome. We reveal that SUVH6 has a distinct 5-methyl-dC (5mC) base-flipping mechanism involving a thumb loop element. Autoinhibition of H3 substrate entry is regulated by a SET domain loop, and a conformational transition in the post-SET domain upon cofactor binding may control catalysis. In vitro DNA binding and in vivo ChIP-seq data reveal that the different SUVH family H3K9 MTases have distinct DNA binding preferences, targeting H3K9 methylation to sites with different methylated DNA sequences, explaining the context biased non-CG DNA methylation in plants.
Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation.,Li X, Harris CJ, Zhong Z, Chen W, Liu R, Jia B, Wang Z, Li S, Jacobsen SE, Du J Proc Natl Acad Sci U S A. 2018 Sep 11;115(37):E8793-E8802. doi:, 10.1073/pnas.1809841115. Epub 2018 Aug 27. PMID:30150382[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Jackson JP, Johnson L, Jasencakova Z, Zhang X, PerezBurgos L, Singh PB, Cheng X, Schubert I, Jenuwein T, Jacobsen SE. Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma. 2004 Mar;112(6):308-15. doi: 10.1007/s00412-004-0275-7. Epub 2004 Mar, 10. PMID:15014946 doi:http://dx.doi.org/10.1007/s00412-004-0275-7
- ↑ Ebbs ML, Bartee L, Bender J. H3 lysine 9 methylation is maintained on a transcribed inverted repeat by combined action of SUVH6 and SUVH4 methyltransferases. Mol Cell Biol. 2005 Dec;25(23):10507-15. PMID:16287862 doi:http://dx.doi.org/10.1128/MCB.25.23.10507-10515.2005
- ↑ Li X, Harris CJ, Zhong Z, Chen W, Liu R, Jia B, Wang Z, Li S, Jacobsen SE, Du J. Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation. Proc Natl Acad Sci U S A. 2018 Sep 11;115(37):E8793-E8802. doi:, 10.1073/pnas.1809841115. Epub 2018 Aug 27. PMID:30150382 doi:http://dx.doi.org/10.1073/pnas.1809841115
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