5vah - Revision history

OCA at 13:44, 4 October 2023

2023-10-04T13:44:55Z

←Older revision		Revision as of 13:44, 4 October 2023
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	<StructureSection load='5vah' size='340' side='right'caption='[[5vah]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='5vah' size='340' side='right'caption='[[5vah]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vah]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VAH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5VAH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vah]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] and [https://en.wikipedia.org/wiki/Ricinus_communis Ricinus communis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VAH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VAH FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SAH:S~~-~~ADENOSYL-L-HOMOCYSTEINE'>SAH</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=DA2:NG,NG-DIMETHYL-L-ARGININE'>DA2</scene>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DA2:NG,NG-DIMETHYL-L-ARGININE'>DA2</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vac\|5vac]]~~, ~~[[5vab\|5vab]]~~<~~/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=5vah FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vah OCA], [https://pdbe.org/5vah PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vah RCSB], [https://www.ebi.ac.uk/pdbsum/5vah PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vah 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~~://proteopedia.org/fgij/fg.htm?mol=5vah FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vah OCA], [~~http~~://pdbe.org/5vah PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vah RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vah PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vah ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ATXR5_RICCO ATXR5_RICCO]] Histone methyltransferase that specifically monomethylates 'Lys-37' of histone H3 (H3K27me1). Has much higher activity on nucleosomes containing H3.1 than H3.3. Involved in the formation of constitutive heterochromatin and the silencing of heterochromatic elements (By similarity).	+	[https://www.uniprot.org/uniprot/ATXR5_RICCO ATXR5_RICCO] Histone methyltransferase that specifically monomethylates 'Lys-37' of histone H3 (H3K27me1). Has much higher activity on nucleosomes containing H3.1 than H3.3. Involved in the formation of constitutive heterochromatin and the silencing of heterochromatic elements (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Histone-lysine N-methyltransferase~~]]	+	[[Category: Arabidopsis thaliana]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bergamin, E]]	+	[[Category: Ricinus communis]]
-	[[Category: Blais, A]]	+	[[Category: Bergamin E]]
-	[[Category: Brunzelle~~, J S~~]]	+	[[Category: Blais A]]
-	[[Category: Couture, J F]]	+	[[Category: Brunzelle JS]]
-	[[Category: Eram, M]]	+	[[Category: Couture J-F]]
-	[[Category: Joshi, M]]	+	[[Category: Eram M]]
-	[[Category: Malette, J]]	+	[[Category: Joshi M]]
-	[[Category: Michaels~~, S D~~]]	+	[[Category: Malette J]]
-	[[Category: Mongeon, V]]	+	[[Category: Michaels SD]]
-	[[Category: Sarvan, S]]	+	[[Category: Mongeon V]]
-	[[Category: Vedadi, M]]	+	[[Category: Sarvan S]]
-	[[Category: Yeung, S]]	+	[[Category: Vedadi M]]
-	~~[[Category: Histone]]~~	+	[[Category: Yeung S]]
-	~~[[Category: Methyltransferase]]~~	+
-	~~[[Category: Nucleosome]]~~	+
-	~~[[Category: Transferase-dna binding protein complex~~]]	+

OCA at 08:33, 30 September 2020

2020-09-30T08:33:46Z

←Older revision		Revision as of 08:33, 30 September 2020
Line 1:		Line 1:

	==Crystal structure of ATXR5 SET domain in complex with histone H3 di-methylated on R26==		==Crystal structure of ATXR5 SET domain in complex with histone H3 di-methylated on R26==
-	<StructureSection load='5vah' size='340' side='right' caption='[[5vah]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='5vah' size='340' side='right'caption='[[5vah]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vah]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VAH OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VAH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vah]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VAH OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5VAH FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DA2:NG,NG-DIMETHYL-L-ARGININE'>DA2</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DA2:NG,NG-DIMETHYL-L-ARGININE'>DA2</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vac\|5vac]], [[5vab\|5vab]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vac\|5vac]], [[5vab\|5vab]]</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='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=5vah FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vah OCA], [http://pdbe.org/5vah PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vah RCSB], [http://www.ebi.ac.uk/pdbsum/5vah PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vah ProSAT]</span></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=5vah FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vah OCA], [http://pdbe.org/5vah PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vah RCSB], [http://www.ebi.ac.uk/pdbsum/5vah PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vah ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 26:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Histone-lysine N-methyltransferase]]		[[Category: Histone-lysine N-methyltransferase]]
		+	[[Category: Large Structures]]
	[[Category: Bergamin, E]]		[[Category: Bergamin, E]]
	[[Category: Blais, A]]		[[Category: Blais, A]]

OCA at 06:12, 19 April 2017

2017-04-19T06:12:18Z

←Older revision		Revision as of 06:12, 19 April 2017
Line 12:		Line 12:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/ATXR5_RICCO ATXR5_RICCO]] Histone methyltransferase that specifically monomethylates 'Lys-37' of histone H3 (H3K27me1). Has much higher activity on nucleosomes containing H3.1 than H3.3. Involved in the formation of constitutive heterochromatin and the silencing of heterochromatic elements (By similarity).		[[http://www.uniprot.org/uniprot/ATXR5_RICCO ATXR5_RICCO]] Histone methyltransferase that specifically monomethylates 'Lys-37' of histone H3 (H3K27me1). Has much higher activity on nucleosomes containing H3.1 than H3.3. Involved in the formation of constitutive heterochromatin and the silencing of heterochromatic elements (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In plants, the histone H3.1 lysine 27 (H3K27) mono-methyltransferases ARABIDOPSIS TRITHORAX RELATED PROTEIN 5 and 6 (ATXR5/6) regulate heterochromatic DNA replication and genome stability. Our initial studies showed that ATXR5/6 discriminate between histone H3 variants and preferentially methylate K27 on H3.1. In this study, we report three regulatory mechanisms contributing to the specificity of ATXR5/6. First, we show that ATXR5 preferentially methylates the R/F-K*-S/C-G/A-P/C motif with striking preference for hydrophobic and aromatic residues in positions flanking this core of five amino acids. Second, we demonstrate that post-transcriptional modifications of residues neighboring K27 that are typically associated with actively transcribed chromatin are detrimental to ATXR5 activity. Third, we show that ATXR5 PHD domain employs a narrow binding pocket to selectively recognize unmethylated K4 of histone H3. Finally, we demonstrate that deletion or mutation of the PHD domain reduces the catalytic efficiency (kcat/Km of AdoMet) of ATXR5 up to 58-fold, highlighting the multifunctional nature of ATXR5 PHD domain. Overall, our results suggest that several molecular determinants regulate ATXR5/6 methyltransferase activity and epigenetic inheritance of H3.1 K27me1 mark in plants.
		+
		+	Molecular basis for the methylation specificity of ATXR5 for histone H3.,Bergamin E, Sarvan S, Malette J, Eram MS, Yeung S, Mongeon V, Joshi M, Brunzelle JS, Michaels SD, Blais A, Vedadi M, Couture JF Nucleic Acids Res. 2017 Apr 5. doi: 10.1093/nar/gkx224. PMID:28383693<ref>PMID:28383693</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5vah" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA: Protected "5vah" [edit=sysop:move=sysop]

2017-04-05T13:32:10Z

Protected "5vah" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:32, 5 April 2017

OCA: New page: ==Crystal structure of ATXR5 SET domain in complex with histone H3 di-methylated on R26== == Structural highlights ==
<table><tr><td colspan='2'>[[5vah]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VAH OCA]. For a guided tour on the structure components use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VAH FirstGlance]. 
</td></tr><tr id='ligand'><td class="sblockLbl">[[Ligand|Ligands:]]</td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl">[[Non-Standard_Residue|NonStd Res:]]</td><td class="sblockDat"><scene name='pdbligand=DA2:NG,NG-DIMETHYL-L-ARGININE'>DA2</scene></td></tr>
<tr id='related'><td class="sblockLbl">[[Related_structure|Related:]]</td><td class="sblockDat">[[5vac|5vac]], [[5vab|5vab]]</td></tr>
<tr id='activity'><td class="sblockLbl">Activity:</td><td class="sblockDat">[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] </td></tr>
<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5vah FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vah OCA], [http://pdbe.org/5vah PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vah RCSB], [http://www.ebi.ac.uk/pdbsum/5vah PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vah ProSAT]</td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/ATXR5_RICCO ATXR5_RICCO]] Histone methyltransferase that specifically monomethylates 'Lys-37' of histone H3 (H3K27me1). Has much higher activity on nucleosomes containing H3.1 than H3.3. Involved in the formation of constitutive heterochromatin and the silencing of heterochromatic elements (By similarity).
TOC
</StructureSection>
[[Category: Histone-lysine N-methyltransferase]]
[[Category: Bergamin, E]]
[[Category: Blais, A]]
[[Category: Brunzelle, J S]]
[[Category: Couture, J F]]
[[Category: Eram, M]]
[[Category: Joshi, M]]
[[Category: Malette, J]]
[[Category: Michaels, S D]]
[[Category: Mongeon, V]]
[[Category: Sarvan, S]]
[[Category: Vedadi, M]]
[[Category: Yeung, S]]
[[Category: Histone]]
[[Category: Methyltransferase]]
[[Category: Nucleosome]]
[[Category: Transferase-dna binding protein complex]]