3u4s - Revision history

OCA at 10:17, 1 March 2024

OCA — Fri, 01 Mar 2024 10:17:08 GMT

←Older revision		Revision as of 10:17, 1 March 2024
Line 3:		Line 3:
	<StructureSection load='3u4s' size='340' side='right'caption='[[3u4s]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='3u4s' size='340' side='right'caption='[[3u4s]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3u4s]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U4S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U4S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3u4s]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U4S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U4S FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=08P:N~~-~~(CARBOXYCARBONYL)-D-CYSTEINE'>08P</scene>~~, ~~<scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <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]] 2.15Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~M3L~~:N-~~TRIMETHYLLYSINE~~'>~~M3L~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=08P:N-(CARBOXYCARBONYL)-D-CYSTEINE'>08P</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td><~~td class="sblockDat"><div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[2oq6\|2oq6]]~~</~~div~~><~~/td></tr>~~	+
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">JHDM3A, JMJD2, JMJD2A, KDM4A, KIAA0677 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=3u4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u4s OCA], [https://pdbe.org/3u4s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u4s RCSB], [https://www.ebi.ac.uk/pdbsum/3u4s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u4s 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=3u4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u4s OCA], [https://pdbe.org/3u4s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u4s RCSB], [https://www.ebi.ac.uk/pdbsum/3u4s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u4s ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/KDM4A_HUMAN KDM4A_HUMAN]] Histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. Participates in transcriptional repression of ASCL2 and E2F-responsive promoters via the recruitment of histone deacetylases and NCOR1, respectively.<ref>PMID:16024779</ref> <ref>PMID:16603238</ref> <ref>PMID:21694756</ref> Isoform 2: Crucial for muscle differentiation, promotes transcriptional activation of the Myog gene by directing the removal of repressive chromatin marks at its promoter. Lacks the N-terminal demethylase domain.<ref>PMID:16024779</ref> <ref>PMID:16603238</ref> <ref>PMID:21694756</ref>	+	[https://www.uniprot.org/uniprot/KDM4A_HUMAN KDM4A_HUMAN] Histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. Participates in transcriptional repression of ASCL2 and E2F-responsive promoters via the recruitment of histone deacetylases and NCOR1, respectively.<ref>PMID:16024779</ref> <ref>PMID:16603238</ref> <ref>PMID:21694756</ref> Isoform 2: Crucial for muscle differentiation, promotes transcriptional activation of the Myog gene by directing the removal of repressive chromatin marks at its promoter. Lacks the N-terminal demethylase domain.<ref>PMID:16024779</ref> <ref>PMID:16603238</ref> <ref>PMID:21694756</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Select an isoform: Linking of cosubstrate and substrate binding sites enables highly selective inhibiton of isoforms of human histone lysine demethylases. The results should provide a basis for the development of potent and selective JmjC inhibitors, possibly suitable for clinical use.	+
-		+
-	Linking of 2-Oxoglutarate and Substrate Binding Sites Enables Potent and Highly Selective Inhibition of JmjC Histone Demethylases.,Woon EC, Tumber A, Kawamura A, Hillringhaus L, Ge W, Rose NR, Ma JH, Chan MC, Walport LJ, Che KH, Ng SS, Marsden BD, Oppermann U, McDonough MA, Schofield CJ Angew Chem Int Ed Engl. 2012 Feb 13;51(7):1631-4. doi:, 10.1002/anie.201107833. Epub 2012 Jan 12. PMID:22241642<ref>PMID:22241642</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3u4s" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 28:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ma, J]]	+	[[Category: Ma J]]
-	[[Category: McDonough~~, M A~~]]	+	[[Category: McDonough MA]]
-	[[Category: Schofield~~, C J]]~~	+	[[Category: Schofield CJ]]
-	~~[[Category: Demethylase]]~~	+
-	~~[[Category: Double-stranded beta-helix]]~~	+
-	~~[[Category: Histone 3 tail]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Oxidoreductase-oxidoreductase substrate complex~~]]	+

OCA at 05:57, 13 July 2022

OCA — Wed, 13 Jul 2022 05:57:57 GMT

←Older revision		Revision as of 05:57, 13 July 2022
Line 1:		Line 1:

	==Histone Lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to N-oxalyl-D-cysteine==		==Histone Lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to N-oxalyl-D-cysteine==
-	<StructureSection load='3u4s' size='340' side='right' caption='[[3u4s]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='3u4s' size='340' side='right'caption='[[3u4s]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3u4s]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U4S OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3U4S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3u4s]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U4S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U4S FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=08P:N-(CARBOXYCARBONYL)-D-CYSTEINE'>08P</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=08P:N-(CARBOXYCARBONYL)-D-CYSTEINE'>08P</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2oq6\|2oq6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2oq6\|2oq6]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">JHDM3A, JMJD2, JMJD2A, KDM4A, KIAA0677 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">JHDM3A, JMJD2, JMJD2A, KDM4A, KIAA0677 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3u4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u4s OCA], [~~http~~://pdbe.org/3u4s PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3u4s RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3u4s PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3u4s 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=3u4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u4s OCA], [https://pdbe.org/3u4s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u4s RCSB], [https://www.ebi.ac.uk/pdbsum/3u4s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u4s ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/KDM4A_HUMAN KDM4A_HUMAN]] Histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. Participates in transcriptional repression of ASCL2 and E2F-responsive promoters via the recruitment of histone deacetylases and NCOR1, respectively.<ref>PMID:16024779</ref> <ref>PMID:16603238</ref> <ref>PMID:21694756</ref> Isoform 2: Crucial for muscle differentiation, promotes transcriptional activation of the Myog gene by directing the removal of repressive chromatin marks at its promoter. Lacks the N-terminal demethylase domain.<ref>PMID:16024779</ref> <ref>PMID:16603238</ref> <ref>PMID:21694756</ref>	+	[[https://www.uniprot.org/uniprot/KDM4A_HUMAN KDM4A_HUMAN]] Histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. Participates in transcriptional repression of ASCL2 and E2F-responsive promoters via the recruitment of histone deacetylases and NCOR1, respectively.<ref>PMID:16024779</ref> <ref>PMID:16603238</ref> <ref>PMID:21694756</ref> Isoform 2: Crucial for muscle differentiation, promotes transcriptional activation of the Myog gene by directing the removal of repressive chromatin marks at its promoter. Lacks the N-terminal demethylase domain.<ref>PMID:16024779</ref> <ref>PMID:16603238</ref> <ref>PMID:21694756</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Jumonji domain-containing protein\|Jumonji domain-containing protein]]	+	*[[Jumonji domain-containing protein 3D structures\|Jumonji domain-containing protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Ma, J]]		[[Category: Ma, J]]
	[[Category: McDonough, M A]]		[[Category: McDonough, M A]]

OCA at 21:57, 5 August 2016

OCA — Fri, 05 Aug 2016 21:57:17 GMT

←Older revision		Revision as of 21:57, 5 August 2016
Line 1:		Line 1:
		+
	==Histone Lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to N-oxalyl-D-cysteine==		==Histone Lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to N-oxalyl-D-cysteine==
	<StructureSection load='3u4s' size='340' side='right' caption='[[3u4s]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='3u4s' size='340' side='right' caption='[[3u4s]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3u4s]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U4S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3U4S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3u4s]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U4S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3U4S FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=08P:N-(CARBOXYCARBONYL)-D-CYSTEINE'>08P</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=08P:N-(CARBOXYCARBONYL)-D-CYSTEINE'>08P</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2oq6\|2oq6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2oq6\|2oq6]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">JHDM3A, JMJD2, JMJD2A, KDM4A, KIAA0677 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">JHDM3A, JMJD2, JMJD2A, KDM4A, KIAA0677 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3u4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u4s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3u4s RCSB], [http://www.ebi.ac.uk/pdbsum/3u4s PDBsum]</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=3u4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u4s OCA], [http://pdbe.org/3u4s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3u4s RCSB], [http://www.ebi.ac.uk/pdbsum/3u4s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3u4s ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3u4s" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Jumonji domain-containing protein\|Jumonji domain-containing protein]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Ma, J]]		[[Category: Ma, J]]
	[[Category: McDonough, M A]]		[[Category: McDonough, M A]]

OCA at 06:10, 25 December 2014

OCA — Thu, 25 Dec 2014 06:10:25 GMT

←Older revision		Revision as of 06:10, 25 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3u4s.~~png~~\|~~left~~\|~~200px~~]]	+	==Histone Lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to N-oxalyl-D-cysteine==
		+	<StructureSection load='3u4s' size='340' side='right' caption='[[3u4s]], [[Resolution\|resolution]] 2.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3u4s]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U4S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3U4S FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=08P:N-(CARBOXYCARBONYL)-D-CYSTEINE'>08P</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2oq6\|2oq6]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">JHDM3A, JMJD2, JMJD2A, KDM4A, KIAA0677 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3u4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u4s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3u4s RCSB], [http://www.ebi.ac.uk/pdbsum/3u4s PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KDM4A_HUMAN KDM4A_HUMAN]] Histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. Participates in transcriptional repression of ASCL2 and E2F-responsive promoters via the recruitment of histone deacetylases and NCOR1, respectively.<ref>PMID:16024779</ref> <ref>PMID:16603238</ref> <ref>PMID:21694756</ref> Isoform 2: Crucial for muscle differentiation, promotes transcriptional activation of the Myog gene by directing the removal of repressive chromatin marks at its promoter. Lacks the N-terminal demethylase domain.<ref>PMID:16024779</ref> <ref>PMID:16603238</ref> <ref>PMID:21694756</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Select an isoform: Linking of cosubstrate and substrate binding sites enables highly selective inhibiton of isoforms of human histone lysine demethylases. The results should provide a basis for the development of potent and selective JmjC inhibitors, possibly suitable for clinical use.

-	<!--	+	Linking of 2-Oxoglutarate and Substrate Binding Sites Enables Potent and Highly Selective Inhibition of JmjC Histone Demethylases.,Woon EC, Tumber A, Kawamura A, Hillringhaus L, Ge W, Rose NR, Ma JH, Chan MC, Walport LJ, Che KH, Ng SS, Marsden BD, Oppermann U, McDonough MA, Schofield CJ Angew Chem Int Ed Engl. 2012 Feb 13;51(7):1631-4. doi:, 10.1002/anie.201107833. Epub 2012 Jan 12. PMID:22241642<ref>PMID:22241642</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3u4s"~~, ~~creates the "Structure Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet)~~	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded~~),	+
-	~~or leave the SCENE parameter empty for the default display~~.	+
-	-->	+
-	~~{{STRUCTURE_3u4s\| PDB=3u4s \| SCENE= }}~~	+

-	~~===Histone Lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to N-oxalyl-D-cysteine===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_22241642}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 22241642 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_22241642}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3u4s]] is a 4 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U4S OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022241642<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Ma, J.]]	+	[[Category: Ma, J]]
-	[[Category: McDonough, M A.]]	+	[[Category: McDonough, M A]]
-	[[Category: Schofield, C J.]]	+	[[Category: Schofield, C J]]
	[[Category: Demethylase]]		[[Category: Demethylase]]
	[[Category: Double-stranded beta-helix]]		[[Category: Double-stranded beta-helix]]

OCA at 06:54, 22 February 2012

OCA — Wed, 22 Feb 2012 06:54:22 GMT

←Older revision		Revision as of 06:54, 22 February 2012
Line 1:		Line 1:
-	[[Image:3u4s.~~jpg~~\|left\|200px]]	+	[[Image:3u4s.png\|left\|200px]]

	<!--		<!--

OCA at 06:26, 8 February 2012

OCA — Wed, 08 Feb 2012 06:26:27 GMT

←Older revision		Revision as of 06:26, 8 February 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3u4s.jpg\|left\|200px]]

-	The ~~entry 3u4s~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3u4s", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3u4s\| PDB=3u4s \| SCENE= }}

-	~~Authors: Ma, J., McDonough, M.A., Schofield, C.J.~~	+	===Histone Lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to N-oxalyl-D-cysteine===

-	~~Description~~: ~~Histone Lysine demethylase JMJD2A in complex~~ with ~~T11C peptide substrate crosslinked to N~~-~~oxalyl~~-D-~~cysteine~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22241642}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22241642 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22241642}}
		+
		+	==About this Structure==
		+	[[3u4s]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U4S OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022241642</ref><references group="xtra"/>
		+	[[Category: Homo sapiens]]
		+	[[Category: Ma, J.]]
		+	[[Category: McDonough, M A.]]
		+	[[Category: Schofield, C J.]]
		+	[[Category: Demethylase]]
		+	[[Category: Double-stranded beta-helix]]
		+	[[Category: Histone 3 tail]]
		+	[[Category: Nucleus]]
		+	[[Category: Oxidoreductase-oxidoreductase substrate complex]]

OCA: Protected "3u4s" [edit=sysop:move=sysop]

OCA — Sun, 30 Oct 2011 08:51:04 GMT

Protected "3u4s" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:51, 30 October 2011

OCA: New page: '''Unreleased structure''' The entry 3u4s is ON HOLD Authors: Ma, J., McDonough, M.A., Schofield, C.J. Description: Histone Lysine demethylase JMJD2A in complex with T11C peptide subst...

OCA — Sun, 30 Oct 2011 08:51:03 GMT

New page: '''Unreleased structure''' The entry 3u4s is ON HOLD Authors: Ma, J., McDonough, M.A., Schofield, C.J. Description: Histone Lysine demethylase JMJD2A in complex with T11C peptide subst...

New page

'''Unreleased structure'''

The entry 3u4s is ON HOLD

Authors: Ma, J., McDonough, M.A., Schofield, C.J.

Description: Histone Lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to N-oxalyl-D-cysteine