4v2w - Revision history

OCA at 10:39, 10 January 2024

OCA — Wed, 10 Jan 2024 10:39:43 GMT

←Older revision		Revision as of 10:39, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4v2w]] is a 3 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=4V2W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4V2W FirstGlance]. <br>		<table><tr><td colspan='2'>[[4v2w]] is a 3 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=4V2W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4V2W FirstGlance]. <br>
-	</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>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</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]] 1.81Å</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>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=4v2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v2w OCA], [https://pdbe.org/4v2w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4v2w RCSB], [https://www.ebi.ac.uk/pdbsum/4v2w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4v2w 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=4v2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v2w OCA], [https://pdbe.org/4v2w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4v2w RCSB], [https://www.ebi.ac.uk/pdbsum/4v2w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4v2w ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:00, 29 March 2023

OCA — Wed, 29 Mar 2023 08:00:45 GMT

←Older revision		Revision as of 08:00, 29 March 2023
Line 1:		Line 1:

	==JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (16-35)==		==JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (16-35)==
-	<StructureSection load='4v2w' size='340' side='right' caption='[[4v2w]], [[Resolution\|resolution]] 1.81Å' scene=''>	+	<StructureSection load='4v2w' size='340' side='right'caption='[[4v2w]], [[Resolution\|resolution]] 1.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4v2w]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens~~] and [http://en.wikipedia.org/wiki/Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V2W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4V2W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4v2w]] is a 3 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=4V2W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4V2W 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>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4v2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v2w OCA], [https://pdbe.org/4v2w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4v2w RCSB], [https://www.ebi.ac.uk/pdbsum/4v2w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4v2w ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4v2v\|4v2v]]~~</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=4v2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v2w OCA], [~~http~~://pdbe.org/4v2w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4v2w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4v2w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4v2w 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> [[http://www.uniprot.org/uniprot/H31T_HUMAN H31T_HUMAN]] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.	+	[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/>
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	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: ~~Human~~]]	+	[[Category: Large Structures]]
-	[[Category: Chowdhury, R]]	+	[[Category: Chowdhury R]]
-	[[Category: Schofield~~, C J~~]]	+	[[Category: Schofield CJ]]
-	[[Category: Zafred, D]]	+	[[Category: Zafred D]]
-	~~[[Category: 2-oxoglutarate]]~~	+
-	~~[[Category: Chromatin regulator]]~~	+
-	~~[[Category: Demethylase]]~~	+
-	~~[[Category: Dioxygenase]]~~	+
-	~~[[Category: Double-stranded beta helix]]~~	+
-	~~[[Category: Dsbh]]~~	+
-	~~[[Category: Epigenetic and transcription regulation]]~~	+
-	~~[[Category: Facial triad]]~~	+
-	~~[[Category: Histone]]~~	+
-	~~[[Category: Hydroxylation]]~~	+
-	~~[[Category: Iron]]~~	+
-	~~[[Category: Jmjc domain]]~~	+
-	~~[[Category: Jmjd2a]]~~	+
-	~~[[Category: Metal binding protein]]~~	+
-	~~[[Category: Non-heme]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Oxygenase~~]]	+

OCA at 08:12, 6 March 2019

OCA — Wed, 06 Mar 2019 08:12:20 GMT

←Older revision		Revision as of 08:12, 6 March 2019
Line 1:		Line 1:

	==JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (16-35)==		==JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (16-35)==
-	<StructureSection load='4v2w' size='340' side='right' caption='[[4v2w]], [[Resolution\|resolution]] 1.81Å' scene=''>	+	<StructureSection load='4v2w' size='340' side='right' caption='[[4v2w]], [[Resolution\|resolution]] 1.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4v2w]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V2W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V2W FirstGlance]. <br>		<table><tr><td colspan='2'>[[4v2w]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V2W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V2W FirstGlance]. <br>

OCA at 09:16, 30 January 2019

OCA — Wed, 30 Jan 2019 09:16:10 GMT

←Older revision		Revision as of 09:16, 30 January 2019
Line 3:		Line 3:
	<StructureSection load='4v2w' size='340' side='right' caption='[[4v2w]], [[Resolution\|resolution]] 1.81Å' scene=''>		<StructureSection load='4v2w' size='340' side='right' caption='[[4v2w]], [[Resolution\|resolution]] 1.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4v2w]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V2W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V2W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4v2w]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V2W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V2W 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>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</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>
Line 28:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
		+	[[Category: Human]]
	[[Category: Chowdhury, R]]		[[Category: Chowdhury, R]]
	[[Category: Schofield, C J]]		[[Category: Schofield, C J]]

OCA at 01:22, 19 January 2017

OCA — Thu, 19 Jan 2017 01:22:40 GMT

←Older revision		Revision as of 01:22, 19 January 2017
Line 1:		Line 1:
		+
	==JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (16-35)==		==JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (16-35)==
	<StructureSection load='4v2w' size='340' side='right' caption='[[4v2w]], [[Resolution\|resolution]] 1.81Å' scene=''>		<StructureSection load='4v2w' size='340' side='right' caption='[[4v2w]], [[Resolution\|resolution]] 1.81Å' scene=''>
Line 6:		Line 7:
	<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">[[4v2v\|4v2v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4v2v\|4v2v]]</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=4v2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v2w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4v2w RCSB], [http://www.ebi.ac.uk/pdbsum/4v2w 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=4v2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v2w OCA], [http://pdbe.org/4v2w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4v2w RCSB], [http://www.ebi.ac.uk/pdbsum/4v2w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4v2w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 4v2w" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Jumonji domain-containing protein\|Jumonji domain-containing protein]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:30, 12 February 2015

OCA — Thu, 12 Feb 2015 06:30:59 GMT

←Older revision		Revision as of 06:30, 12 February 2015
Line 10:		Line 10:
	== 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> [[http://www.uniprot.org/uniprot/H31T_HUMAN H31T_HUMAN]] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.		[[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> [[http://www.uniprot.org/uniprot/H31T_HUMAN H31T_HUMAN]] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The JmjC-domain-containing 2-oxoglutarate-dependent oxygenases catalyze protein hydroxylation and N()-methyllysine demethylation via hydroxylation. A subgroup of this family, the JmjC lysine demethylases (JmjC KDMs) are involved in histone modifications at multiple sites. There are conflicting reports as to the substrate selectivity of some JmjC oxygenases with respect to KDM activities. In this study, a panel of modified histone H3 peptides was tested for demethylation against 15 human JmjC-domain-containing proteins. The results largely confirmed known N()-methyllysine substrates. However, the purified KDM4 catalytic domains showed greater substrate promiscuity than previously reported (i.e., KDM4A was observed to catalyze demethylation at H3K27 as well as H3K9/K36). Crystallographic analyses revealed that the N()-methyllysine of an H3K27me3 peptide binds similarly to N()-methyllysines of H3K9me3/H3K36me3 with KDM4A. A subgroup of JmjC proteins known to catalyze hydroxylation did not display demethylation activity. Overall, the results reveal that the catalytic domains of the KDM4 enzymes may be less selective than previously identified. They also draw a distinction between the N()-methyllysine demethylation and hydroxylation activities within the JmjC subfamily. These results will be of use to those working on functional studies of the JmjC enzymes.
		+
		+	Studies on the catalytic domains of multiple JmjC oxygenases using peptide substrates.,Williams ST, Walport LJ, Hopkinson RJ, Madden SK, Chowdhury R, Schofield CJ, Kawamura A Epigenetics. 2014 Dec 2;9(12):1596-603. doi: 10.4161/15592294.2014.983381. PMID:25625844<ref>PMID:25625844</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:31, 24 December 2014

OCA — Wed, 24 Dec 2014 11:31:55 GMT

←Older revision		Revision as of 11:31, 24 December 2014
Line 8:		Line 8:
	<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=4v2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v2w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4v2w RCSB], [http://www.ebi.ac.uk/pdbsum/4v2w 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=4v2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v2w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4v2w RCSB], [http://www.ebi.ac.uk/pdbsum/4v2w PDBsum]</span></td></tr>
	</table>		</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> [[http://www.uniprot.org/uniprot/H31T_HUMAN H31T_HUMAN]] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:18, 26 November 2014

OCA — Wed, 26 Nov 2014 08:18:20 GMT

←Older revision		Revision as of 08:18, 26 November 2014
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (16-35)==
-		+	<StructureSection load='4v2w' size='340' side='right' caption='[[4v2w]], [[Resolution\|resolution]] 1.81Å' scene=''>
-	~~The entry~~ 4v2w is ~~ON HOLD~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4v2w]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V2W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V2W FirstGlance]. <br>
-	~~Authors~~: ~~CHOWDHURY~~, R., ~~Zafred~~, D., ~~SCHOFIELD~~, C.J.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</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>
-	~~Description~~: ~~JMJD2A COMPLEXED WITH NI(II)~~, ~~NOG AND HISTONE H3K27me3 PEPTIDE (16~~-~~35)~~	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4v2v\|4v2v]]</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=4v2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v2w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4v2w RCSB], [http://www.ebi.ac.uk/pdbsum/4v2w PDBsum]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Homo sapiens]]
		+	[[Category: Chowdhury, R]]
		+	[[Category: Schofield, C J]]
		+	[[Category: Zafred, D]]
		+	[[Category: 2-oxoglutarate]]
		+	[[Category: Chromatin regulator]]
		+	[[Category: Demethylase]]
		+	[[Category: Dioxygenase]]
		+	[[Category: Double-stranded beta helix]]
		+	[[Category: Dsbh]]
		+	[[Category: Epigenetic and transcription regulation]]
		+	[[Category: Facial triad]]
		+	[[Category: Histone]]
		+	[[Category: Hydroxylation]]
		+	[[Category: Iron]]
		+	[[Category: Jmjc domain]]
		+	[[Category: Jmjd2a]]
		+	[[Category: Metal binding protein]]
		+	[[Category: Non-heme]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Oxygenase]]

OCA: Protected "4v2w" [edit=sysop:move=sysop]

OCA — Wed, 22 Oct 2014 10:04:34 GMT

Protected "4v2w" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:04, 22 October 2014

OCA: New page: '''Unreleased structure''' The entry 4v2w is ON HOLD Authors: CHOWDHURY, R., Zafred, D., SCHOFIELD, C.J. Description: JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (16...

OCA — Wed, 22 Oct 2014 10:04:33 GMT

New page: '''Unreleased structure''' The entry 4v2w is ON HOLD Authors: CHOWDHURY, R., Zafred, D., SCHOFIELD, C.J. Description: JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (16...

New page

'''Unreleased structure'''

The entry 4v2w is ON HOLD

Authors: CHOWDHURY, R., Zafred, D., SCHOFIELD, C.J.

Description: JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (16-35)