3pua - Revision history

OCA at 10:01, 6 September 2023

2023-09-06T10:01:19Z

←Older revision		Revision as of 10:01, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3pua' size='340' side='right'caption='[[3pua]], [[Resolution\|resolution]] 1.89Å' scene=''>		<StructureSection load='3pua' size='340' side='right'caption='[[3pua]], [[Resolution\|resolution]] 1.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3pua]] is a 1 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=3PUA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PUA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3pua]] is a 1 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=3PUA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PUA 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</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]] 1.89Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ptr\|3ptr]], [[3pu3\|3pu3]], [[3pu8\|3pu8]]</div></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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PHF2, KIAA0662 ([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=3pua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pua OCA], [https://pdbe.org/3pua PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pua RCSB], [https://www.ebi.ac.uk/pdbsum/3pua PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pua 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=3pua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pua OCA], [https://pdbe.org/3pua PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pua RCSB], [https://www.ebi.ac.uk/pdbsum/3pua PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pua ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PHF2_HUMAN PHF2_HUMAN]] Lysine demethylase that demethylates both histones and non-histone proteins. Enzymatically inactive by itself, and becomes active following phosphorylation by PKA: forms a complex with ARID5B and mediates demethylation of methylated ARID5B. Demethylation of ARID5B leads to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. PHF2 is recruited to trimethylated 'Lys-4' of histone H3 (H3K4me3) at rDNA promoters and promotes expression of rDNA.<ref>PMID:21532585</ref> <ref>PMID:20129925</ref> <ref>PMID:21167174</ref>	+	[https://www.uniprot.org/uniprot/PHF2_HUMAN PHF2_HUMAN] Lysine demethylase that demethylates both histones and non-histone proteins. Enzymatically inactive by itself, and becomes active following phosphorylation by PKA: forms a complex with ARID5B and mediates demethylation of methylated ARID5B. Demethylation of ARID5B leads to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. PHF2 is recruited to trimethylated 'Lys-4' of histone H3 (H3K4me3) at rDNA promoters and promotes expression of rDNA.<ref>PMID:21532585</ref> <ref>PMID:20129925</ref> <ref>PMID:21167174</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cheng, X]]	+	[[Category: Cheng X]]
-	[[Category: Hashimoto, H]]	+	[[Category: Hashimoto H]]
-	[[Category: Horton~~, J R~~]]	+	[[Category: Horton JR]]
-	[[Category: Upadhyay~~, A K~~]]	+	[[Category: Upadhyay AK]]
-	[[Category: Zhang, X]]	+	[[Category: Zhang X]]
-	~~[[Category: Alpha-ketoglutarate-fe2+ dependent dioxygenase]]~~	+
-	~~[[Category: Histone tail binding protein]]~~	+
-	~~[[Category: Protein binding~~]]	+

OCA at 08:55, 25 May 2022

2022-05-25T08:55:07Z

←Older revision		Revision as of 08:55, 25 May 2022
Line 1:		Line 1:

	==PHF2 Jumonji-NOG-Ni(II)==		==PHF2 Jumonji-NOG-Ni(II)==
-	<StructureSection load='3pua' size='340' side='right' caption='[[3pua]], [[Resolution\|resolution]] 1.89Å' scene=''>	+	<StructureSection load='3pua' size='340' side='right'caption='[[3pua]], [[Resolution\|resolution]] 1.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3pua]] is a 1 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=3PUA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3PUA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3pua]] is a 1 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=3PUA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PUA 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ptr\|3ptr]], [[3pu3\|3pu3]], [[3pu8\|3pu8]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ptr\|3ptr]], [[3pu3\|3pu3]], [[3pu8\|3pu8]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PHF2, KIAA0662 ([~~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">PHF2, KIAA0662 ([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=3pua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pua OCA], [~~http~~://pdbe.org/3pua PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3pua RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3pua PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3pua 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=3pua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pua OCA], [https://pdbe.org/3pua PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pua RCSB], [https://www.ebi.ac.uk/pdbsum/3pua PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pua ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PHF2_HUMAN PHF2_HUMAN]] Lysine demethylase that demethylates both histones and non-histone proteins. Enzymatically inactive by itself, and becomes active following phosphorylation by PKA: forms a complex with ARID5B and mediates demethylation of methylated ARID5B. Demethylation of ARID5B leads to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. PHF2 is recruited to trimethylated 'Lys-4' of histone H3 (H3K4me3) at rDNA promoters and promotes expression of rDNA.<ref>PMID:21532585</ref> <ref>PMID:20129925</ref> <ref>PMID:21167174</ref>	+	[[https://www.uniprot.org/uniprot/PHF2_HUMAN PHF2_HUMAN]] Lysine demethylase that demethylates both histones and non-histone proteins. Enzymatically inactive by itself, and becomes active following phosphorylation by PKA: forms a complex with ARID5B and mediates demethylation of methylated ARID5B. Demethylation of ARID5B leads to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. PHF2 is recruited to trimethylated 'Lys-4' of histone H3 (H3K4me3) at rDNA promoters and promotes expression of rDNA.<ref>PMID:21532585</ref> <ref>PMID:20129925</ref> <ref>PMID:21167174</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Cheng, X]]		[[Category: Cheng, X]]
	[[Category: Hashimoto, H]]		[[Category: Hashimoto, H]]

OCA at 15:03, 5 August 2016

2016-08-05T15:03:40Z

←Older revision		Revision as of 15:03, 5 August 2016
Line 1:		Line 1:
		+
	==PHF2 Jumonji-NOG-Ni(II)==		==PHF2 Jumonji-NOG-Ni(II)==
	<StructureSection load='3pua' size='340' side='right' caption='[[3pua]], [[Resolution\|resolution]] 1.89Å' scene=''>		<StructureSection load='3pua' size='340' side='right' caption='[[3pua]], [[Resolution\|resolution]] 1.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3pua]] is a 1 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=3PUA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PUA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3pua]] is a 1 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=3PUA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PUA 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ptr\|3ptr]], [[3pu3\|3pu3]], [[3pu8\|3pu8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ptr\|3ptr]], [[3pu3\|3pu3]], [[3pu8\|3pu8]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PHF2, KIAA0662 ([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">PHF2, KIAA0662 ([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=3pua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pua OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pua RCSB], [http://www.ebi.ac.uk/pdbsum/3pua 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=3pua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pua OCA], [http://pdbe.org/3pua PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3pua RCSB], [http://www.ebi.ac.uk/pdbsum/3pua PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3pua 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 3pua" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Cheng, X]]		[[Category: Cheng, X]]
	[[Category: Hashimoto, H]]		[[Category: Hashimoto, H]]

OCA at 19:47, 25 December 2014

2014-12-25T19:47:34Z

←Older revision		Revision as of 19:47, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3pua]] is a 1 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=3PUA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PUA FirstGlance]. <br>		<table><tr><td colspan='2'>[[3pua]] is a 1 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=3PUA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PUA FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene><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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ptr\|3ptr]], [[3pu3\|3pu3]], [[3pu8\|3pu8]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ptr\|3ptr]], [[3pu3\|3pu3]], [[3pu8\|3pu8]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PHF2, KIAA0662 ([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">PHF2, KIAA0662 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3pua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pua OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pua RCSB], [http://www.ebi.ac.uk/pdbsum/3pua 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=3pua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pua OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pua RCSB], [http://www.ebi.ac.uk/pdbsum/3pua PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PHF2_HUMAN PHF2_HUMAN]] Lysine demethylase that demethylates both histones and non-histone proteins. Enzymatically inactive by itself, and becomes active following phosphorylation by PKA: forms a complex with ARID5B and mediates demethylation of methylated ARID5B. Demethylation of ARID5B leads to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. PHF2 is recruited to trimethylated 'Lys-4' of histone H3 (H3K4me3) at rDNA promoters and promotes expression of rDNA.<ref>PMID:21532585</ref> <ref>PMID:20129925</ref> <ref>PMID:21167174</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 14:		Line 16:
	Structural Basis for Human PHF2 Jumonji Domain Interaction with Metal Ions.,Horton JR, Upadhyay AK, Hashimoto H, Zhang X, Cheng X J Mol Biol. 2010 Dec 15. PMID:21167174<ref>PMID:21167174</ref>		Structural Basis for Human PHF2 Jumonji Domain Interaction with Metal Ions.,Horton JR, Upadhyay AK, Hashimoto H, Zhang X, Cheng X J Mol Biol. 2010 Dec 15. PMID:21167174<ref>PMID:21167174</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 21:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Cheng, X.]]	+	[[Category: Cheng, X]]
-	[[Category: Hashimoto, H.]]	+	[[Category: Hashimoto, H]]
-	[[Category: Horton, J R.]]	+	[[Category: Horton, J R]]
-	[[Category: Upadhyay, A K.]]	+	[[Category: Upadhyay, A K]]
-	[[Category: Zhang, X.]]	+	[[Category: Zhang, X]]
	[[Category: Alpha-ketoglutarate-fe2+ dependent dioxygenase]]		[[Category: Alpha-ketoglutarate-fe2+ dependent dioxygenase]]
	[[Category: Histone tail binding protein]]		[[Category: Histone tail binding protein]]
	[[Category: Protein binding]]		[[Category: Protein binding]]

OCA at 05:24, 4 June 2014

2014-06-04T05:24:44Z

←Older revision		Revision as of 05:24, 4 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3pua.~~png~~\|~~left~~\|~~200px~~]]	+	==PHF2 Jumonji-NOG-Ni(II)==
		+	<StructureSection load='3pua' size='340' side='right' caption='[[3pua]], [[Resolution\|resolution]] 1.89Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3pua]] is a 1 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=3PUA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PUA FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ptr\|3ptr]], [[3pu3\|3pu3]], [[3pu8\|3pu8]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PHF2, KIAA0662 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3pua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pua OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pua RCSB], [http://www.ebi.ac.uk/pdbsum/3pua PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	PHF2 belongs to a class of alpha-ketoglutarate-Fe(2)(+)-dependent dioxygenases. PHF2 harbors a plant homeodomain (PHD) and a Jumonji domain. PHF2, via its PHD, binds Lys4-trimethylated histone 3 in submicromolar affinity and has been reported to have the demethylase activity of monomethylated lysine 9 of histone 3 in vivo. However, we did not detect demethylase activity for PHF2 Jumonji domain (with and without its linked PHD) in the context of histone peptides. We determined the crystal structures of PHF2 Jumonji domain in the absence and presence of additional exogenous metal ions. When Fe(2+) or Ni(2+) was added at a high concentration (50 mM) and allowed to soak in the preformed crystals, Fe(2+) or Ni(2+) was bound by six ligands in an octahedral coordination. The side chains of H249 and D251 and the two oxygen atoms of N-oxalylglycine (an analog of alpha-ketoglutarate) provide four coordinations in the equatorial plane, while the hydroxyl oxygen atom of Y321 and one water molecule provide the two axial coordinations as the fifth and sixth ligands, respectively. The metal binding site in PHF2 closely resembles the Fe(2+) sites in other Jumonji domains examined, with one important difference-a tyrosine (Y321 of PHF2) replaces histidine as the fifth ligand. However, neither Y321H mutation nor high metal concentration renders PHF2 an active demethylase on histone peptides. Wild type and Y321H mutant bind Ni(2+) with an approximately equal affinity of 50 muM. We propose that there must be other regulatory factors required for the enzymatic activity of PHF2 in vivo or that perhaps PHF2 acts on non-histone substrates. Furthermore, PHF2 shares significant sequence homology throughout the entire region, including the above-mentioned tyrosine at the corresponding iron-binding position, with that of Schizosaccharomyces pombe Epe1, which plays an essential role in heterochromatin function but has no known enzymatic activity.

-	~~<!--~~	+	Structural Basis for Human PHF2 Jumonji Domain Interaction with Metal Ions.,Horton JR, Upadhyay AK, Hashimoto H, Zhang X, Cheng X J Mol Biol. 2010 Dec 15. PMID:21167174<ref>PMID:21167174</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3pua"~~, ~~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_3pua\| PDB=3pua \| SCENE= }}~~	+

-	~~===PHF2 Jumonji-NOG-Ni(II)===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_21167174}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 21167174 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_21167174}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3pua]] is a 1 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=3PUA OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:021167174<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Cheng, X.]]		[[Category: Cheng, X.]]

OCA at 07:34, 2 November 2011

2011-11-02T07:34:09Z

←Older revision		Revision as of 07:34, 2 November 2011
Line 1:		Line 1:
-	[[Image:3pua.~~jpg~~\|left\|200px]]	+	[[Image:3pua.png\|left\|200px]]

	<!--		<!--
Line 22:		Line 22:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~21167174~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021167174</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Cheng, X.]]		[[Category: Cheng, X.]]
Line 29:		Line 29:
	[[Category: Upadhyay, A K.]]		[[Category: Upadhyay, A K.]]
	[[Category: Zhang, X.]]		[[Category: Zhang, X.]]
		+	[[Category: Alpha-ketoglutarate-fe2+ dependent dioxygenase]]
		+	[[Category: Histone tail binding protein]]
		+	[[Category: Protein binding]]

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

2011-01-26T13:05:45Z

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

←Older revision

Revision as of 13:05, 26 January 2011

OCA at 13:05, 26 January 2011

2011-01-26T13:05:44Z

←Older revision		Revision as of 13:05, 26 January 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3pua.jpg\|left\|200px]]

-	The ~~entry 3pua~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3pua", 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_3pua\| PDB=3pua \| SCENE= }}

-	~~Authors: Horton, J.R., Upadhyay, A.K., Hashimoto, H., Zhang, X., Cheng, X.~~	+	===PHF2 Jumonji-NOG-Ni(II)===

-	Description: PHF2 Jumonji-NOG-Ni(II)

-	~~''Page seeded by~~ [http://oca.weizmann.ac.il/oca OCA ] ~~on Wed Dec 22 09~~:37:~~27 2010''~~	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21167174}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21167174 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21167174}}
		+
		+	==About this Structure==
		+	[[3pua]] is a 1 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=3PUA OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:21167174</ref><references group="xtra"/>
		+	[[Category: Homo sapiens]]
		+	[[Category: Cheng, X.]]
		+	[[Category: Hashimoto, H.]]
		+	[[Category: Horton, J R.]]
		+	[[Category: Upadhyay, A K.]]
		+	[[Category: Zhang, X.]]

OCA at 06:24, 22 December 2010

2010-12-22T06:24:50Z

←Older revision		Revision as of 06:24, 22 December 2010
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3pua is ON HOLD	+	The entry 3pua is ON HOLD until Paper Publication

	Authors: Horton, J.R., Upadhyay, A.K., Hashimoto, H., Zhang, X., Cheng, X.		Authors: Horton, J.R., Upadhyay, A.K., Hashimoto, H., Zhang, X., Cheng, X.
Line 7:		Line 7:
	Description: PHF2 Jumonji-NOG-Ni(II)		Description: PHF2 Jumonji-NOG-Ni(II)

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec ~~15 08~~:25:35 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 22 09:37:27 2010''

OCA: New page: '''Unreleased structure''' The entry 3pua is ON HOLD Authors: Horton, J.R., Upadhyay, A.K., Hashimoto, H., Zhang, X., Cheng, X. Description: PHF2 Jumonji-NOG-Ni(II) ''Page seeded by [...

2010-12-15T05:13:15Z

New page: '''Unreleased structure''' The entry 3pua is ON HOLD Authors: Horton, J.R., Upadhyay, A.K., Hashimoto, H., Zhang, X., Cheng, X. Description: PHF2 Jumonji-NOG-Ni(II) ''Page seeded by [...

New page

'''Unreleased structure'''

The entry 3pua is ON HOLD

Authors: Horton, J.R., Upadhyay, A.K., Hashimoto, H., Zhang, X., Cheng, X.

Description: PHF2 Jumonji-NOG-Ni(II)

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 15 08:25:35 2010''