3opt - Revision history

OCA at 11:18, 21 February 2024

2024-02-21T11:18:12Z

← Older revision		Revision as of 11:18, 21 February 2024
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	<StructureSection load='3opt' size='340' side='right'caption='[[3opt]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='3opt' size='340' side='right'caption='[[3opt]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3opt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OPT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OPT FirstGlance]. <br>		<table><tr><td colspan='2'>[[3opt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OPT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OPT FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=AKG:2~~-~~OXOGLUTARIC+ACID'>AKG</scene>~~, ~~<scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 2.2Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[3opw\|3opw]]</div>~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>RPH1, YER169W ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~4932 ATCC 18824])</td~~><~~/tr>~~
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/[Histone_H3]-lysine-36_demethylase [Histone H3]-lysine-36 demethylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.27 1.14.11.27]~~ </~~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=3opt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3opt OCA], [https://pdbe.org/3opt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3opt RCSB], [https://www.ebi.ac.uk/pdbsum/3opt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3opt 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=3opt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3opt OCA], [https://pdbe.org/3opt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3opt RCSB], [https://www.ebi.ac.uk/pdbsum/3opt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3opt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/RPH1_YEAST RPH1_YEAST]] Transcriptional repressor of photolyase PHR1. Recognizes and binds the sequence AG(4) in the upstream repressing sequence of PHR1. Derepresses PHR1 transcription when phosphorylated.<ref>PMID:10523651</ref> <ref>PMID:11809875</ref>		[https://www.uniprot.org/uniprot/RPH1_YEAST RPH1_YEAST] Transcriptional repressor of photolyase PHR1. Recognizes and binds the sequence AG(4) in the upstream repressing sequence of PHR1. Derepresses PHR1 transcription when phosphorylated.<ref>PMID:10523651</ref> <ref>PMID:11809875</ref>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Saccharomyces cerevesiae Rph1 is a histone demethylase orthologous to human JMJD2A that can specifically demethylate tri- and dimethylated Lys36 of histone H3. The catalytic core of Rph1 (c-Rph1) is responsible for the demethylase activity which is essential for the transcription elongation of some actively transcribed genes. We report here the crystal structures of c-Rph1 in apo form and in complex with Ni2+ and alpha-ketoglutarate (alpha-KG). The structure of c-Rph1 is composed of a JmjN domain, a long beta-hairpin, a mixed structural motif, and a JmjC domain. The alpha-KG co-factor forms hydrogen-bonding interactions with the side chains of conserved residues, and the Ni2+ ion at the active site is chelated by conserved residues and the cofactor. Structural comparison of Rph1 with JMJD2A indicates that the substrate-binding cleft of Rph1 is formed with several structural elements of the JmjC domain, the long beta-hairpin, and the mixed structural motif; and the methylated Lys36 of H3 is recognized by several conserved residues of the JmjC domain. In vitro biochemical data show that mutations of the key residues at the catalytic center and in the substrate-binding cleft abolish the demethylase activity. In vivo growth phenotype analyses also demonstrate that these residues are essential for its functional roles in transcription elongation. Taken together, our structural and biological data provide insights into the molecular basis of the histone demethylase activity and the substrate specificity of Rph1.

	Crystal structure of the catalytic core of Saccharomyces cerevesiae histone demethylase Rph1: insights into the substrate specificity and catalytic mechanism.,Chang Y, Wu J, Tong XJ, Zhou JQ, Ding J Biochem J. 2010 Nov 10. PMID:21067515<ref>PMID:21067515</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 3opt" style="background-color:#fffaf0;"></div~~>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Atcc 18824]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Chang, Y]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Ding, J]]		[[Category: Chang Y]]
	[[Category: Tong, X]]		[[Category: Ding J]]
	[[Category: Wu, J]]		[[Category: Tong X]]
	[[Category: Zhou, J]]		[[Category: Wu J]]
	~~[[Category: Catalytic core]]~~		[[Category: Zhou J]]
	~~[[Category: Histone demethylase]]~~
	~~[[Category: Oxidoreductase]]~~
	~~[[Category: Rph1~~]]

OCA at 10:52, 18 May 2022

2022-05-18T10:52:31Z

← Older revision		Revision as of 10:52, 18 May 2022
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	==Crystal structure of the Rph1 catalytic core with a-ketoglutarate==		==Crystal structure of the Rph1 catalytic core with a-ketoglutarate==
	<StructureSection load='3opt' size='340' side='right' caption='[[3opt]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='3opt' size='340' side='right'caption='[[3opt]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3opt]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OPT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3OPT FirstGlance]. <br>		<table><tr><td colspan='2'>[[3opt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OPT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OPT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3opw\|3opw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3opw\|3opw]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RPH1, YER169W ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RPH1, YER169W ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/[Histone_H3]-lysine-36_demethylase [Histone H3]-lysine-36 demethylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.27 1.14.11.27] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/[Histone_H3]-lysine-36_demethylase [Histone H3]-lysine-36 demethylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.27 1.14.11.27] </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=3opt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3opt OCA], [~~http~~://pdbe.org/3opt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3opt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3opt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3opt 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=3opt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3opt OCA], [https://pdbe.org/3opt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3opt RCSB], [https://www.ebi.ac.uk/pdbsum/3opt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3opt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/RPH1_YEAST RPH1_YEAST]] Transcriptional repressor of photolyase PHR1. Recognizes and binds the sequence AG(4) in the upstream repressing sequence of PHR1. Derepresses PHR1 transcription when phosphorylated.<ref>PMID:10523651</ref> <ref>PMID:11809875</ref>		[[https://www.uniprot.org/uniprot/RPH1_YEAST RPH1_YEAST]] Transcriptional repressor of photolyase PHR1. Recognizes and binds the sequence AG(4) in the upstream repressing sequence of PHR1. Derepresses PHR1 transcription when phosphorylated.<ref>PMID:10523651</ref> <ref>PMID:11809875</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
			[[Category: Large Structures]]
	[[Category: Chang, Y]]		[[Category: Chang, Y]]
	[[Category: Ding, J]]		[[Category: Ding, J]]

OCA at 08:29, 4 August 2016

2016-08-04T08:29:00Z

← Older revision		Revision as of 08:29, 4 August 2016
Line 1:		Line 1:

	==Crystal structure of the Rph1 catalytic core with a-ketoglutarate==		==Crystal structure of the Rph1 catalytic core with a-ketoglutarate==
	<StructureSection load='3opt' size='340' side='right' caption='[[3opt]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='3opt' size='340' side='right' caption='[[3opt]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RPH1, YER169W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RPH1, YER169W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Histone_H3]-lysine-36_demethylase [Histone H3]-lysine-36 demethylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.27 1.14.11.27] </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_H3]-lysine-36_demethylase [Histone H3]-lysine-36 demethylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.27 1.14.11.27] </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=3opt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3opt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3opt RCSB], [http://www.ebi.ac.uk/pdbsum/3opt 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=3opt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3opt OCA], [http://pdbe.org/3opt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3opt RCSB], [http://www.ebi.ac.uk/pdbsum/3opt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3opt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 3opt" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:41, 24 December 2014

2014-12-24T07:41:32Z

← Older revision		Revision as of 07:41, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3opt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OPT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OPT FirstGlance]. <br>		<table><tr><td colspan='2'>[[3opt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OPT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OPT FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3opw\|3opw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3opw\|3opw]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RPH1, YER169W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RPH1, YER169W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Histone_H3]-lysine-36_demethylase [Histone H3]-lysine-36 demethylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.27 1.14.11.27] </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_H3]-lysine-36_demethylase [Histone H3]-lysine-36 demethylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.27 1.14.11.27] </span></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=3opt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3opt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3opt RCSB], [http://www.ebi.ac.uk/pdbsum/3opt 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=3opt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3opt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3opt RCSB], [http://www.ebi.ac.uk/pdbsum/3opt PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/RPH1_YEAST RPH1_YEAST]] Transcriptional repressor of photolyase PHR1. Recognizes and binds the sequence AG(4) in the upstream repressing sequence of PHR1. Derepresses PHR1 transcription when phosphorylated.<ref>PMID:10523651</ref> <ref>PMID:11809875</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 17:
	Crystal structure of the catalytic core of Saccharomyces cerevesiae histone demethylase Rph1: insights into the substrate specificity and catalytic mechanism.,Chang Y, Wu J, Tong XJ, Zhou JQ, Ding J Biochem J. 2010 Nov 10. PMID:21067515<ref>PMID:21067515</ref>		Crystal structure of the catalytic core of Saccharomyces cerevesiae histone demethylase Rph1: insights into the substrate specificity and catalytic mechanism.,Chang Y, Wu J, Tong XJ, Zhou JQ, Ding J Biochem J. 2010 Nov 10. PMID:21067515<ref>PMID:21067515</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 22:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
	[[Category: Chang, Y.]]		[[Category: Chang, Y]]
	[[Category: Ding, J.]]		[[Category: Ding, J]]
	[[Category: Tong, X.]]		[[Category: Tong, X]]
	[[Category: Wu, J.]]		[[Category: Wu, J]]
	[[Category: Zhou, J.]]		[[Category: Zhou, J]]
	[[Category: Catalytic core]]		[[Category: Catalytic core]]
	[[Category: Histone demethylase]]		[[Category: Histone demethylase]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Rph1]]		[[Category: Rph1]]

OCA at 13:10, 18 May 2014

2014-05-18T13:10:44Z

← Older revision		Revision as of 13:10, 18 May 2014
Line 1:		Line 1:
	~~{{STRUCTURE_3opt\| PDB=3opt \| SCENE= }}~~		==Crystal structure of the Rph1 catalytic core with a-ketoglutarate==
	===Crystal structure of the Rph1 catalytic core with a-ketoglutarate===		<StructureSection load='3opt' size='340' side='right' caption='[[3opt]], [[Resolution\|resolution]] 2.20Å' scene=''>
	~~{{ABSTRACT_PUBMED_21067515}}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[3opt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OPT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OPT FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3opw\|3opw]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RPH1, YER169W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Histone_H3]-lysine-36_demethylase [Histone H3]-lysine-36 demethylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.27 1.14.11.27] </span></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=3opt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3opt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3opt RCSB], [http://www.ebi.ac.uk/pdbsum/3opt PDBsum]</span></td></tr>
			<table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Saccharomyces cerevesiae Rph1 is a histone demethylase orthologous to human JMJD2A that can specifically demethylate tri- and dimethylated Lys36 of histone H3. The catalytic core of Rph1 (c-Rph1) is responsible for the demethylase activity which is essential for the transcription elongation of some actively transcribed genes. We report here the crystal structures of c-Rph1 in apo form and in complex with Ni2+ and alpha-ketoglutarate (alpha-KG). The structure of c-Rph1 is composed of a JmjN domain, a long beta-hairpin, a mixed structural motif, and a JmjC domain. The alpha-KG co-factor forms hydrogen-bonding interactions with the side chains of conserved residues, and the Ni2+ ion at the active site is chelated by conserved residues and the cofactor. Structural comparison of Rph1 with JMJD2A indicates that the substrate-binding cleft of Rph1 is formed with several structural elements of the JmjC domain, the long beta-hairpin, and the mixed structural motif; and the methylated Lys36 of H3 is recognized by several conserved residues of the JmjC domain. In vitro biochemical data show that mutations of the key residues at the catalytic center and in the substrate-binding cleft abolish the demethylase activity. In vivo growth phenotype analyses also demonstrate that these residues are essential for its functional roles in transcription elongation. Taken together, our structural and biological data provide insights into the molecular basis of the histone demethylase activity and the substrate specificity of Rph1.

	~~==Function==~~		Crystal structure of the catalytic core of Saccharomyces cerevesiae histone demethylase Rph1: insights into the substrate specificity and catalytic mechanism.,Chang Y, Wu J, Tong XJ, Zhou JQ, Ding J Biochem J. 2010 Nov 10. PMID:21067515<ref>PMID:21067515</ref>
	~~[[http://www.uniprot.org/uniprot/RPH1_YEAST RPH1_YEAST]] Transcriptional repressor~~ of ~~photolyase PHR1. Recognizes and binds~~ the ~~sequence AG(4) in~~ the ~~upstream repressing sequence of PHR1~~. ~~Derepresses PHR1 transcription when phosphorylated~~.~~<ref>~~PMID:~~10523651</ref>~~ <ref>PMID:~~11809875~~</ref>

	~~==About this Structure==~~		From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
	~~[[3opt]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3OPT OCA].~~		</div>
			== References ==
	==~~Reference~~==		<references/>
	~~<ref group="xtra">PMID:021067515</ref>~~<references ~~group="xtra"~~/><~~references~~/>		__TOC__
	[[Category: ~~Saccharomyces cerevisiae~~]]		</StructureSection>
			[[Category: Atcc 18824]]
	[[Category: Chang, Y.]]		[[Category: Chang, Y.]]
	[[Category: Ding, J.]]		[[Category: Ding, J.]]

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

2013-05-02T08:12:04Z

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

← Older revision	Revision as of 08:12, 2 May 2013
(No difference)

OCA at 08:12, 2 May 2013

2013-05-02T08:12:00Z

← Older revision		Revision as of 08:12, 2 May 2013
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	~~{{Seed}}~~
	~~[[Image:3opt.jpg\|left\|200px]]~~

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3opt", 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_3opt\| PDB=3opt \| SCENE= }}		{{STRUCTURE_3opt\| PDB=3opt \| SCENE= }}

	===Crystal structure of the Rph1 catalytic core with a-ketoglutarate===		===Crystal structure of the Rph1 catalytic core with a-ketoglutarate===
			{{ABSTRACT_PUBMED_21067515}}

			==Function==
	~~<!--~~		[[http://www.uniprot.org/uniprot/RPH1_YEAST RPH1_YEAST]] Transcriptional repressor of photolyase PHR1. Recognizes and binds the sequence AG(4) in the upstream repressing sequence of PHR1. Derepresses PHR1 transcription when phosphorylated.<ref>PMID:10523651</ref> <ref>PMID:11809875</ref>
	~~The line below this paragraph, {{ABSTRACT_PUBMED_21067515}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov~~)~~, where 21067515 is~~ the ~~PubMed ID number~~.
	-->
	~~{{ABSTRACT_PUBMED_21067515}}~~

	==About this Structure==		==About this Structure==
	~~3OPT~~ is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OPT OCA].		[[3opt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OPT OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~21067515~~</ref><references group="xtra"/>		<ref group="xtra">PMID:021067515</ref><references group="xtra"/><references/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Chang, Y.]]		[[Category: Chang, Y.]]
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	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Rph1]]		[[Category: Rph1]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 22 09:57:29 2010''~~

OCA at 06:44, 22 December 2010

2010-12-22T06:44:53Z

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-'''Unreleased structure'''
+{{Seed}}
-The entry 3opt is ON HOLD  until Paper Publication
+<!--
-Authors: Chang, Y., Wu, J., Tong, X., Zhou, J., Ding, J.
+===Crystal structure of the Rph1 catalytic core with a-ketoglutarate===
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 10 06:30:37 2010''
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OCA at 03:19, 10 November 2010

2010-11-10T03:19:41Z

← Older revision		Revision as of 03:19, 10 November 2010
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 3opt is ON HOLD		The entry 3opt is ON HOLD until Paper Publication

	Authors: Chang, Y., Wu, J., Tong, X., Zhou, J., Ding, J.		Authors: Chang, Y., Wu, J., Tong, X., Zhou, J., Ding, J.
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	Description: Crystal structure of the Rph1 catalytic core with a-ketoglutarate		Description: Crystal structure of the Rph1 catalytic core with a-ketoglutarate

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Sep 22 14~~:34:05 2010''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 10 06:30:37 2010''

OCA at 11:25, 22 September 2010

2010-09-22T11:25:06Z

← Older revision		Revision as of 11:25, 22 September 2010
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	The entry 3opt is ON HOLD		The entry 3opt is ON HOLD

	Authors: Chang, Y, Wu, J, Tong, X, Zhou, J, Ding, J		Authors: Chang, Y., Wu, J., Tong, X., Zhou, J., Ding, J.

	Description: Crystal structure of the Rph1 catalytic core with a-ketoglutarate		Description: Crystal structure of the Rph1 catalytic core with a-ketoglutarate

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep ~~15 10~~:38:29 2010''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 14:34:05 2010''