2z5u - Revision history

OCA at 13:23, 1 November 2023

2023-11-01T13:23:03Z

←Older revision		Revision as of 13:23, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='2z5u' size='340' side='right'caption='[[2z5u]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='2z5u' size='340' side='right'caption='[[2z5u]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z5u]] 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=2Z5U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z5U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z5u]] 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=2Z5U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z5U FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FAJ:FAD-TRANS~~-2~~-PHENYLCYCLOPROPYLAMINE+ADDUCT'>FAJ</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]] 2.25Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[2ejr\|2ejr]], [[2z3y\|2z3y]]~~</~~div~~>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAJ:FAD-TRANS-2-PHENYLCYCLOPROPYLAMINE+ADDUCT'>FAJ</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KIAA0601, LSD1 ([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=2z5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z5u OCA], [https://pdbe.org/2z5u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z5u RCSB], [https://www.ebi.ac.uk/pdbsum/2z5u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z5u 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=2z5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z5u OCA], [https://pdbe.org/2z5u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z5u RCSB], [https://www.ebi.ac.uk/pdbsum/2z5u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z5u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/KDM1A_HUMAN KDM1A_HUMAN]] Histone demethylase that demethylates both 'Lys-4' (H3K4me) and 'Lys-9' (H3K9me) of histone H3, thereby acting as a coactivator or a corepressor, depending on the context. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Acts as a corepressor by mediating demethylation of H3K4me, a specific tag for epigenetic transcriptional activation. Demethylates both mono- (H3K4me1) and di-methylated (H3K4me2) H3K4me. May play a role in the repression of neuronal genes. Alone, it is unable to demethylate H3K4me on nucleosomes and requires the presence of RCOR1/CoREST to achieve such activity. Also acts as a coactivator of androgen receptor (ANDR)-dependent transcription, by being recruited to ANDR target genes and mediating demethylation of H3K9me, a specific tag for epigenetic transcriptional repression. The presence of PRKCB in ANDR-containing complexes, which mediates phosphorylation of 'Thr-6' of histone H3 (H3T6ph), a specific tag that prevents demethylation H3K4me, prevents H3K4me demethylase activity of KDM1A. Demethylates di-methylated 'Lys-370' of p53/TP53 which prevents interaction of p53/TP53 with TP53BP1 and represses p53/TP53-mediated transcriptional activation. Demethylates and stabilizes the DNA methylase DNMT1. Required for gastrulation during embryogenesis. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development.<ref>PMID:12032298</ref> <ref>PMID:15620353</ref> <ref>PMID:16079795</ref> <ref>PMID:17805299</ref> <ref>PMID:20228790</ref>	+	[https://www.uniprot.org/uniprot/KDM1A_HUMAN KDM1A_HUMAN] Histone demethylase that demethylates both 'Lys-4' (H3K4me) and 'Lys-9' (H3K9me) of histone H3, thereby acting as a coactivator or a corepressor, depending on the context. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Acts as a corepressor by mediating demethylation of H3K4me, a specific tag for epigenetic transcriptional activation. Demethylates both mono- (H3K4me1) and di-methylated (H3K4me2) H3K4me. May play a role in the repression of neuronal genes. Alone, it is unable to demethylate H3K4me on nucleosomes and requires the presence of RCOR1/CoREST to achieve such activity. Also acts as a coactivator of androgen receptor (ANDR)-dependent transcription, by being recruited to ANDR target genes and mediating demethylation of H3K9me, a specific tag for epigenetic transcriptional repression. The presence of PRKCB in ANDR-containing complexes, which mediates phosphorylation of 'Thr-6' of histone H3 (H3T6ph), a specific tag that prevents demethylation H3K4me, prevents H3K4me demethylase activity of KDM1A. Demethylates di-methylated 'Lys-370' of p53/TP53 which prevents interaction of p53/TP53 with TP53BP1 and represses p53/TP53-mediated transcriptional activation. Demethylates and stabilizes the DNA methylase DNMT1. Required for gastrulation during embryogenesis. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development.<ref>PMID:12032298</ref> <ref>PMID:15620353</ref> <ref>PMID:16079795</ref> <ref>PMID:17805299</ref> <ref>PMID:20228790</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Mimasu, S]]	+	[[Category: Mimasu S]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Sengoku T]]
-	[[Category: Sengoku, T]]	+	[[Category: Yokoyama S]]
-	[[Category: Yokoyama, S]]	+
-	~~[[Category: Chromatin]]~~	+
-	~~[[Category: Chromatin regulator]]~~	+
-	~~[[Category: Fad]]~~	+
-	~~[[Category: Histone demethylase]]~~	+
-	~~[[Category: Lsd1]]~~	+
-	~~[[Category: Lysine-specific]]~~	+
-	~~[[Category: National project on protein structural and functional analyse]]~~	+
-	~~[[Category: Nppsfa]]~~	+
-	~~[[Category: Nucleosome]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Phosphorylation]]~~	+
-	~~[[Category: Repressor]]~~	+
-	~~[[Category: Rsgi]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription regulation~~]]	+

OCA at 10:46, 8 December 2021

2021-12-08T10:46:23Z

←Older revision		Revision as of 10:46, 8 December 2021
Line 3:		Line 3:
	<StructureSection load='2z5u' size='340' side='right'caption='[[2z5u]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='2z5u' size='340' side='right'caption='[[2z5u]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z5u]] 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=2Z5U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2Z5U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z5u]] 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=2Z5U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z5U FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAJ:FAD-TRANS-2-PHENYLCYCLOPROPYLAMINE+ADDUCT'>FAJ</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAJ:FAD-TRANS-2-PHENYLCYCLOPROPYLAMINE+ADDUCT'>FAJ</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ejr\|2ejr]], [[2z3y\|2z3y]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ejr\|2ejr]], [[2z3y\|2z3y]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KIAA0601, LSD1 ([~~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">KIAA0601, LSD1 ([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=2z5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z5u OCA], [~~http~~://pdbe.org/2z5u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2z5u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2z5u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2z5u 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=2z5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z5u OCA], [https://pdbe.org/2z5u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z5u RCSB], [https://www.ebi.ac.uk/pdbsum/2z5u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z5u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/KDM1A_HUMAN KDM1A_HUMAN]] Histone demethylase that demethylates both 'Lys-4' (H3K4me) and 'Lys-9' (H3K9me) of histone H3, thereby acting as a coactivator or a corepressor, depending on the context. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Acts as a corepressor by mediating demethylation of H3K4me, a specific tag for epigenetic transcriptional activation. Demethylates both mono- (H3K4me1) and di-methylated (H3K4me2) H3K4me. May play a role in the repression of neuronal genes. Alone, it is unable to demethylate H3K4me on nucleosomes and requires the presence of RCOR1/CoREST to achieve such activity. Also acts as a coactivator of androgen receptor (ANDR)-dependent transcription, by being recruited to ANDR target genes and mediating demethylation of H3K9me, a specific tag for epigenetic transcriptional repression. The presence of PRKCB in ANDR-containing complexes, which mediates phosphorylation of 'Thr-6' of histone H3 (H3T6ph), a specific tag that prevents demethylation H3K4me, prevents H3K4me demethylase activity of KDM1A. Demethylates di-methylated 'Lys-370' of p53/TP53 which prevents interaction of p53/TP53 with TP53BP1 and represses p53/TP53-mediated transcriptional activation. Demethylates and stabilizes the DNA methylase DNMT1. Required for gastrulation during embryogenesis. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development.<ref>PMID:12032298</ref> <ref>PMID:15620353</ref> <ref>PMID:16079795</ref> <ref>PMID:17805299</ref> <ref>PMID:20228790</ref>	+	[[https://www.uniprot.org/uniprot/KDM1A_HUMAN KDM1A_HUMAN]] Histone demethylase that demethylates both 'Lys-4' (H3K4me) and 'Lys-9' (H3K9me) of histone H3, thereby acting as a coactivator or a corepressor, depending on the context. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Acts as a corepressor by mediating demethylation of H3K4me, a specific tag for epigenetic transcriptional activation. Demethylates both mono- (H3K4me1) and di-methylated (H3K4me2) H3K4me. May play a role in the repression of neuronal genes. Alone, it is unable to demethylate H3K4me on nucleosomes and requires the presence of RCOR1/CoREST to achieve such activity. Also acts as a coactivator of androgen receptor (ANDR)-dependent transcription, by being recruited to ANDR target genes and mediating demethylation of H3K9me, a specific tag for epigenetic transcriptional repression. The presence of PRKCB in ANDR-containing complexes, which mediates phosphorylation of 'Thr-6' of histone H3 (H3T6ph), a specific tag that prevents demethylation H3K4me, prevents H3K4me demethylase activity of KDM1A. Demethylates di-methylated 'Lys-370' of p53/TP53 which prevents interaction of p53/TP53 with TP53BP1 and represses p53/TP53-mediated transcriptional activation. Demethylates and stabilizes the DNA methylase DNMT1. Required for gastrulation during embryogenesis. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development.<ref>PMID:12032298</ref> <ref>PMID:15620353</ref> <ref>PMID:16079795</ref> <ref>PMID:17805299</ref> <ref>PMID:20228790</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 09:44, 25 December 2019

2019-12-25T09:44:49Z

←Older revision		Revision as of 09:44, 25 December 2019
Line 1:		Line 1:

	==Crystal structure of Lysine-specific histone demethylase 1==		==Crystal structure of Lysine-specific histone demethylase 1==
-	<StructureSection load='2z5u' size='340' side='right' caption='[[2z5u]], [[Resolution\|resolution]] 2.25Å' scene=''>	+	<StructureSection load='2z5u' size='340' side='right'caption='[[2z5u]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2z5u]] 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=2Z5U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z5U FirstGlance]. <br>		<table><tr><td colspan='2'>[[2z5u]] 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=2Z5U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z5U FirstGlance]. <br>
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[Lysine-specific histone demethylase\|Lysine-specific histone demethylase]]	+	*[[Lysine-specific histone demethylase 3D structures\|Lysine-specific histone demethylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Mimasu, S]]		[[Category: Mimasu, S]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

OCA at 09:32, 17 October 2018

2018-10-17T09:32:58Z

←Older revision		Revision as of 09:32, 17 October 2018
Line 1:		Line 1:
		+
	==Crystal structure of Lysine-specific histone demethylase 1==		==Crystal structure of Lysine-specific histone demethylase 1==
	<StructureSection load='2z5u' size='340' side='right' caption='[[2z5u]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='2z5u' size='340' side='right' caption='[[2z5u]], [[Resolution\|resolution]] 2.25Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ejr\|2ejr]], [[2z3y\|2z3y]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ejr\|2ejr]], [[2z3y\|2z3y]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KIAA0601, LSD1 ([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">KIAA0601, LSD1 ([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=2z5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z5u OCA], [http://pdbe.org/2z5u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z5u RCSB], [http://www.ebi.ac.uk/pdbsum/2z5u 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=2z5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z5u OCA], [http://pdbe.org/2z5u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z5u RCSB], [http://www.ebi.ac.uk/pdbsum/2z5u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z5u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z5/2z5u_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z5/2z5u_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 17:56, 9 February 2016

2016-02-09T17:56:46Z

←Older revision		Revision as of 17:56, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='2z5u' size='340' side='right' caption='[[2z5u]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='2z5u' size='340' side='right' caption='[[2z5u]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z5u]] 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=2Z5U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z5U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z5u]] 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=2Z5U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z5U FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAJ:FAD-TRANS-2-PHENYLCYCLOPROPYLAMINE+ADDUCT'>FAJ</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAJ:FAD-TRANS-2-PHENYLCYCLOPROPYLAMINE+ADDUCT'>FAJ</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ejr\|2ejr]], [[2z3y\|2z3y]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ejr\|2ejr]], [[2z3y\|2z3y]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KIAA0601, LSD1 ([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">KIAA0601, LSD1 ([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=2z5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z5u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z5u RCSB], [http://www.ebi.ac.uk/pdbsum/2z5u 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=2z5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z5u OCA], [http://pdbe.org/2z5u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z5u RCSB], [http://www.ebi.ac.uk/pdbsum/2z5u PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2z5u ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 28:
	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 2z5u" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[Lysine-specific histone demethylase 1\|Lysine-specific histone demethylase 1]]	+	*[[Lysine-specific histone demethylase\|Lysine-specific histone demethylase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Mimasu, S]]		[[Category: Mimasu, S]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

OCA at 08:29, 25 December 2014

2014-12-25T08:29:17Z

←Older revision		Revision as of 08:29, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2z5u]] 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=2Z5U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z5U FirstGlance]. <br>		<table><tr><td colspan='2'>[[2z5u]] 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=2Z5U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z5U FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAJ:FAD-TRANS-2-PHENYLCYCLOPROPYLAMINE+ADDUCT'>FAJ</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAJ:FAD-TRANS-2-PHENYLCYCLOPROPYLAMINE+ADDUCT'>FAJ</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ejr\|2ejr]], [[2z3y\|2z3y]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ejr\|2ejr]], [[2z3y\|2z3y]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KIAA0601, LSD1 ([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">KIAA0601, LSD1 ([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=2z5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z5u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z5u RCSB], [http://www.ebi.ac.uk/pdbsum/2z5u 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=2z5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z5u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z5u RCSB], [http://www.ebi.ac.uk/pdbsum/2z5u PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KDM1A_HUMAN KDM1A_HUMAN]] Histone demethylase that demethylates both 'Lys-4' (H3K4me) and 'Lys-9' (H3K9me) of histone H3, thereby acting as a coactivator or a corepressor, depending on the context. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Acts as a corepressor by mediating demethylation of H3K4me, a specific tag for epigenetic transcriptional activation. Demethylates both mono- (H3K4me1) and di-methylated (H3K4me2) H3K4me. May play a role in the repression of neuronal genes. Alone, it is unable to demethylate H3K4me on nucleosomes and requires the presence of RCOR1/CoREST to achieve such activity. Also acts as a coactivator of androgen receptor (ANDR)-dependent transcription, by being recruited to ANDR target genes and mediating demethylation of H3K9me, a specific tag for epigenetic transcriptional repression. The presence of PRKCB in ANDR-containing complexes, which mediates phosphorylation of 'Thr-6' of histone H3 (H3T6ph), a specific tag that prevents demethylation H3K4me, prevents H3K4me demethylase activity of KDM1A. Demethylates di-methylated 'Lys-370' of p53/TP53 which prevents interaction of p53/TP53 with TP53BP1 and represses p53/TP53-mediated transcriptional activation. Demethylates and stabilizes the DNA methylase DNMT1. Required for gastrulation during embryogenesis. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development.<ref>PMID:12032298</ref> <ref>PMID:15620353</ref> <ref>PMID:16079795</ref> <ref>PMID:17805299</ref> <ref>PMID:20228790</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Mimasu, S.]]	+	[[Category: Mimasu, S]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Sengoku, T.]]	+	[[Category: Sengoku, T]]
-	[[Category: Yokoyama, S.]]	+	[[Category: Yokoyama, S]]
	[[Category: Chromatin]]		[[Category: Chromatin]]
	[[Category: Chromatin regulator]]		[[Category: Chromatin regulator]]
Line 51:		Line 53:
	[[Category: Phosphorylation]]		[[Category: Phosphorylation]]
	[[Category: Repressor]]		[[Category: Repressor]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]
	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]

OCA at 05:12, 2 October 2014

2014-10-02T05:12:33Z

←Older revision		Revision as of 05:12, 2 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_2z5u~~\| ~~PDB~~=2z5u \| ~~SCENE~~= }}	+	==Crystal structure of Lysine-specific histone demethylase 1==
-	===~~Crystal~~ structure of ~~Lysine~~-~~specific histone demethylase 1~~===	+	<StructureSection load='2z5u' size='340' side='right' caption='[[2z5u]], [[Resolution\|resolution]] 2.25Å' scene=''>
-	~~{{ABSTRACT_PUBMED_18039463}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2z5u]] 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=2Z5U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z5U FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAJ:FAD-TRANS-2-PHENYLCYCLOPROPYLAMINE+ADDUCT'>FAJ</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ejr\|2ejr]], [[2z3y\|2z3y]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KIAA0601, LSD1 ([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=2z5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z5u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z5u RCSB], [http://www.ebi.ac.uk/pdbsum/2z5u PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z5/2z5u_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Transcriptional activity and chromatin structure accessibility are correlated with the methylation of specific histone residues. Lysine-specific demethylase 1 (LSD1) is the first discovered histone demethylase, which demethylates Lys4 or Lys9 of histone H3, using FAD. Among the known monoamine oxidase inhibitors, tranylcypromine (Parnate) showed the most potent inhibitory effect on LSD1. Recently, the crystal structure of LSD1 and tranylcypromine was solved at 2.75 A, revealing a five-membered ring fused to the flavin of LSD1. In this study, we refined the crystal structure of the LSD1-tranylcypromine complex to 2.25 A. The five-membered ring model did not fit completely with the electron density, giving R(work)/R(free) values of 0.226/0.254. On the other hand, the N(5) adduct gave the lowest R(work)/R(free) values of 0.218/0.248, among the tested models. These results imply that the LSD1-tranylcypromine complex is not completely composed of the five-membered adduct, but partially contains an intermediate, such as the N(5) adduct.

-	~~==About this Structure==~~	+	Crystal structure of histone demethylase LSD1 and tranylcypromine at 2.25 A.,Mimasu S, Sengoku T, Fukuzawa S, Umehara T, Yokoyama S Biochem Biophys Res Commun. 2008 Feb 1;366(1):15-22. Epub 2007 Nov 26. PMID:18039463<ref>PMID:18039463</ref>
-	~~[[2z5u]] 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=2Z5U OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Lysine-specific histone demethylase 1\|Lysine-specific histone demethylase 1]]		*[[Lysine-specific histone demethylase 1\|Lysine-specific histone demethylase 1]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:018039463</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Mimasu, S.]]		[[Category: Mimasu, S.]]

OCA at 07:42, 27 March 2013

2013-03-27T07:42:54Z

←Older revision		Revision as of 07:42, 27 March 2013
Line 1:		Line 1:
-	[[Image:2z5u.png\|left\|200px]]
-
	{{STRUCTURE_2z5u\| PDB=2z5u \| SCENE= }}		{{STRUCTURE_2z5u\| PDB=2z5u \| SCENE= }}
-
	===Crystal structure of Lysine-specific histone demethylase 1===		===Crystal structure of Lysine-specific histone demethylase 1===
-
	{{ABSTRACT_PUBMED_18039463}}		{{ABSTRACT_PUBMED_18039463}}

Line 14:		Line 10:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:018039463</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018039463</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Mimasu, S.]]		[[Category: Mimasu, S.]]

OCA at 14:38, 20 October 2012

2012-10-20T14:38:59Z

←Older revision		Revision as of 14:38, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2z5u]] is a 1 chain structure ~~of [[Lysine-specific histone demethylase 1]]~~ 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=2Z5U OCA].	+	[[2z5u]] 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=2Z5U OCA].

	==See Also==		==See Also==

OCA: Protected "2z5u" [edit=sysop:move=sysop]

2012-07-26T15:48:07Z

Protected "2z5u" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:48, 26 July 2012