3zmt - Revision history

OCA at 11:06, 20 December 2023

OCA — Wed, 20 Dec 2023 11:06:23 GMT

←Older revision		Revision as of 11:06, 20 December 2023
Line 3:		Line 3:
	<StructureSection load='3zmt' size='340' side='right'caption='[[3zmt]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='3zmt' size='340' side='right'caption='[[3zmt]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3zmt]] is a 3 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=3ZMT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZMT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3zmt]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZMT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZMT FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FAD:FLAVIN~~-~~ADENINE+DINUCLEOTIDE'>FAD</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]] 3.1Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[3zms\|3zms]], [[3zmu\|3zmu]], [[3zmv\|3zmv]], [[3zmz\|3zmz]], [[3zn0\|3zn0]], [[3zn1\|3zn1]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3zmt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zmt OCA], [https://pdbe.org/3zmt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zmt RCSB], [https://www.ebi.ac.uk/pdbsum/3zmt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zmt 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=3zmt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zmt OCA], [https://pdbe.org/3zmt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zmt RCSB], [https://www.ebi.ac.uk/pdbsum/3zmt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zmt 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/RCOR1_HUMAN RCOR1_HUMAN]] Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. The BHC complex is recruited at RE1/NRSE sites by REST and acts by deacetylating and demethylating specific sites on histones, thereby acting as a chromatin modifier. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. It also protects KDM1A from the proteasome. 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 and controls hematopoietic differentiation.<ref>PMID:11516394</ref> <ref>PMID:11171972</ref> <ref>PMID:12032298</ref> <ref>PMID:12399542</ref> <ref>PMID:12493763</ref> <ref>PMID:16140033</ref> <ref>PMID:16079794</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>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Baron, R]]	+	[[Category: Baron R]]
-	[[Category: Borrello~~, M T~~]]	+	[[Category: Borrello MT]]
-	[[Category: Chiarelli~~, L R~~]]	+	[[Category: Chiarelli LR]]
-	[[Category: Ciossani, G]]	+	[[Category: Ciossani G]]
-	[[Category: ~~Connell, M O~~]]	+	[[Category: Cowan J]]
-	[[Category: ~~Cowan, J~~]]	+	[[Category: Ganesan A]]
-	[[Category: ~~Ganesan,~~ A]]	+	[[Category: Mai A]]
-	[[Category: ~~Mai,~~ A]]	+	[[Category: Mattevi A]]
-	[[Category: ~~Mattevi, A~~]]	+	[[Category: O'Connell M]]
-	[[Category: Pilotto, S]]	+	[[Category: Pilotto S]]
-	[[Category: Tardugno, M]]	+	[[Category: Tardugno M]]
-	[[Category: Tortorici, M]]	+	[[Category: Tortorici M]]
-	[[Category: Vellore~~, N A]]~~	+	[[Category: Vellore NA]]
-	~~[[Category: Chromatin]]~~	+
-	~~[[Category: Demethylase]]~~	+
-	~~[[Category: Oxidoreductase-peptide complex]]~~	+
-	~~[[Category: Transcription factor~~]]	+

OCA at 07:01, 18 August 2022

OCA — Thu, 18 Aug 2022 07:01:56 GMT

←Older revision		Revision as of 07:01, 18 August 2022
Line 1:		Line 1:

	==LSD1-CoREST in complex with PRSFLV peptide==		==LSD1-CoREST in complex with PRSFLV peptide==
-	<StructureSection load='3zmt' size='340' side='right' caption='[[3zmt]], [[Resolution\|resolution]] 3.10Å' scene=''>	+	<StructureSection load='3zmt' size='340' side='right'caption='[[3zmt]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3zmt]] is a 3 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=3ZMT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3ZMT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3zmt]] is a 3 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=3ZMT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZMT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zms\|3zms]], [[3zmu\|3zmu]], [[3zmv\|3zmv]], [[3zmz\|3zmz]], [[3zn0\|3zn0]], [[3zn1\|3zn1]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3zms\|3zms]], [[3zmu\|3zmu]], [[3zmv\|3zmv]], [[3zmz\|3zmz]], [[3zn0\|3zn0]], [[3zn1\|3zn1]]</div></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=3zmt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zmt OCA], [~~http~~://pdbe.org/3zmt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3zmt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3zmt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3zmt 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=3zmt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zmt OCA], [https://pdbe.org/3zmt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zmt RCSB], [https://www.ebi.ac.uk/pdbsum/3zmt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zmt 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> [[~~http~~://www.uniprot.org/uniprot/RCOR1_HUMAN RCOR1_HUMAN]] Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. The BHC complex is recruited at RE1/NRSE sites by REST and acts by deacetylating and demethylating specific sites on histones, thereby acting as a chromatin modifier. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. It also protects KDM1A from the proteasome. 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 and controls hematopoietic differentiation.<ref>PMID:11516394</ref> <ref>PMID:11171972</ref> <ref>PMID:12032298</ref> <ref>PMID:12399542</ref> <ref>PMID:12493763</ref> <ref>PMID:16140033</ref> <ref>PMID:16079794</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> [[https://www.uniprot.org/uniprot/RCOR1_HUMAN RCOR1_HUMAN]] Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. The BHC complex is recruited at RE1/NRSE sites by REST and acts by deacetylating and demethylating specific sites on histones, thereby acting as a chromatin modifier. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. It also protects KDM1A from the proteasome. 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 and controls hematopoietic differentiation.<ref>PMID:11516394</ref> <ref>PMID:11171972</ref> <ref>PMID:12032298</ref> <ref>PMID:12399542</ref> <ref>PMID:12493763</ref> <ref>PMID:16140033</ref> <ref>PMID:16079794</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:

	==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 27:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Baron, R]]		[[Category: Baron, R]]
	[[Category: Borrello, M T]]		[[Category: Borrello, M T]]

OCA at 22:19, 4 August 2016

OCA — Thu, 04 Aug 2016 22:19:55 GMT

←Older revision		Revision as of 22:19, 4 August 2016
Line 1:		Line 1:
		+
	==LSD1-CoREST in complex with PRSFLV peptide==		==LSD1-CoREST in complex with PRSFLV peptide==
	<StructureSection load='3zmt' size='340' side='right' caption='[[3zmt]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='3zmt' size='340' side='right' caption='[[3zmt]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3zmt]] is a 3 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=3ZMT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZMT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3zmt]] is a 3 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=3ZMT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZMT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zms\|3zms]], [[3zmu\|3zmu]], [[3zmv\|3zmv]], [[3zmz\|3zmz]], [[3zn0\|3zn0]], [[3zn1\|3zn1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zms\|3zms]], [[3zmu\|3zmu]], [[3zmv\|3zmv]], [[3zmz\|3zmz]], [[3zn0\|3zn0]], [[3zn1\|3zn1]]</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=3zmt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zmt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3zmt RCSB], [http://www.ebi.ac.uk/pdbsum/3zmt 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=3zmt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zmt OCA], [http://pdbe.org/3zmt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3zmt RCSB], [http://www.ebi.ac.uk/pdbsum/3zmt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3zmt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/RCOR1_HUMAN RCOR1_HUMAN]] Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. The BHC complex is recruited at RE1/NRSE sites by REST and acts by deacetylating and demethylating specific sites on histones, thereby acting as a chromatin modifier. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. It also protects KDM1A from the proteasome. 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 and controls hematopoietic differentiation.<ref>PMID:11516394</ref> <ref>PMID:11171972</ref> <ref>PMID:12032298</ref> <ref>PMID:12399542</ref> <ref>PMID:12493763</ref> <ref>PMID:16140033</ref> <ref>PMID:16079794</ref>	+	[[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> [[http://www.uniprot.org/uniprot/RCOR1_HUMAN RCOR1_HUMAN]] Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. The BHC complex is recruited at RE1/NRSE sites by REST and acts by deacetylating and demethylating specific sites on histones, thereby acting as a chromatin modifier. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. It also protects KDM1A from the proteasome. 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 and controls hematopoietic differentiation.<ref>PMID:11516394</ref> <ref>PMID:11171972</ref> <ref>PMID:12032298</ref> <ref>PMID:12399542</ref> <ref>PMID:12493763</ref> <ref>PMID:16140033</ref> <ref>PMID:16079794</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 18:
	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 3zmt" 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: Baron, R]]		[[Category: Baron, R]]
	[[Category: Borrello, M T]]		[[Category: Borrello, M T]]

OCA at 13:36, 25 December 2014

OCA — Thu, 25 Dec 2014 13:36:10 GMT

←Older revision		Revision as of 13:36, 25 December 2014
Line 7:		Line 7:
	<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=3zmt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zmt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3zmt RCSB], [http://www.ebi.ac.uk/pdbsum/3zmt 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=3zmt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zmt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3zmt RCSB], [http://www.ebi.ac.uk/pdbsum/3zmt PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RCOR1_HUMAN RCOR1_HUMAN]] Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. The BHC complex is recruited at RE1/NRSE sites by REST and acts by deacetylating and demethylating specific sites on histones, thereby acting as a chromatin modifier. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. It also protects KDM1A from the proteasome. 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 and controls hematopoietic differentiation.<ref>PMID:11516394</ref> <ref>PMID:11171972</ref> <ref>PMID:12032298</ref> <ref>PMID:12399542</ref> <ref>PMID:12493763</ref> <ref>PMID:16140033</ref> <ref>PMID:16079794</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 09:59, 21 December 2014

OCA — Sun, 21 Dec 2014 09:59:14 GMT

←Older revision		Revision as of 09:59, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3zmt~~\| ~~PDB~~=3zmt \| ~~SCENE~~= }}	+	==LSD1-CoREST in complex with PRSFLV peptide==
-	===LSD1-CoREST in ~~complex~~ with ~~PRSFLV~~ peptide~~===~~	+	<StructureSection load='3zmt' size='340' side='right' caption='[[3zmt]], [[Resolution\|resolution]] 3.10Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23721412}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3zmt]] is a 3 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=3ZMT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZMT FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zms\|3zms]], [[3zmu\|3zmu]], [[3zmv\|3zmv]], [[3zmz\|3zmz]], [[3zn0\|3zn0]], [[3zn1\|3zn1]]</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=3zmt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zmt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3zmt RCSB], [http://www.ebi.ac.uk/pdbsum/3zmt PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The combinatorial assembly of protein complexes is at the heart of chromatin biology. Lysine demethylase LSD1(KDM1A)/CoREST beautifully exemplifies this concept. The active site of the enzyme tightly associates to the N-terminal domain of transcription factors of the SNAIL1 family, which therefore can competitively inhibit the binding of the N-terminal tail of the histone substrate. Our enzymatic, crystallographic, spectroscopic, and computational studies reveal that LSD1/CoREST can bind to a hexapeptide derived from the SNAIL sequence through recognition of a positively charged alpha-helical turn that forms upon binding to the enzyme. Variations in sequence and length of this six amino acid ligand modulate affinities enabling the same binding site to differentially interact with proteins that exert distinct biological functions. The discovered short peptide inhibitors exhibit antiproliferative activities and lay the foundation for the development of peptidomimetic small molecule inhibitors of LSD1.

-	~~==Function==~~	+	PROTEIN RECOGNITION BY SMALL PEPTIDE REVERSIBLE INHIBITORS OF THE CHROMATIN-MODIFYING LSD1/CoREST LYSINE DEMETHYLASE.,Tortorici M, Borrello MT, Tardugno M, Chiarelli LR, Pilotto S, Ciossani G, Vellore NA, Bailey SG, Cowan J, O'Connell M, Crabb SJ, Packham GK, Mai A, Baron R, Ganesan A, Mattevi A ACS Chem Biol. 2013 May 30. PMID:23721412<ref>PMID:23721412</ref>
-	~~[[http:/~~/~~www~~.~~uniprot.org/uniprot/RCOR1_HUMAN RCOR1_HUMAN]] Essential component of the BHC complex~~, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. The BHC complex is recruited at RE1/NRSE sites by REST and acts by deacetylating and demethylating specific sites on histones, ~~thereby acting as a chromatin modifier. In the BHC complex~~, ~~it serves as a molecular beacon for the recruitment of molecular machinery~~, ~~including MeCP2 and SUV39H1~~, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. It also protects KDM1A from the proteasome. 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 and controls hematopoietic differentiation~~.~~<ref>~~PMID:~~11516394</ref> <ref>PMID:11171972</ref> <ref>PMID:12032298</ref> <ref>PMID:12399542</ref> <ref>PMID:12493763</ref> <ref>PMID:16140033</ref>~~ <ref>PMID:~~16079794~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3zmt]] is~~ a ~~3 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=3ZMT OCA].~~	+	</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:023721412</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Baron, R.]]	+	[[Category: Baron, R]]
-	[[Category: Borrello, M T.]]	+	[[Category: Borrello, M T]]
-	[[Category: Chiarelli, L R.]]	+	[[Category: Chiarelli, L R]]
-	[[Category: Ciossani, G.]]	+	[[Category: Ciossani, G]]
-	[[Category: Connell, M O.]]	+	[[Category: Connell, M O]]
-	[[Category: Cowan, J.]]	+	[[Category: Cowan, J]]
-	[[Category: Ganesan, A.]]	+	[[Category: Ganesan, A]]
-	[[Category: Mai, A.]]	+	[[Category: Mai, A]]
-	[[Category: Mattevi, A.]]	+	[[Category: Mattevi, A]]
-	[[Category: Pilotto, S.]]	+	[[Category: Pilotto, S]]
-	[[Category: Tardugno, M.]]	+	[[Category: Tardugno, M]]
-	[[Category: Tortorici, M.]]	+	[[Category: Tortorici, M]]
-	[[Category: Vellore, N A.]]	+	[[Category: Vellore, N A]]
	[[Category: Chromatin]]		[[Category: Chromatin]]
	[[Category: Demethylase]]		[[Category: Demethylase]]
	[[Category: Oxidoreductase-peptide complex]]		[[Category: Oxidoreductase-peptide complex]]
	[[Category: Transcription factor]]		[[Category: Transcription factor]]

OCA at 05:38, 28 August 2013

OCA — Wed, 28 Aug 2013 05:38:37 GMT

←Older revision		Revision as of 05:38, 28 August 2013
Line 8:		Line 8:
	==About this Structure==		==About this Structure==
	[[3zmt]] is a 3 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=3ZMT OCA].		[[3zmt]] is a 3 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=3ZMT OCA].
		+
		+	==See Also==
		+	*[[Lysine-specific histone demethylase 1\|Lysine-specific histone demethylase 1]]

	==Reference==		==Reference==

OCA at 17:58, 19 June 2013

OCA — Wed, 19 Jun 2013 17:58:14 GMT

←Older revision		Revision as of 17:58, 19 June 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_3zmt\| PDB=3zmt \| SCENE= }}
		+	===LSD1-CoREST in complex with PRSFLV peptide===
		+	{{ABSTRACT_PUBMED_23721412}}

-	The ~~entry 3zmt~~ is ~~ON HOLD~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/RCOR1_HUMAN RCOR1_HUMAN]] Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. The BHC complex is recruited at RE1/NRSE sites by REST and acts by deacetylating and demethylating specific sites on histones, thereby acting as a chromatin modifier. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. It also protects KDM1A from the proteasome. 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 and controls hematopoietic differentiation.<ref>PMID:11516394</ref> <ref>PMID:11171972</ref> <ref>PMID:12032298</ref> <ref>PMID:12399542</ref> <ref>PMID:12493763</ref> <ref>PMID:16140033</ref> <ref>PMID:16079794</ref>

-	~~Authors~~: ~~Tortorici, M~~.~~, Borrello, M~~.T.~~, Tardugno, M., Chiarelli, L.R., Pilotto, S., Ciossani, G., Vellore, N.A., Cowan, J., O'Connell, M., Mai, A~~.~~, Baron, R~~.~~, Ganesan, A~~.~~, Mattevi, A~~.	+	==About this Structure==
		+	[[3zmt]] is a 3 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=3ZMT OCA].

-	~~Description~~:	+	==Reference==
		+	<ref group="xtra">PMID:023721412</ref><references group="xtra"/><references/>
		+	[[Category: Homo sapiens]]
		+	[[Category: Baron, R.]]
		+	[[Category: Borrello, M T.]]
		+	[[Category: Chiarelli, L R.]]
		+	[[Category: Ciossani, G.]]
		+	[[Category: Connell, M O.]]
		+	[[Category: Cowan, J.]]
		+	[[Category: Ganesan, A.]]
		+	[[Category: Mai, A.]]
		+	[[Category: Mattevi, A.]]
		+	[[Category: Pilotto, S.]]
		+	[[Category: Tardugno, M.]]
		+	[[Category: Tortorici, M.]]
		+	[[Category: Vellore, N A.]]
		+	[[Category: Chromatin]]
		+	[[Category: Demethylase]]
		+	[[Category: Oxidoreductase-peptide complex]]
		+	[[Category: Transcription factor]]

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

OCA — Wed, 20 Feb 2013 13:13:05 GMT

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

←Older revision

Revision as of 13:13, 20 February 2013

OCA: New page: '''Unreleased structure''' The entry 3zmt is ON HOLD Authors: Tortorici, M., Borrello, M.T., Tardugno, M., Chiarelli, L.R., Pilotto, S., Ciossani, G., Vellore, N.A., Cowan, J., O'Connel...

OCA — Wed, 20 Feb 2013 13:13:04 GMT

New page: '''Unreleased structure''' The entry 3zmt is ON HOLD Authors: Tortorici, M., Borrello, M.T., Tardugno, M., Chiarelli, L.R., Pilotto, S., Ciossani, G., Vellore, N.A., Cowan, J., O'Connel...

New page

'''Unreleased structure'''

The entry 3zmt is ON HOLD

Authors: Tortorici, M., Borrello, M.T., Tardugno, M., Chiarelli, L.R., Pilotto, S., Ciossani, G., Vellore, N.A., Cowan, J., O'Connell, M., Mai, A., Baron, R., Ganesan, A., Mattevi, A.

Description: