4bay - Revision history

OCA at 11:46, 20 December 2023

2023-12-20T11:46:57Z

←Older revision		Revision as of 11:46, 20 December 2023
Line 3:		Line 3:
	<StructureSection load='4bay' size='340' side='right'caption='[[4bay]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='4bay' size='340' side='right'caption='[[4bay]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4bay]] is a 2 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=4BAY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BAY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4bay]] is a 2 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=4BAY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BAY 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;~~'>[[2com\|2com]], [[2h94\|2h94]], [[2iw5\|2iw5]], [[2uxn\|2uxn]], [[2uxx\|2uxx]], [[2v1d\|2v1d]], [[2x0l\|2x0l]], [[2xaf\|2xaf]], [[2xag\|2xag]], [[2xah\|2xah]], [[2xaj\|2xaj]], [[2xaq\|2xaq]], [[2xas\|2xas]], [[2y48\|2y48]]</~~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=4bay FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bay OCA], [https://pdbe.org/4bay PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bay RCSB], [https://www.ebi.ac.uk/pdbsum/4bay PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bay 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=4bay FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bay OCA], [https://pdbe.org/4bay PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bay RCSB], [https://www.ebi.ac.uk/pdbsum/4bay PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bay 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: Battaglioli, E]]	+	[[Category: Battaglioli E]]
-	[[Category: Maffioli, E]]	+	[[Category: Maffioli E]]
-	[[Category: Mattevi, A]]	+	[[Category: Mattevi A]]
-	[[Category: Paganini, L]]	+	[[Category: Paganini L]]
-	[[Category: Pilotto, S]]	+	[[Category: Pilotto S]]
-	[[Category: Rusconi, F]]	+	[[Category: Rusconi F]]
-	[[Category: Sala, C]]	+	[[Category: Sala C]]
-	[[Category: Tedeschi, G]]	+	[[Category: Tedeschi G]]
-	[[Category: Toffolo, E]]	+	[[Category: Toffolo E]]
-	[[Category: Tortorici, M]]	+	[[Category: Tortorici M]]
-	[[Category: Verpelli, C]]	+	[[Category: Verpelli C]]
-	~~[[Category: Demethylase splicing chromatin]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 07:06, 31 August 2022

2022-08-31T07:06:18Z

←Older revision		Revision as of 07:06, 31 August 2022
Line 3:		Line 3:
	<StructureSection load='4bay' size='340' side='right'caption='[[4bay]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='4bay' size='340' side='right'caption='[[4bay]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4bay]] is a 2 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=4BAY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4BAY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4bay]] is a 2 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=4BAY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BAY 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">[[2com\|2com]], [[2h94\|2h94]], [[2iw5\|2iw5]], [[2uxn\|2uxn]], [[2uxx\|2uxx]], [[2v1d\|2v1d]], [[2x0l\|2x0l]], [[2xaf\|2xaf]], [[2xag\|2xag]], [[2xah\|2xah]], [[2xaj\|2xaj]], [[2xaq\|2xaq]], [[2xas\|2xas]], [[2y48\|2y48]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2com\|2com]], [[2h94\|2h94]], [[2iw5\|2iw5]], [[2uxn\|2uxn]], [[2uxx\|2uxx]], [[2v1d\|2v1d]], [[2x0l\|2x0l]], [[2xaf\|2xaf]], [[2xag\|2xag]], [[2xah\|2xah]], [[2xaj\|2xaj]], [[2xaq\|2xaq]], [[2xas\|2xas]], [[2y48\|2y48]]</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=4bay FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bay OCA], [~~http~~://pdbe.org/4bay PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4bay RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4bay PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4bay 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=4bay FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bay OCA], [https://pdbe.org/4bay PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bay RCSB], [https://www.ebi.ac.uk/pdbsum/4bay PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bay 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/>

OCA at 13:10, 13 March 2019

2019-03-13T13:10:52Z

←Older revision		Revision as of 13:10, 13 March 2019
Line 1:		Line 1:

	==Phosphomimetic mutant of LSD1-8a splicing variant in complex with CoREST==		==Phosphomimetic mutant of LSD1-8a splicing variant in complex with CoREST==
-	<StructureSection load='4bay' size='340' side='right' caption='[[4bay]], [[Resolution\|resolution]] 3.10Å' scene=''>	+	<StructureSection load='4bay' size='340' side='right'caption='[[4bay]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4bay]] is a 2 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=4BAY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4BAY FirstGlance]. <br>		<table><tr><td colspan='2'>[[4bay]] is a 2 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=4BAY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4BAY FirstGlance]. <br>
Line 27:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Battaglioli, E]]		[[Category: Battaglioli, E]]
	[[Category: Maffioli, E]]		[[Category: Maffioli, E]]

OCA at 00:09, 5 August 2016

2016-08-05T00:09:38Z

←Older revision		Revision as of 00:09, 5 August 2016
Line 1:		Line 1:
		+
	==Phosphomimetic mutant of LSD1-8a splicing variant in complex with CoREST==		==Phosphomimetic mutant of LSD1-8a splicing variant in complex with CoREST==
	<StructureSection load='4bay' size='340' side='right' caption='[[4bay]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='4bay' size='340' side='right' caption='[[4bay]], [[Resolution\|resolution]] 3.10Å' scene=''>
Line 5:		Line 6:
	</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">[[2com\|2com]], [[2h94\|2h94]], [[2iw5\|2iw5]], [[2uxn\|2uxn]], [[2uxx\|2uxx]], [[2v1d\|2v1d]], [[2x0l\|2x0l]], [[2xaf\|2xaf]], [[2xag\|2xag]], [[2xah\|2xah]], [[2xaj\|2xaj]], [[2xaq\|2xaq]], [[2xas\|2xas]], [[2y48\|2y48]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2com\|2com]], [[2h94\|2h94]], [[2iw5\|2iw5]], [[2uxn\|2uxn]], [[2uxx\|2uxx]], [[2v1d\|2v1d]], [[2x0l\|2x0l]], [[2xaf\|2xaf]], [[2xag\|2xag]], [[2xah\|2xah]], [[2xaj\|2xaj]], [[2xaq\|2xaq]], [[2xas\|2xas]], [[2y48\|2y48]]</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=4bay FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bay OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4bay RCSB], [http://www.ebi.ac.uk/pdbsum/4bay 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=4bay FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bay OCA], [http://pdbe.org/4bay PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4bay RCSB], [http://www.ebi.ac.uk/pdbsum/4bay PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4bay ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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 4bay" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Lysine-specific histone demethylase\|Lysine-specific histone demethylase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:02, 24 December 2014

2014-12-24T21:02:56Z

←Older revision		Revision as of 21:02, 24 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4bay\| PDB=4bay \| SCENE= }}~~	+	==Phosphomimetic mutant of LSD1-8a splicing variant in complex with CoREST==
-	===Phosphomimetic mutant of LSD1-8a splicing variant in complex with CoREST===	+	<StructureSection load='4bay' size='340' side='right' caption='[[4bay]], [[Resolution\|resolution]] 3.10Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24111946}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4bay]] is a 2 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=4BAY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4BAY FirstGlance]. <br>
-	==Function==	+	</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">[[2com\|2com]], [[2h94\|2h94]], [[2iw5\|2iw5]], [[2uxn\|2uxn]], [[2uxx\|2uxx]], [[2v1d\|2v1d]], [[2x0l\|2x0l]], [[2xaf\|2xaf]], [[2xag\|2xag]], [[2xah\|2xah]], [[2xaj\|2xaj]], [[2xaq\|2xaq]], [[2xas\|2xas]], [[2y48\|2y48]]</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=4bay FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bay OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4bay RCSB], [http://www.ebi.ac.uk/pdbsum/4bay PDBsum]</span></td></tr>
		+	</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> [[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;">
		+	== Publication Abstract from PubMed ==
		+	Epigenetic mechanisms play important roles in brain development, orchestrating proliferation, differentiation, and morphogenesis. Lysine-Specific Demethylase 1 (LSD1 also known as KDM1A and AOF2) is a histone modifier involved in transcriptional repression, forming a stable core complex with the corepressors corepressor of REST (CoREST) and histone deacetylases (HDAC1/2). Importantly, in the mammalian CNS, neuronal LSD1-8a, an alternative splicing isoform of LSD1 including the mini-exon E8a, sets alongside LSD1 and is capable of enhancing neurite growth and morphogenesis. Here, we describe that the morphogenic properties of neuronal LSD1-8a require switching off repressive activity and this negative modulation is mediated in vivo by phosphorylation of the Thr369b residue coded by exon E8a. Three-dimensional crystal structure analysis using a phospho-mimetic mutant (Thr369bAsp), indicate that phosphorylation affects the residues surrounding the exon E8a-coded amino acids, causing a local conformational change. We suggest that phosphorylation, without affecting demethylase activity, causes in neurons CoREST and HDAC1/2 corepressors detachment from LSD1-8a and impairs neuronal LSD1-8a repressive activity. In neurons, Thr369b phosphorylation is required for morphogenic activity, converting neuronal LSD1-8a in a dominant-negative isoform, challenging LSD1-mediated transcriptional repression on target genes.

-	~~==About this Structure==~~	+	Phosphorylation of neuronal Lysine-Specific Demethylase 1LSD1/KDM1A impairs transcriptional repression by regulating interaction with CoREST and histone deacetylases HDAC1/2.,Toffolo E, Rusconi F, Paganini L, Tortorici M, Pilotto S, Heise C, Verpelli C, Tedeschi G, Maffioli E, Sala C, Mattevi A, Battaglioli E J Neurochem. 2013 Sep 20. doi: 10.1111/jnc.12457. PMID:24111946<ref>PMID:24111946</ref>
-	~~[[4bay]] is a 2 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=4BAY OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024111946</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Human]]		[[Category: Human]]
-	[[Category: Battaglioli, E.]]	+	[[Category: Battaglioli, E]]
-	[[Category: Maffioli, E.]]	+	[[Category: Maffioli, E]]
-	[[Category: Mattevi, A.]]	+	[[Category: Mattevi, A]]
-	[[Category: Paganini, L.]]	+	[[Category: Paganini, L]]
-	[[Category: Pilotto, S.]]	+	[[Category: Pilotto, S]]
-	[[Category: Rusconi, F.]]	+	[[Category: Rusconi, F]]
-	[[Category: Sala, C.]]	+	[[Category: Sala, C]]
-	[[Category: Tedeschi, G.]]	+	[[Category: Tedeschi, G]]
-	[[Category: Toffolo, E.]]	+	[[Category: Toffolo, E]]
-	[[Category: Tortorici, M.]]	+	[[Category: Tortorici, M]]
-	[[Category: Verpelli, C.]]	+	[[Category: Verpelli, C]]
	[[Category: Demethylase splicing chromatin]]		[[Category: Demethylase splicing chromatin]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 09:49, 19 March 2014

2014-03-19T09:49:18Z

←Older revision		Revision as of 09:49, 19 March 2014
Line 7:		Line 7:

	==About this Structure==		==About this Structure==
-	[[4bay]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BAY OCA].	+	[[4bay]] is a 2 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=4BAY OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:024111946</ref><references group="xtra"/><references/>		<ref group="xtra">PMID:024111946</ref><references group="xtra"/><references/>
		+	[[Category: Human]]
	[[Category: Battaglioli, E.]]		[[Category: Battaglioli, E.]]
	[[Category: Maffioli, E.]]		[[Category: Maffioli, E.]]

OCA at 10:26, 27 November 2013

2013-11-27T10:26:20Z

←Older revision		Revision as of 10:26, 27 November 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4bay\| PDB=4bay \| SCENE= }}
		+	===Phosphomimetic mutant of LSD1-8a splicing variant in complex with CoREST===
		+	{{ABSTRACT_PUBMED_24111946}}

-	~~The entry 4bay~~ is ~~ON HOLD~~ ~~until sometime~~ in the ~~future~~	+	==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>

-	~~Authors~~: ~~Toffolo, E., Paganini, L., Rusconi, F., Tortorici, M., Pilotto, S., Verpelli, C., Tedeschi, G., Maffioli, E~~.~~, Sala, C~~.~~, Mattevi, A~~.~~, Battaglioli, E~~.	+	==About this Structure==
		+	[[4bay]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BAY OCA].

-	~~Description~~: ~~Phosphomimetic mutant of LSD1-8a~~ splicing ~~variant in complex with CoREST~~	+	==Reference==
		+	<ref group="xtra">PMID:024111946</ref><references group="xtra"/><references/>
		+	[[Category: Battaglioli, E.]]
		+	[[Category: Maffioli, E.]]
		+	[[Category: Mattevi, A.]]
		+	[[Category: Paganini, L.]]
		+	[[Category: Pilotto, S.]]
		+	[[Category: Rusconi, F.]]
		+	[[Category: Sala, C.]]
		+	[[Category: Tedeschi, G.]]
		+	[[Category: Toffolo, E.]]
		+	[[Category: Tortorici, M.]]
		+	[[Category: Verpelli, C.]]
		+	[[Category: Demethylase splicing chromatin]]
		+	[[Category: Oxidoreductase]]

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

2012-09-26T19:59:51Z

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

←Older revision

Revision as of 19:59, 26 September 2012

OCA: New page: '''Unreleased structure''' The entry 4bay is ON HOLD until sometime in the future Authors: Toffolo, E., Paganini, L., Rusconi, F., Tortorici, M., Pilotto, S., Verpelli, C., Tedeschi, G....

2012-09-26T19:59:50Z

New page: '''Unreleased structure''' The entry 4bay is ON HOLD until sometime in the future Authors: Toffolo, E., Paganini, L., Rusconi, F., Tortorici, M., Pilotto, S., Verpelli, C., Tedeschi, G....

New page

'''Unreleased structure'''

The entry 4bay is ON HOLD until sometime in the future

Authors: Toffolo, E., Paganini, L., Rusconi, F., Tortorici, M., Pilotto, S., Verpelli, C., Tedeschi, G., Maffioli, E., Sala, C., Mattevi, A., Battaglioli, E.

Description: Phosphomimetic mutant of LSD1-8a splicing variant in complex with CoREST