Histone deacetylase - Revision history

Michal Harel at 07:36, 11 February 2021

Michal Harel — Thu, 11 Feb 2021 07:36:35 GMT

←Older revision		Revision as of 07:36, 11 February 2021
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	* '''HDAC class III''' called '''sirtuin''' - (Silent Information Regulator) (SIRT) are NAD-dependent HDAC. This protein is bifunctional and can act as a deacylase or as mono-ADP-acetyltransferase. <ref>PMID:18249170</ref>.<br />		* '''HDAC class III''' called '''sirtuin''' - (Silent Information Regulator) (SIRT) are NAD-dependent HDAC. This protein is bifunctional and can act as a deacylase or as mono-ADP-acetyltransferase. <ref>PMID:18249170</ref>.<br />

-	For HDAC8 see - [[Histone deacetylase 8 (HDAC8)]].	+	For HDAC8 see - [[Histone deacetylase 8 (HDAC8)]].<br />
	For additional details see<br />		For additional details see<br />
	* [[Understanding of the Recruitment of HDACs by MEF2, Based on Their Structure]]<br />		* [[Understanding of the Recruitment of HDACs by MEF2, Based on Their Structure]]<br />

Michal Harel at 07:36, 11 February 2021

Michal Harel — Thu, 11 Feb 2021 07:36:11 GMT

←Older revision		Revision as of 07:36, 11 February 2021
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	* '''HDAC class II''' are homologous to yeast HdaI.<br />		* '''HDAC class II''' are homologous to yeast HdaI.<br />
	* '''HDAC class III''' called '''sirtuin''' - (Silent Information Regulator) (SIRT) are NAD-dependent HDAC. This protein is bifunctional and can act as a deacylase or as mono-ADP-acetyltransferase. <ref>PMID:18249170</ref>.<br />		* '''HDAC class III''' called '''sirtuin''' - (Silent Information Regulator) (SIRT) are NAD-dependent HDAC. This protein is bifunctional and can act as a deacylase or as mono-ADP-acetyltransferase. <ref>PMID:18249170</ref>.<br />
		+
		+	For HDAC8 see - [[Histone deacetylase 8 (HDAC8)]].
	For additional details see<br />		For additional details see<br />
	* [[Understanding of the Recruitment of HDACs by MEF2, Based on Their Structure]]<br />		* [[Understanding of the Recruitment of HDACs by MEF2, Based on Their Structure]]<br />

Michal Harel at 09:10, 31 July 2019

Michal Harel — Wed, 31 Jul 2019 09:10:59 GMT

←Older revision		Revision as of 09:10, 31 July 2019
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	</StructureSection>		</StructureSection>
-	== 3D Structures of histone deacetylase ==

-	Updated on {{REVISIONDAY2}}-{{MONTHNAME\|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
-	{{#tree:id=OrganizedByTopic\|openlevels=0\|
-
-	*'''HDAC class I'''
-
-	*HDAC1
-
-	**[[4bkx]] – hHDAC1 + MTA1 – human<br />
-	**[[3hgq]], [[3hgt]] – hHDAC1 subunit 3<br />
-	**[[5icn]] – hHDAC1 + MTA1 + peptide<br />
-	**[[5j8j]] – yHDAC1 residues 457-698 – yeast<br />
-
-	*HDAC2
-
-	**[[3max]] – hHDAC2 + amide derivative <br />
-	**[[4lxz]] – hHDAC2 core domain + SAHA<br />
-	**[[4ly1]], [[5iwg]], [[5ix0]] – hHDAC2 core domain + inhibitor<br />
-
-	*HDAC3
-
-	**[[4a69]] – hHDAC3 + nuclear receptor corepressor 2 + inositol tetraphosphate
-
-	*HDAC8
-
-	**[[3ew8]], [[3ezp]], [[3ezt]], [[3f06]] – hHDAC8 (mutant)<br />
-	**[[3sff]], [[3sfh]] – hHDAC8 + inhibitor<br />
-	**[[1t64]], [[3f0r]], [[5ths]] – hHDAC8 + trichostatin A <br />
-	**[[5tht]], [[5thu]], [[5thv]], [[5dc5]], [[5d1b]] - hHDAC8 (mutant) + amide derivative<br />
-	**[[1t67]], [[1w22]], [[1vkg]], [[3f07]] - hHDAC8 + amide derivative<br />
-	**[[1t69]] - hHDAC8 + SAHA<br />
-	**[[4qa0]] - hHDAC8 (mutant) + SAHA<br />
-	**[[5fcw]], [[5fue]] - hHDAC8 + hydroxamate<br />
-	**[[5vi6]] - hHDAC8 + trapoxin A<br />
-	**[[4qa1]], [[4qa2]], [[4qa3]], [[4qa4]] - hHDAC8 (mutant) + inhibitor<br />
-	**[[2v5w]] – hHDAC8 + tripeptide substrate<br />
-	**[[4qa5]], [[4qa6]], [[4qa7]], [[3ewf]], [[5dc8]], [[5dc7]], [[5dc6]], [[5d1d]], [[5d1c]] - hHDAC8 (mutant) + tetrapeptide substrate<br />
-	**[[3rqd]] - hHDAC8 + largazole<br />
-	**[[4rn0]], [[4rn1]], [[4rn2]] - hHDAC8 (mutant) + largazole analog<br />
-	**[[5bwz]] - hHDAC8 (mutant) + droxinostat<br />
-	**[[3mz3]] - hHDAC8 (Co) + amide derivative<br />
-	**[[3mz7]] - hHDAC8 (Co) (mutant) + amide derivative<br />
-	**[[3mz4]] - hHDAC8 (Mn) (mutant) + amide derivative<br />
-	**[[3mz6]] - hHDAC8 (Fe) (mutant) + amide derivative<br />
-	**[[2v5x]] - hHDAC8 (mutant) + octanediamide derivative<br />
-	**[[4bz5]] – SmHDAC8 – ''Schistosoma mansoni''<br />
-	**[[4bz7]], [[4bz8]], [[4bz9]], [[4cqf]], [[6hsz]], [[6ht8]], [[6htg]], [[6hth]], [[6hti]], [[6htt]], [[6htz]], [[6hu0]], [[6hu1]], [[6hu2]], [[6hu3]], [[6hsh]], [[6hrq]], [[6hqy]] – SmHDAC8 + inhibitor<br />
-	**[[6hsk]], [[6hsf]], [[6hsg]] – SmHDAC8 (mutant) + inhibitor<br />
-	**[[4bz6]], [[6gxw]], [[6gxu]], [[6gxa]], [[6gx3]], [[6fu1]] – SmHDAC8 + SAHA derivative<br />
-
-	*'''HDAC class IIA'''
-
-	*HDAC4
-
-	**[[2h8n]] – hHDAC4 N terminal <br />
-	**[[2o94]] - hHDAC4 N terminal (mutant)<br />
-	**[[2vqw]] - hHDAC4 catalytic domain (mutant)<br />
-	**[[2vqj]], [[2vqm]], [[4cbt]], [[5a2s]] – hHDAC4 catalytic domain + inhibitor<br />
-	**[[6fyz]] - hHDAC4 catalytic domain + SAHA derivative<br />
-	**[[2vqo]], [[2vqq]], [[2vqv]], [[4cby]] – hHDAC4 catalytic domain (mutant) + inhibitor<br />
-	**[[5zop]], [[5zoo]] - hHDAC4 catalytic domain (mutant) + SMRT corepressor<br />
-
-	*HDAC5
-
-	**[[5uwi]] – hHDAC5 + RAN + RANBP1 + exportin<br />
-
-	*HDAC7
-
-	**[[3c0y]] – hHDAC7 catalytic domain<br />
-	**[[3c0z]] - hHDAC7 catalytic domain + octanedioic acid hydroxyamide phenylamide<br />
-	**[[3c10]] - hHDAC7 catalytic domain + trichostatin A<br />
-	**[[3znr]], [[3zns]] - hHDAC7 catalytic domain + inhibitor<br />
-
-	*HDAC9
-
-	**[[1tqe]] – mHDAC9 + myocyte-specific enhancer factor + DNA – mouse
-
-	*HDAC
-
-	**[[4a6q]], [[4a90]] - hHDAC subunit SAP18 <br />
-	**[[2hde]] – hHDAC subunit SAP18 (mutant) – NMR<br />
-	**[[4a8x]] - hHDAC subunit SAP18 + RNA-binding protein + hook-like<br />
-	**[[2kdp]] – hHDAC subunit SAP30 – NMR<br />
-	**[[2ld7]] – hHDAC subunit SAP30 +SIN3A PAH 3 domain – NMR<br />
-	**[[5ikk]] – HDAC CLR3 – fission yeast<br />
-
-	*'''HDAC class IIB'''
-
-	*HDAC6
-
-	**[[3c5k]] – hHDAC6 zinc finger domain<br />
-	**[[3gv4]] - hHDAC6 zinc finger domain + ubiquitin peptide<br />
-	**[[3phd]] - hHDAC6 + polyubiquitin<br />
-	**[[5kh3]], [[5kh7]], [[5kh9]], [[5b8d]], [[6ce6]], [[6ce8]], [[6cea]], [[6cec]], [[6ced]], [[6cee]], [[6cef]], [[5wpb]], [[5wbn]] – hHDAC6 zinc finger + inhibitor<br />
-	**[[5eem]] – zHDAC6 catalytic domain - zebrafish<br />
-	**[[6cgp]], [[5wgm]], [[5wgl]], [[5wgi]], [[5wgk]], [[5g0j]], [[5g0i]], [[5g0h]], [[5g0g]], [[5g0f]], [[5efh]], [[5efg]], [[5efb]], [[5ef7]], [[5ef8]], [[5een]], [[5eek]], [[5eef]], [[6mr5]], [[6dvo]], [[6dvn]], [[6dvm]], [[6dvl]], [[6cw8]] – zHDAC6 catalytic domain + inhibitor <br />
-	**[[5eei]], [[6css]], [[6csr]], [[6csq]], [[6csp]], [[5w5k]] – zHDAC6 catalytic domain + SAHA derivative<br />
-	**[[5efn]], [[5efk]], [[53fj]] – zHDAC6 catalytic domain (mutant) + peptide <br />
-
-
-	*'''HDAC class III'''
-	*SIRT1
-
-	**[[4ig9]] – hSIRT1 + Zn<br />
-	**[[4i5i]] – hSIRT1 + NAD + indole + Zn<br />
-	**[[4if6]], [[4kxq]] – hSIRT1 + ADP-ribose + Zn<br />
-	**[[5btr]] – hSIRT1 + acetyl lysine peptide + resveratol + Zn<br />
-	**[[4zzh]] – hSIRT1 + activator + Zn<br />
-	**[[4zzi]] – hSIRT1 + activator + inhibitor + Zn<br />
-	**[[4zzj]] – hSIRT1 + acetyl lysine peptide + activator + Zn<br />
-
-	*SIRT2
-
-	**[[2hjh]] – ySIRT2 + pseudosubstrate + nicotinamide + Zn <br />
-	**[[4iao]] – ySIRT2 + SIRT4 + ADP-ribose + Zn<br />
-	**[[1j8f]], [[3zgo]] – hSIRT2 + Zn<br />
-	**[[5yqo]], [[5yqn]], [[5yqm]], [[5yql]] – hSIRT2 + inhibitor + Zn<br />
-	**[[5y0z]] – hSIRT2 (mutant) + inhibitor + Zn<br />
-	**[[3zgv]], [[5d7o]] – hSIRT2+ ADP ribose + Zn<br />
-	**[[4y6q]] – hSIRT2+ ADP ribose derivative + Zn<br />
-	**[[4l3o]], [[4y6l]], [[4y6o]] – hSIRT2 + acetyl lysine peptide + Zn<br />
-	**[[4x3o]], [[4x3p]] – hSIRT2 + myristoyl peptide + Zn<br />
-	**[[4rmg]], [[5dy4]], [[5dy5]], [[5y5n]], [[5mat]] – hSIRT2 + inhibitor + Zn<br />
-	**[[5d7p]], [[5d7q]], [[5mar]] – hSIRT2 + inhibitor + ADP-ribose + Zn<br />
-	**[[4rmh]], [[4rmi]] – hSIRT2 + acetyl lysine peptide + inhibitor + Zn<br />
-	**[[4r8m]] – hSIRT2 + peptide + tridecanethial + Zn<br />
-	**[[4rmj]] – hSIRT2 + ADP-ribose + nicotinamide + Zn <br />
-	**[[5g4c]] – hSIRT2 + carba-NAD + Zn<br/ >
-	**[[5fyq]] – hSIRT2 + RAN AA peptide + Zn<br/ >
-	**[[5dy5]] – hSIRT2 + thiazole derivative + piperazine derivative + Zn<br/ >
-	**[[5dy4]] – hSIRT2 + thiazole derivative + NAD + Zn<br/ >
-	**[[5d7q]], [[5d7p]], [[5d7o]] – hSIRT2 + oxolan derivative + Zn<br/ >
-
-	*SIRT3
-
-	**[[5d7n]] – hSIRT3 + Zn<br />
-	**[[3gls]] – hSIRT3 (mutant) + Zn<br />
-	**[[3glu]], [[5ytk]], [[5y4h]] – hSIRT3 + peptide + Zn<br />
-	**[[5bwo]], [[5bwn]] – hSIRT3 + palmitoyl H3K9 peptide + Zn<br />
-	**[[5bwl]] – hSIRT3 + succinyl peptide + Zn<br />
-	**[[3glr]], [[3glt]], [[4fvt]], [[4bve]], [[6iso]] – hSIRT3 + acetyl lysine peptide + Zn<br />
-	**[[4hd8]] – hSIRT3 + acetyl lysine peptide + piceatannol + Zn<br />
-	**[[4fz3]] – hSIRT3 + acetyl lysine peptide + coumarine derivative + Zn<br />
-	**[[4c78]], [[4c7b]] – hSIRT3 + acetyl lysine peptide + resveratol derivative + Zn<br />
-	**[[5zgc]], [[5z94]], [[5z93]] – hSIRT3 + histone peptide + Zn<br />
-	**[[4jsr]], [[4jt8]], [[4jt9]], [[4o8z]] – hSIRT3 + inhibitor + Zn<br />
-	**[[4gbn5]] – hSIRT3 + inhibitor + carba-NAD + Zn<br/ >
-	**[[4bv3]] – hSIRT3 + inhibitor + NAD + ADP-ribose + Zn<br />
-	**[[4bvb]], [[4bvh]] – hSIRT3 + inhibitor + ADP-ribose + Zn<br />
-	**[[4bvf]], [[4bvg]] – hSIRT3 + acetyl lysine peptide + inhibitor + Zn<br />
-	**[[5h4d]] – hSIRT3 + agonist + NAD + Zn<br/ >
-
-	*SIRT4
-
-	**[[5ojn]] – hSIRT4 + ADP-ribose + Zn – ''Xenopus tropicalis''<br />
-
-	*SIRT5
-
-	**[[2b4y]], [[4bn4]] – hSIRT5 + ADP-ribose + Zn<br />
-	**[[2nyr]], [[5xhs]] – hSIRT5 + inhibitor + Zn<br />
-	**[[3rig]], [[3riy]], [[4f4u]] – hSIRT5 + acetyl lysine peptide + Zn<br />
-	**[[4gic]] – hSIRT5 + acetyl lysine peptide + carba-NAD + Zn<br/ >
-	**[[4f56]] – hSIRT5 + peptide + intermediate + Zn<br />
-	**[[4hda]] – hSIRT5 + acetyl lysine peptide + resveratrol + Zn<br />
-	**[[6acp]], [[6aco]], [[6acl]], [[6ace]] – hSIRT5 + succinyl peptide + Zn<br />
-	**[[4utn]], [[4utr]], [[4utv]], [[4utx]], [[4utz]], [[4uu7]], [[4uu8]], [[4uua]], [[4uub]], [[6flg]], [[6fkz]], [[6fky]] – zSIRT5 + acetyl lysine peptide + inhibitor + Zn <br />
-	**[[6enx]], [[6eo0]], [[6eqs]] – zSIRT5 + inhibitor + Zn <br />
-	**[[5ojo]] – zSIRT5 + CPS1 peptide + Zn <br />
-
-	*SIRT6
-
-	**[[3k35]] – hSIRT6 + ADP-ribose + Zn<br />
-	**[[5x16]] – hSIRT6 + oxolan derivative + Zn<br />
-	**[[6hoy]] – hSIRT6 + ADP-ribose + trichostatin + Zn<br />
-	**[[3pki]], [[3pkj]] – hSIRT6 (mutant) + ADP-ribose derivative + Zn<br />
-	**[[3zg6]] – hSIRT6 + acetyl lysine peptide + ADP-ribose + Zn<br />
-	**[[5mgn]], [[5mfz]], [[5mfp]], [[5mf6]] – hSIRT6 + activator + Zn<br />
-	**[[5y2f]] – hSIRT6 + peptide activator + Zn<br />
-
-	*SIRT7
-
-	**[[5iqz]] – hSIRT7 N-terminal<br />
-
-	}}
	== References ==		== References ==
	<references/>		<references/>
	[[Category:Topic Page]]		[[Category:Topic Page]]

Michal Harel at 09:09, 31 July 2019

Michal Harel — Wed, 31 Jul 2019 09:09:45 GMT

←Older revision		Revision as of 09:09, 31 July 2019
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	== Structural highlights ==		== Structural highlights ==
	The biological assembly of Human sirtuin-3 is <scene name='48/483191/Cv/5'>homodimer</scene>. The <scene name='48/483191/Cv/6'>acetylated lysine of the peptide is inserted in an extended conformation</scene> between the 2 domains of SIRT3 - a large Rossman fold, NAD-binding domain and a small Zn-binding one)<ref>PMID:19535340</ref>. Water molecule shown as red sphere.		The biological assembly of Human sirtuin-3 is <scene name='48/483191/Cv/5'>homodimer</scene>. The <scene name='48/483191/Cv/6'>acetylated lysine of the peptide is inserted in an extended conformation</scene> between the 2 domains of SIRT3 - a large Rossman fold, NAD-binding domain and a small Zn-binding one)<ref>PMID:19535340</ref>. Water molecule shown as red sphere.
		+
		+	== 3D Structures of histone deacetylase ==
		+	[[Histone deacetylase 3D structures]]
		+
	</StructureSection>		</StructureSection>
	== 3D Structures of histone deacetylase ==		== 3D Structures of histone deacetylase ==
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	**[[4iao]] – ySIRT2 + SIRT4 + ADP-ribose + Zn<br />		**[[4iao]] – ySIRT2 + SIRT4 + ADP-ribose + Zn<br />
	**[[1j8f]], [[3zgo]] – hSIRT2 + Zn<br />		**[[1j8f]], [[3zgo]] – hSIRT2 + Zn<br />
		+	**[[5yqo]], [[5yqn]], [[5yqm]], [[5yql]] – hSIRT2 + inhibitor + Zn<br />
		+	**[[5y0z]] – hSIRT2 (mutant) + inhibitor + Zn<br />
	**[[3zgv]], [[5d7o]] – hSIRT2+ ADP ribose + Zn<br />		**[[3zgv]], [[5d7o]] – hSIRT2+ ADP ribose + Zn<br />
	**[[4y6q]] – hSIRT2+ ADP ribose derivative + Zn<br />		**[[4y6q]] – hSIRT2+ ADP ribose derivative + Zn<br />
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	**[[4fz3]] – hSIRT3 + acetyl lysine peptide + coumarine derivative + Zn<br />		**[[4fz3]] – hSIRT3 + acetyl lysine peptide + coumarine derivative + Zn<br />
	**[[4c78]], [[4c7b]] – hSIRT3 + acetyl lysine peptide + resveratol derivative + Zn<br />		**[[4c78]], [[4c7b]] – hSIRT3 + acetyl lysine peptide + resveratol derivative + Zn<br />
		+	**[[5zgc]], [[5z94]], [[5z93]] – hSIRT3 + histone peptide + Zn<br />
	**[[4jsr]], [[4jt8]], [[4jt9]], [[4o8z]] – hSIRT3 + inhibitor + Zn<br />		**[[4jsr]], [[4jt8]], [[4jt9]], [[4o8z]] – hSIRT3 + inhibitor + Zn<br />
	**[[4gbn5]] – hSIRT3 + inhibitor + carba-NAD + Zn<br/ >		**[[4gbn5]] – hSIRT3 + inhibitor + carba-NAD + Zn<br/ >
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	**[[4f56]] – hSIRT5 + peptide + intermediate + Zn<br />		**[[4f56]] – hSIRT5 + peptide + intermediate + Zn<br />
	**[[4hda]] – hSIRT5 + acetyl lysine peptide + resveratrol + Zn<br />		**[[4hda]] – hSIRT5 + acetyl lysine peptide + resveratrol + Zn<br />
		+	**[[6acp]], [[6aco]], [[6acl]], [[6ace]] – hSIRT5 + succinyl peptide + Zn<br />
	**[[4utn]], [[4utr]], [[4utv]], [[4utx]], [[4utz]], [[4uu7]], [[4uu8]], [[4uua]], [[4uub]], [[6flg]], [[6fkz]], [[6fky]] – zSIRT5 + acetyl lysine peptide + inhibitor + Zn <br />		**[[4utn]], [[4utr]], [[4utv]], [[4utx]], [[4utz]], [[4uu7]], [[4uu8]], [[4uua]], [[4uub]], [[6flg]], [[6fkz]], [[6fky]] – zSIRT5 + acetyl lysine peptide + inhibitor + Zn <br />
	**[[6enx]], [[6eo0]], [[6eqs]] – zSIRT5 + inhibitor + Zn <br />		**[[6enx]], [[6eo0]], [[6eqs]] – zSIRT5 + inhibitor + Zn <br />
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	**[[3k35]] – hSIRT6 + ADP-ribose + Zn<br />		**[[3k35]] – hSIRT6 + ADP-ribose + Zn<br />
		+	**[[5x16]] – hSIRT6 + oxolan derivative + Zn<br />
		+	**[[6hoy]] – hSIRT6 + ADP-ribose + trichostatin + Zn<br />
	**[[3pki]], [[3pkj]] – hSIRT6 (mutant) + ADP-ribose derivative + Zn<br />		**[[3pki]], [[3pkj]] – hSIRT6 (mutant) + ADP-ribose derivative + Zn<br />
	**[[3zg6]] – hSIRT6 + acetyl lysine peptide + ADP-ribose + Zn<br />		**[[3zg6]] – hSIRT6 + acetyl lysine peptide + ADP-ribose + Zn<br />
	**[[5mgn]], [[5mfz]], [[5mfp]], [[5mf6]] – hSIRT6 + activator + Zn<br />		**[[5mgn]], [[5mfz]], [[5mfp]], [[5mf6]] – hSIRT6 + activator + Zn<br />
		+	**[[5y2f]] – hSIRT6 + peptide activator + Zn<br />

	*SIRT7		*SIRT7

Michal Harel at 08:35, 31 July 2019

Michal Harel — Wed, 31 Jul 2019 08:35:15 GMT

←Older revision		Revision as of 08:35, 31 July 2019
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	**[[2v5x]] - hHDAC8 (mutant) + octanediamide derivative<br />		**[[2v5x]] - hHDAC8 (mutant) + octanediamide derivative<br />
	**[[4bz5]] – SmHDAC8 – ''Schistosoma mansoni''<br />		**[[4bz5]] – SmHDAC8 – ''Schistosoma mansoni''<br />
-	**[[4bz7]], [[4bz8]], [[4bz9]], [[4cqf]] – SmHDAC8 + inhibitor<br />	+	**[[4bz7]], [[4bz8]], [[4bz9]], [[4cqf]], [[6hsz]], [[6ht8]], [[6htg]], [[6hth]], [[6hti]], [[6htt]], [[6htz]], [[6hu0]], [[6hu1]], [[6hu2]], [[6hu3]], [[6hsh]], [[6hrq]], [[6hqy]] – SmHDAC8 + inhibitor<br />
-	**[[4bz6]] – SmHDAC8 + SAHA<br />	+	**[[6hsk]], [[6hsf]], [[6hsg]] – SmHDAC8 (mutant) + inhibitor<br />
		+	**[[4bz6]], [[6gxw]], [[6gxu]], [[6gxa]], [[6gx3]], [[6fu1]] – SmHDAC8 + SAHA derivative<br />

	*'''HDAC class IIA'''		*'''HDAC class IIA'''
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	**[[2vqw]] - hHDAC4 catalytic domain (mutant)<br />		**[[2vqw]] - hHDAC4 catalytic domain (mutant)<br />
	**[[2vqj]], [[2vqm]], [[4cbt]], [[5a2s]] – hHDAC4 catalytic domain + inhibitor<br />		**[[2vqj]], [[2vqm]], [[4cbt]], [[5a2s]] – hHDAC4 catalytic domain + inhibitor<br />
-	**[[2vqo]], [[2vqq]], [[2vqv]], [[4cby]] – hHDAC4 catalytic domain (mutant) + inhibitor	+	**[[6fyz]] - hHDAC4 catalytic domain + SAHA derivative<br />
		+	**[[2vqo]], [[2vqq]], [[2vqv]], [[4cby]] – hHDAC4 catalytic domain (mutant) + inhibitor<br />
		+	**[[5zop]], [[5zoo]] - hHDAC4 catalytic domain (mutant) + SMRT corepressor<br />

	*HDAC5		*HDAC5
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	**[[5kh3]], [[5kh7]], [[5kh9]], [[5b8d]], [[6ce6]], [[6ce8]], [[6cea]], [[6cec]], [[6ced]], [[6cee]], [[6cef]], [[5wpb]], [[5wbn]] – hHDAC6 zinc finger + inhibitor<br />		**[[5kh3]], [[5kh7]], [[5kh9]], [[5b8d]], [[6ce6]], [[6ce8]], [[6cea]], [[6cec]], [[6ced]], [[6cee]], [[6cef]], [[5wpb]], [[5wbn]] – hHDAC6 zinc finger + inhibitor<br />
	**[[5eem]] – zHDAC6 catalytic domain - zebrafish<br />		**[[5eem]] – zHDAC6 catalytic domain - zebrafish<br />
-	**[[6cgp]], [[5wgm]], [[5wgl]], [[5wgi]], [[5wgk]], [[5g0j]], [[5g0i]], [[5g0h]], [[5g0g]], [[5g0f]], [[5efh]], [[5efg]], [[5efb]], [[5ef7]], [[5ef8]], [[5een]], [[5eek]], [[5eef]] – zHDAC6 catalytic domain + inhibitor <br />	+	**[[6cgp]], [[5wgm]], [[5wgl]], [[5wgi]], [[5wgk]], [[5g0j]], [[5g0i]], [[5g0h]], [[5g0g]], [[5g0f]], [[5efh]], [[5efg]], [[5efb]], [[5ef7]], [[5ef8]], [[5een]], [[5eek]], [[5eef]], [[6mr5]], [[6dvo]], [[6dvn]], [[6dvm]], [[6dvl]], [[6cw8]] – zHDAC6 catalytic domain + inhibitor <br />
-	**[[5eei]] – zHDAC6 catalytic domain + SAHA<br />	+	**[[5eei]], [[6css]], [[6csr]], [[6csq]], [[6csp]], [[5w5k]] – zHDAC6 catalytic domain + SAHA derivative<br />
	**[[5efn]], [[5efk]], [[53fj]] – zHDAC6 catalytic domain (mutant) + peptide <br />		**[[5efn]], [[5efk]], [[53fj]] – zHDAC6 catalytic domain (mutant) + peptide <br />

Alexander Berchansky at 12:48, 16 May 2019

Alexander Berchansky — Thu, 16 May 2019 12:48:39 GMT

←Older revision		Revision as of 12:48, 16 May 2019
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	== Structural highlights ==		== Structural highlights ==
-	The biological assembly of Human sirtuin-3 is <scene name='48/483191/Cv/2'>homodimer</scene>. The <scene name='48/483191/Cv/4'>acetylated lysine of the peptide is inserted in an extended conformation</scene> between the 2 domains of SIRT3 - a large Rossman fold, NAD-binding domain and a small Zn-binding one)<ref>PMID:19535340</ref~~>.<br /~~>. Water molecule shown as red sphere.	+	The biological assembly of Human sirtuin-3 is <scene name='48/483191/Cv/5'>homodimer</scene>. The <scene name='48/483191/Cv/6'>acetylated lysine of the peptide is inserted in an extended conformation</scene> between the 2 domains of SIRT3 - a large Rossman fold, NAD-binding domain and a small Zn-binding one)<ref>PMID:19535340</ref>. Water molecule shown as red sphere.
	</StructureSection>		</StructureSection>
	== 3D Structures of histone deacetylase ==		== 3D Structures of histone deacetylase ==

Joel L. Sussman at 13:53, 30 January 2019

Joel L. Sussman — Wed, 30 Jan 2019 13:53:25 GMT

←Older revision		Revision as of 13:53, 30 January 2019
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	**[[5bwo]], [[5bwn]] – hSIRT3 + palmitoyl H3K9 peptide + Zn<br />		**[[5bwo]], [[5bwn]] – hSIRT3 + palmitoyl H3K9 peptide + Zn<br />
	**[[5bwl]] – hSIRT3 + succinyl peptide + Zn<br />		**[[5bwl]] – hSIRT3 + succinyl peptide + Zn<br />
-	**[[3glr]], [[3glt]], [[4fvt]], [[4bve]], [[~~4v1c~~]] – hSIRT3 + acetyl lysine peptide + Zn<br />	+	**[[3glr]], [[3glt]], [[4fvt]], [[4bve]], [[6iso]] – hSIRT3 + acetyl lysine peptide + Zn<br />
	**[[4hd8]] – hSIRT3 + acetyl lysine peptide + piceatannol + Zn<br />		**[[4hd8]] – hSIRT3 + acetyl lysine peptide + piceatannol + Zn<br />
	**[[4fz3]] – hSIRT3 + acetyl lysine peptide + coumarine derivative + Zn<br />		**[[4fz3]] – hSIRT3 + acetyl lysine peptide + coumarine derivative + Zn<br />

Michal Harel at 05:58, 17 July 2018

Michal Harel — Tue, 17 Jul 2018 05:58:41 GMT

←Older revision		Revision as of 05:58, 17 July 2018
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	* '''HDAC class I''' are homologous to yeast Rpd3.<br />		* '''HDAC class I''' are homologous to yeast Rpd3.<br />
	* '''HDAC class II''' are homologous to yeast HdaI.<br />		* '''HDAC class II''' are homologous to yeast HdaI.<br />
-	* '''HDAC class III''' called '''sirtuin''' - (Silent Information Regulator) (SIRT) are NAD-dependent HDAC <ref>PMID:18249170</ref>.<br />	+	* '''HDAC class III''' called '''sirtuin''' - (Silent Information Regulator) (SIRT) are NAD-dependent HDAC. This protein is bifunctional and can act as a deacylase or as mono-ADP-acetyltransferase. <ref>PMID:18249170</ref>.<br />
	For additional details see<br />		For additional details see<br />
	* [[Understanding of the Recruitment of HDACs by MEF2, Based on Their Structure]]<br />		* [[Understanding of the Recruitment of HDACs by MEF2, Based on Their Structure]]<br />
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	**[[4qa0]] - hHDAC8 (mutant) + SAHA<br />		**[[4qa0]] - hHDAC8 (mutant) + SAHA<br />
	**[[5fcw]], [[5fue]] - hHDAC8 + hydroxamate<br />		**[[5fcw]], [[5fue]] - hHDAC8 + hydroxamate<br />
		+	**[[5vi6]] - hHDAC8 + trapoxin A<br />
	**[[4qa1]], [[4qa2]], [[4qa3]], [[4qa4]] - hHDAC8 (mutant) + inhibitor<br />		**[[4qa1]], [[4qa2]], [[4qa3]], [[4qa4]] - hHDAC8 (mutant) + inhibitor<br />
	**[[2v5w]] – hHDAC8 + tripeptide substrate<br />		**[[2v5w]] – hHDAC8 + tripeptide substrate<br />
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	**[[2vqj]], [[2vqm]], [[4cbt]], [[5a2s]] – hHDAC4 catalytic domain + inhibitor<br />		**[[2vqj]], [[2vqm]], [[4cbt]], [[5a2s]] – hHDAC4 catalytic domain + inhibitor<br />
	**[[2vqo]], [[2vqq]], [[2vqv]], [[4cby]] – hHDAC4 catalytic domain (mutant) + inhibitor		**[[2vqo]], [[2vqq]], [[2vqv]], [[4cby]] – hHDAC4 catalytic domain (mutant) + inhibitor
		+
		+	*HDAC5
		+
		+	**[[5uwi]] – hHDAC5 + RAN + RANBP1 + exportin<br />

	*HDAC7		*HDAC7
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	**[[3gv4]] - hHDAC6 zinc finger domain + ubiquitin peptide<br />		**[[3gv4]] - hHDAC6 zinc finger domain + ubiquitin peptide<br />
	**[[3phd]] - hHDAC6 + polyubiquitin<br />		**[[3phd]] - hHDAC6 + polyubiquitin<br />
-	**[[5kh3]], [[5kh7]], [[5kh9]], [[5b8d]] – hHDAC6 zinc finger + inhibitor<br />	+	**[[5kh3]], [[5kh7]], [[5kh9]], [[5b8d]], [[6ce6]], [[6ce8]], [[6cea]], [[6cec]], [[6ced]], [[6cee]], [[6cef]], [[5wpb]], [[5wbn]] – hHDAC6 zinc finger + inhibitor<br />
		+	**[[5eem]] – zHDAC6 catalytic domain - zebrafish<br />
		+	**[[6cgp]], [[5wgm]], [[5wgl]], [[5wgi]], [[5wgk]], [[5g0j]], [[5g0i]], [[5g0h]], [[5g0g]], [[5g0f]], [[5efh]], [[5efg]], [[5efb]], [[5ef7]], [[5ef8]], [[5een]], [[5eek]], [[5eef]] – zHDAC6 catalytic domain + inhibitor <br />
		+	**[[5eei]] – zHDAC6 catalytic domain + SAHA<br />
		+	**[[5efn]], [[5efk]], [[53fj]] – zHDAC6 catalytic domain (mutant) + peptide <br />
		+

	*'''HDAC class III'''		*'''HDAC class III'''
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	**[[4l3o]], [[4y6l]], [[4y6o]] – hSIRT2 + acetyl lysine peptide + Zn<br />		**[[4l3o]], [[4y6l]], [[4y6o]] – hSIRT2 + acetyl lysine peptide + Zn<br />
	**[[4x3o]], [[4x3p]] – hSIRT2 + myristoyl peptide + Zn<br />		**[[4x3o]], [[4x3p]] – hSIRT2 + myristoyl peptide + Zn<br />
-	**[[4rmg]], [[5dy4]], [[5dy5]] – hSIRT2 + inhibitor + Zn<br />	+	**[[4rmg]], [[5dy4]], [[5dy5]], [[5y5n]], [[5mat]] – hSIRT2 + inhibitor + Zn<br />
-	**[[5d7p]], [[5d7q]] – hSIRT2 + inhibitor + ADP-ribose + Zn<br />	+	**[[5d7p]], [[5d7q]], [[5mar]] – hSIRT2 + inhibitor + ADP-ribose + Zn<br />
	**[[4rmh]], [[4rmi]] – hSIRT2 + acetyl lysine peptide + inhibitor + Zn<br />		**[[4rmh]], [[4rmi]] – hSIRT2 + acetyl lysine peptide + inhibitor + Zn<br />
	**[[4r8m]] – hSIRT2 + peptide + tridecanethial + Zn<br />		**[[4r8m]] – hSIRT2 + peptide + tridecanethial + Zn<br />
	**[[4rmj]] – hSIRT2 + ADP-ribose + nicotinamide + Zn <br />		**[[4rmj]] – hSIRT2 + ADP-ribose + nicotinamide + Zn <br />
		+	**[[5g4c]] – hSIRT2 + carba-NAD + Zn<br/ >
		+	**[[5fyq]] – hSIRT2 + RAN AA peptide + Zn<br/ >
		+	**[[5dy5]] – hSIRT2 + thiazole derivative + piperazine derivative + Zn<br/ >
		+	**[[5dy4]] – hSIRT2 + thiazole derivative + NAD + Zn<br/ >
		+	**[[5d7q]], [[5d7p]], [[5d7o]] – hSIRT2 + oxolan derivative + Zn<br/ >

	*SIRT3		*SIRT3
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	**[[5d7n]] – hSIRT3 + Zn<br />		**[[5d7n]] – hSIRT3 + Zn<br />
	**[[3gls]] – hSIRT3 (mutant) + Zn<br />		**[[3gls]] – hSIRT3 (mutant) + Zn<br />
-	**[[3glu]] – hSIRT3 + peptide + Zn<br />	+	**[[3glu]], [[5ytk]], [[5y4h]] – hSIRT3 + peptide + Zn<br />
		+	**[[5bwo]], [[5bwn]] – hSIRT3 + palmitoyl H3K9 peptide + Zn<br />
		+	**[[5bwl]] – hSIRT3 + succinyl peptide + Zn<br />
	**[[3glr]], [[3glt]], [[4fvt]], [[4bve]], [[4v1c]] – hSIRT3 + acetyl lysine peptide + Zn<br />		**[[3glr]], [[3glt]], [[4fvt]], [[4bve]], [[4v1c]] – hSIRT3 + acetyl lysine peptide + Zn<br />
	**[[4hd8]] – hSIRT3 + acetyl lysine peptide + piceatannol + Zn<br />		**[[4hd8]] – hSIRT3 + acetyl lysine peptide + piceatannol + Zn<br />
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	**[[4bvb]], [[4bvh]] – hSIRT3 + inhibitor + ADP-ribose + Zn<br />		**[[4bvb]], [[4bvh]] – hSIRT3 + inhibitor + ADP-ribose + Zn<br />
	**[[4bvf]], [[4bvg]] – hSIRT3 + acetyl lysine peptide + inhibitor + Zn<br />		**[[4bvf]], [[4bvg]] – hSIRT3 + acetyl lysine peptide + inhibitor + Zn<br />
		+	**[[5h4d]] – hSIRT3 + agonist + NAD + Zn<br/ >
		+
		+	*SIRT4
		+
		+	**[[5ojn]] – hSIRT4 + ADP-ribose + Zn – ''Xenopus tropicalis''<br />

	*SIRT5		*SIRT5

	**[[2b4y]], [[4bn4]] – hSIRT5 + ADP-ribose + Zn<br />		**[[2b4y]], [[4bn4]] – hSIRT5 + ADP-ribose + Zn<br />
-	**[[2nyr]] – hSIRT5 + ~~suramine~~ + Zn<br />	+	**[[2nyr]], [[5xhs]] – hSIRT5 + inhibitor + Zn<br />
-		+
	**[[3rig]], [[3riy]], [[4f4u]] – hSIRT5 + acetyl lysine peptide + Zn<br />		**[[3rig]], [[3riy]], [[4f4u]] – hSIRT5 + acetyl lysine peptide + Zn<br />
	**[[4gic]] – hSIRT5 + acetyl lysine peptide + carba-NAD + Zn<br/ >		**[[4gic]] – hSIRT5 + acetyl lysine peptide + carba-NAD + Zn<br/ >
	**[[4f56]] – hSIRT5 + peptide + intermediate + Zn<br />		**[[4f56]] – hSIRT5 + peptide + intermediate + Zn<br />
	**[[4hda]] – hSIRT5 + acetyl lysine peptide + resveratrol + Zn<br />		**[[4hda]] – hSIRT5 + acetyl lysine peptide + resveratrol + Zn<br />
-	**[[4utn]], [[4utr]], [[4utv]], [[4utx]], [[4utz]], [[4uu7]], [[4uu8]], [[4uua]], [[4uub]] – ~~zeSIRT5~~ + acetyl lysine peptide + inhibitor + Zn ~~- zebrafish~~<br />	+	**[[4utn]], [[4utr]], [[4utv]], [[4utx]], [[4utz]], [[4uu7]], [[4uu8]], [[4uua]], [[4uub]], [[6flg]], [[6fkz]], [[6fky]] – zSIRT5 + acetyl lysine peptide + inhibitor + Zn <br />
-		+	**[[6enx]], [[6eo0]], [[6eqs]] – zSIRT5 + inhibitor + Zn <br />
		+	**[[5ojo]] – zSIRT5 + CPS1 peptide + Zn <br />

	*SIRT6		*SIRT6
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	**[[3pki]], [[3pkj]] – hSIRT6 (mutant) + ADP-ribose derivative + Zn<br />		**[[3pki]], [[3pkj]] – hSIRT6 (mutant) + ADP-ribose derivative + Zn<br />
	**[[3zg6]] – hSIRT6 + acetyl lysine peptide + ADP-ribose + Zn<br />		**[[3zg6]] – hSIRT6 + acetyl lysine peptide + ADP-ribose + Zn<br />
		+	**[[5mgn]], [[5mfz]], [[5mfp]], [[5mf6]] – hSIRT6 + activator + Zn<br />
		+
		+	*SIRT7
		+
		+	**[[5iqz]] – hSIRT7 N-terminal<br />

	}}		}}

Michal Harel at 09:08, 7 January 2018

Michal Harel — Sun, 07 Jan 2018 09:08:38 GMT

←Older revision		Revision as of 09:08, 7 January 2018
Line 10:		Line 10:

	== Relevance ==		== Relevance ==
-	HDAC inhibitors are used in cancer therapy<ref>PMID:11902574</ref>. Sirtuins play a role in cancer, metabolic activity and neurodegenerative diseases<ref>PMID:17456799</ref>. HDAC inhibitor SAHA or Vorinostat is used in the treatment of cutaneous T cell lymphoma<ref>PMID:17962618</ref>.	+	HDAC inhibitors are used in cancer therapy<ref>PMID:11902574</ref>. Sirtuins play a role in cancer, metabolic activity and neurodegenerative diseases<ref>PMID:17456799</ref>. HDAC inhibitor SAHA or [[Zolinza (Vorinostat)]] is used in the treatment of cutaneous T cell lymphoma<ref>PMID:17962618</ref>.

	== Structural highlights ==		== Structural highlights ==

Joel L. Sussman at 06:37, 20 October 2017

Joel L. Sussman — Fri, 20 Oct 2017 06:37:51 GMT

←Older revision		Revision as of 06:37, 20 October 2017
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-	<StructureSection load='~~3glr~~' size='350' side='right' caption='Human sirtuin-3 complex with peptide containing acetylated lysine, sulfate, carbonate, glycerol and Zn+2 ion (PDB entry [[3glr]])' scene='48/483191/Cv/1'>	+	<StructureSection load='' size='350' side='right' caption='Human sirtuin-3 complex with peptide containing acetylated lysine, sulfate, carbonate, glycerol and Zn+2 ion (PDB entry [[3glr]])' scene='48/483191/Cv/1'>
	== Function ==		== Function ==
	'''Histone deacetylase''' (HDAC) catalyzes the removal of acetyl group from ε-N-acetyl lysine in histones<ref>PMID:23752268</ref>. HDAC contains Zn. DNA expression is regulated by acetylation and de-acetylation. SAHA is a common inhibitor of HDAC. HDAC are classified according to their domain organization into 4 classes. <br />		'''Histone deacetylase''' (HDAC) catalyzes the removal of acetyl group from ε-N-acetyl lysine in histones<ref>PMID:23752268</ref>. HDAC contains Zn. DNA expression is regulated by acetylation and de-acetylation. SAHA is a common inhibitor of HDAC. HDAC are classified according to their domain organization into 4 classes. <br />