3phd - Revision history

OCA at 09:54, 6 September 2023

2023-09-06T09:54:38Z

← Older revision		Revision as of 09:54, 6 September 2023
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	<StructureSection load='3phd' size='340' side='right'caption='[[3phd]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='3phd' size='340' side='right'caption='[[3phd]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3phd]] is a 8 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=3PHD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PHD FirstGlance]. <br>		<table><tr><td colspan='2'>[[3phd]] is a 8 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=3PHD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PHD FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 3Å</td></tr>
	~~<tr id='related'><td class="sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[3c5k\|3c5k]]~~, [[~~3gv4~~\|~~3gv4]], [[2znv\|2znv]], [[3nhe\|3nhe~~]]~~</div>~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>HDAC6, KIAA0901, JM21 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9606 HUMAN]), UBB, UBA52, UBCEP2, UBC, RPS27A, UBA80, UBCEP1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td~~><~~/tr>~~
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Histone_deacetylase Histone deacetylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.98 3.5.1.98]~~ </~~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=3phd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3phd OCA], [https://pdbe.org/3phd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3phd RCSB], [https://www.ebi.ac.uk/pdbsum/3phd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3phd 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=3phd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3phd OCA], [https://pdbe.org/3phd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3phd RCSB], [https://www.ebi.ac.uk/pdbsum/3phd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3phd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/HDAC6_HUMAN HDAC6_HUMAN]] Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes (By similarity). Plays a central role in microtubule-dependent cell motility via deacetylation of tubulin.<ref>PMID:12024216</ref> <ref>PMID:17846173</ref> In addition to its protein deacetylase activity, plays a key role in the degradation of misfolded proteins: when misfolded proteins are too abundant to be degraded by the chaperone refolding system and the ubiquitin-proteasome, mediates the transport of misfolded proteins to a cytoplasmic juxtanuclear structure called aggresome. Probably acts as an adapter that recognizes polyubiquitinated misfolded proteins and target them to the aggresome, facilitating their clearance by autophagy.<ref>PMID:12024216</ref> <ref>PMID:17846173</ref> [[https://www.uniprot.org/uniprot/UBB_HUMAN UBB_HUMAN]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>		[https://www.uniprot.org/uniprot/HDAC6_HUMAN HDAC6_HUMAN] Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes (By similarity). Plays a central role in microtubule-dependent cell motility via deacetylation of tubulin.<ref>PMID:12024216</ref> <ref>PMID:17846173</ref> In addition to its protein deacetylase activity, plays a key role in the degradation of misfolded proteins: when misfolded proteins are too abundant to be degraded by the chaperone refolding system and the ubiquitin-proteasome, mediates the transport of misfolded proteins to a cytoplasmic juxtanuclear structure called aggresome. Probably acts as an adapter that recognizes polyubiquitinated misfolded proteins and target them to the aggresome, facilitating their clearance by autophagy.<ref>PMID:12024216</ref> <ref>PMID:17846173</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: ~~Histone deacetylase]]~~		[[Category: Homo sapiens]]
	~~[[Category: Human~~]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Dong, A]]		[[Category: Dong A]]
	[[Category: Kozieradzki, I]]		[[Category: Kozieradzki I]]
	[[Category: Li, F]]		[[Category: Li F]]
	[[Category: Loppnau, P]]		[[Category: Loppnau P]]
	[[Category: Mackenzie, F]]		[[Category: Mackenzie F]]
	[[Category: Ouyang, H]]		[[Category: Ouyang H]]
	[[Category: Qui, W]]		[[Category: Qui W]]
	[[Category: Ravichandran, M]]		[[Category: Ravichandran M]]
	~~[[Category: Structural genomic~~]]		[[Category: Schuetz A]]
	[[Category: Schuetz, A]]
	~~[[Category: Hdac6]]~~
	~~[[Category: Protein binding]]~~
	~~[[Category: Sgc]]~~
	~~[[Category: Ubiquitin~~]]

OCA at 08:39, 25 May 2022

2022-05-25T08:39:33Z

← Older revision		Revision as of 08:39, 25 May 2022
Line 1:		Line 1:

	==Crystal structure of human HDAC6 in complex with ubiquitin==		==Crystal structure of human HDAC6 in complex with ubiquitin==
	<StructureSection load='3phd' size='340' side='right' caption='[[3phd]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='3phd' size='340' side='right'caption='[[3phd]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3phd]] is a 8 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=3PHD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3PHD FirstGlance]. <br>		<table><tr><td colspan='2'>[[3phd]] is a 8 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=3PHD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PHD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3c5k\|3c5k]], [[3gv4\|3gv4]], [[2znv\|2znv]], [[3nhe\|3nhe]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3c5k\|3c5k]], [[3gv4\|3gv4]], [[2znv\|2znv]], [[3nhe\|3nhe]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HDAC6, KIAA0901, JM21 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), UBB, UBA52, UBCEP2, UBC, RPS27A, UBA80, UBCEP1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HDAC6, KIAA0901, JM21 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), UBB, UBA52, UBCEP2, UBC, RPS27A, UBA80, UBCEP1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Histone_deacetylase Histone deacetylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.98 3.5.1.98] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Histone_deacetylase Histone deacetylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.98 3.5.1.98] </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=3phd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3phd OCA], [~~http~~://pdbe.org/3phd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3phd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3phd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3phd 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=3phd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3phd OCA], [https://pdbe.org/3phd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3phd RCSB], [https://www.ebi.ac.uk/pdbsum/3phd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3phd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/HDAC6_HUMAN HDAC6_HUMAN]] Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes (By similarity). Plays a central role in microtubule-dependent cell motility via deacetylation of tubulin.<ref>PMID:12024216</ref> <ref>PMID:17846173</ref> In addition to its protein deacetylase activity, plays a key role in the degradation of misfolded proteins: when misfolded proteins are too abundant to be degraded by the chaperone refolding system and the ubiquitin-proteasome, mediates the transport of misfolded proteins to a cytoplasmic juxtanuclear structure called aggresome. Probably acts as an adapter that recognizes polyubiquitinated misfolded proteins and target them to the aggresome, facilitating their clearance by autophagy.<ref>PMID:12024216</ref> <ref>PMID:17846173</ref> [[~~http~~://www.uniprot.org/uniprot/UBB_HUMAN UBB_HUMAN]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>		[[https://www.uniprot.org/uniprot/HDAC6_HUMAN HDAC6_HUMAN]] Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes (By similarity). Plays a central role in microtubule-dependent cell motility via deacetylation of tubulin.<ref>PMID:12024216</ref> <ref>PMID:17846173</ref> In addition to its protein deacetylase activity, plays a key role in the degradation of misfolded proteins: when misfolded proteins are too abundant to be degraded by the chaperone refolding system and the ubiquitin-proteasome, mediates the transport of misfolded proteins to a cytoplasmic juxtanuclear structure called aggresome. Probably acts as an adapter that recognizes polyubiquitinated misfolded proteins and target them to the aggresome, facilitating their clearance by autophagy.<ref>PMID:12024216</ref> <ref>PMID:17846173</ref> [[https://www.uniprot.org/uniprot/UBB_HUMAN UBB_HUMAN]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
	*[[Histone deacetylase\|Histone deacetylase]]		*[[Histone deacetylase 3D structures\|Histone deacetylase 3D structures]]
	*[[~~Ubiquitin~~\|~~Ubiquitin~~]]		*[[3D structures of ubiquitin\|3D structures of ubiquitin]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Histone deacetylase]]		[[Category: Histone deacetylase]]
	[[Category: Human]]		[[Category: Human]]
			[[Category: Large Structures]]
	[[Category: Dong, A]]		[[Category: Dong, A]]
	[[Category: Kozieradzki, I]]		[[Category: Kozieradzki, I]]

OCA at 11:26, 5 August 2016

2016-08-05T11:26:53Z

← Older revision		Revision as of 11:26, 5 August 2016
Line 1:		Line 1:

	==Crystal structure of human HDAC6 in complex with ubiquitin==		==Crystal structure of human HDAC6 in complex with ubiquitin==
	<StructureSection load='3phd' size='340' side='right' caption='[[3phd]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='3phd' size='340' side='right' caption='[[3phd]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3phd]] is a 8 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=3PHD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PHD FirstGlance]. <br>		<table><tr><td colspan='2'>[[3phd]] is a 8 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=3PHD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PHD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3c5k\|3c5k]], [[3gv4\|3gv4]], [[2znv\|2znv]], [[3nhe\|3nhe]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3c5k\|3c5k]], [[3gv4\|3gv4]], [[2znv\|2znv]], [[3nhe\|3nhe]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HDAC6, KIAA0901, JM21 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~]), UBB, UBA52, UBCEP2, UBC, RPS27A, UBA80, UBCEP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HDAC6, KIAA0901, JM21 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), UBB, UBA52, UBCEP2, UBC, RPS27A, UBA80, UBCEP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_deacetylase Histone deacetylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.98 3.5.1.98] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_deacetylase Histone deacetylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.98 3.5.1.98] </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=3phd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3phd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3phd RCSB], [http://www.ebi.ac.uk/pdbsum/3phd 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=3phd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3phd OCA], [http://pdbe.org/3phd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3phd RCSB], [http://www.ebi.ac.uk/pdbsum/3phd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3phd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 3phd" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	</StructureSection>		</StructureSection>
	[[Category: Histone deacetylase]]		[[Category: Histone deacetylase]]
	[[Category: ~~Homo sapiens~~]]		[[Category: Human]]
	[[Category: Dong, A]]		[[Category: Dong, A]]
	[[Category: Kozieradzki, I]]		[[Category: Kozieradzki, I]]

OCA at 18:26, 25 December 2014

2014-12-25T18:26:02Z

← Older revision		Revision as of 18:26, 25 December 2014
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	<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=3phd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3phd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3phd RCSB], [http://www.ebi.ac.uk/pdbsum/3phd 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=3phd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3phd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3phd RCSB], [http://www.ebi.ac.uk/pdbsum/3phd PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/HDAC6_HUMAN HDAC6_HUMAN]] Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes (By similarity). Plays a central role in microtubule-dependent cell motility via deacetylation of tubulin.<ref>PMID:12024216</ref> <ref>PMID:17846173</ref> In addition to its protein deacetylase activity, plays a key role in the degradation of misfolded proteins: when misfolded proteins are too abundant to be degraded by the chaperone refolding system and the ubiquitin-proteasome, mediates the transport of misfolded proteins to a cytoplasmic juxtanuclear structure called aggresome. Probably acts as an adapter that recognizes polyubiquitinated misfolded proteins and target them to the aggresome, facilitating their clearance by autophagy.<ref>PMID:12024216</ref> <ref>PMID:17846173</ref> [[http://www.uniprot.org/uniprot/UBB_HUMAN UBB_HUMAN]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 11:57, 9 December 2014

2014-12-09T11:57:16Z

← Older revision		Revision as of 11:57, 9 December 2014
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	[[~~Image~~:~~3phd~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of human HDAC6 in complex with ubiquitin==
			<StructureSection load='3phd' size='340' side='right' caption='[[3phd]], [[Resolution\|resolution]] 3.00Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[3phd]] is a 8 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=3PHD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PHD FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3c5k\|3c5k]], [[3gv4\|3gv4]], [[2znv\|2znv]], [[3nhe\|3nhe]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HDAC6, KIAA0901, JM21 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), UBB, UBA52, UBCEP2, UBC, RPS27A, UBA80, UBCEP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
			<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_deacetylase Histone deacetylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.98 3.5.1.98] </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=3phd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3phd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3phd RCSB], [http://www.ebi.ac.uk/pdbsum/3phd PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The aggresome pathway is activated when proteasomal clearance of misfolded proteins is hindered. Misfolded polyubiquitinated protein aggregates are recruited and transported to the aggresome via the microtubule network by a protein complex consisting of histone deacetylase 6 (HDAC6) and the dynein motor complex. Current model suggests that HDAC6 recognizes protein aggregates by binding directly to polyubiquitinated proteins. Here, we show that there are substantial amounts of unanchored ubiquitin in protein aggregates with solvent accessible C-termini. The ubiquitin binding domain (ZnF-UBP) of HDAC6 binds exclusively to the unanchored C-terminal diglycine motif of ubiquitin instead of conjugated polyubiquitin. The unanchored ubiquitin C-termini in the aggregates are generated in situ by aggregate-associated deubiquitinase ataxin-3. These results provide structural and mechanistic bases for the role of HDAC6 in aggresome formation and further suggest a novel ubiquitin-mediated signaling pathway, where the exposure of ubiquitin C-termini within protein aggregates enables HDAC6 recognition and transport to the aggresome.

	~~{{STRUCTURE_3phd\| PDB=3phd \| SCENE= }}~~		Protein aggregates are recruited to the aggresome by histone deacetylase 6 via unanchored ubiquitin C-termini.,Ouyang H, Ali YO, Ravichandran M, Dong A, Qiu W, Mackenzie F, Dhe-Paganon S, Arrowsmith CH, Zhai RG J Biol Chem. 2011 Nov 8. PMID:22069321<ref>PMID:22069321</ref>

	~~===Crystal structure~~ of ~~human HDAC6 in complex with ubiquitin===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_22069321}}~~

	~~==About this Structure==~~
	~~[[3phd]] is a 8 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=3PHD OCA].~~

	==See Also==		==See Also==
	*[[Histone deacetylase\|Histone deacetylase]]		*[[Histone deacetylase\|Histone deacetylase]]
	*[[Ubiquitin\|Ubiquitin]]		*[[Ubiquitin\|Ubiquitin]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:022069321<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Histone deacetylase]]		[[Category: Histone deacetylase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Dong, A.]]		[[Category: Dong, A]]
	[[Category: Kozieradzki, I.]]		[[Category: Kozieradzki, I]]
	[[Category: Li, F.]]		[[Category: Li, F]]
	[[Category: Loppnau, P.]]		[[Category: Loppnau, P]]
	[[Category: Mackenzie, F.]]		[[Category: Mackenzie, F]]
	[[Category: Ouyang, H.]]		[[Category: Ouyang, H]]
	[[Category: Qui, W.]]		[[Category: Qui, W]]
	[[Category: Ravichandran, M.]]		[[Category: Ravichandran, M]]
	[[Category: ~~SGC,~~ Structural ~~Genomics Consortium.~~]]		[[Category: Structural genomic]]
	[[Category: Schuetz, A.]]		[[Category: Schuetz, A]]
	[[Category: Hdac6]]		[[Category: Hdac6]]
	[[Category: Protein binding]]		[[Category: Protein binding]]
	[[Category: Sgc]]		[[Category: Sgc]]
	~~[[Category: Structural genomic]]~~
	~~[[Category: Structural genomics consortium]]~~
	[[Category: Ubiquitin]]		[[Category: Ubiquitin]]

OCA at 19:58, 20 October 2012

2012-10-20T19:58:07Z

← Older revision		Revision as of 19:58, 20 October 2012
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	==About this Structure==		==About this Structure==
	[[3phd]] is a 8 chain structure ~~of [[Histone deacetylase]] and [[Ubiquitin]]~~ 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=3PHD OCA].		[[3phd]] is a 8 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=3PHD OCA].

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

OCA at 09:01, 27 July 2012

2012-07-27T09:01:30Z

← Older revision		Revision as of 09:01, 27 July 2012
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	[[Image:3phd.png\|left\|200px]]		[[Image:3phd.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3phd", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_3phd\| PDB=3phd \| SCENE= }}		{{STRUCTURE_3phd\| PDB=3phd \| SCENE= }}

	===Crystal structure of human HDAC6 in complex with ubiquitin===		===Crystal structure of human HDAC6 in complex with ubiquitin===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_22069321}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 22069321 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_22069321}}		{{ABSTRACT_PUBMED_22069321}}

	==About this Structure==		==About this Structure==
	[[3phd]] is a 8 chain structure of [[Ubiquitin]] 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=3PHD OCA].		[[3phd]] is a 8 chain structure of [[Histone deacetylase]] and [[Ubiquitin]] 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=3PHD OCA].

	==See Also==		==See Also==
	*[[Ubiquitin]]		*[[Histone deacetylase\|Histone deacetylase]]
			*[[Ubiquitin\|Ubiquitin]]

	==Reference==		==Reference==

OCA at 18:22, 23 November 2011

2011-11-23T18:22:01Z

← Older revision		Revision as of 18:22, 23 November 2011
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	===Crystal structure of human HDAC6 in complex with ubiquitin===		===Crystal structure of human HDAC6 in complex with ubiquitin===


			<!--
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			(as it appears on PubMed at http://www.pubmed.gov), where 22069321 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_22069321}}

	==About this Structure==		==About this Structure==
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	==See Also==		==See Also==
	*[[Ubiquitin]]		*[[Ubiquitin]]

			==Reference==
			<ref group="xtra">PMID:022069321</ref><references group="xtra"/>
	[[Category: Histone deacetylase]]		[[Category: Histone deacetylase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]

OCA at 11:04, 16 November 2011

2011-11-16T11:04:06Z

← Older revision		Revision as of 11:04, 16 November 2011
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	[[Image:3phd.~~jpg~~\|left\|200px]]		[[Image:3phd.png\|left\|200px]]

	<!--		<!--
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	==About this Structure==		==About this Structure==
	[[3phd]] is a 8 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=3PHD OCA].		[[3phd]] is a 8 chain structure of [[Ubiquitin]] 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=3PHD OCA].

			==See Also==
			*[[Ubiquitin]]
	[[Category: Histone deacetylase]]		[[Category: Histone deacetylase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
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	[[Category: SGC, Structural Genomics Consortium.]]		[[Category: SGC, Structural Genomics Consortium.]]
	[[Category: Schuetz, A.]]		[[Category: Schuetz, A.]]
			[[Category: Hdac6]]
			[[Category: Protein binding]]
			[[Category: Sgc]]
			[[Category: Structural genomic]]
			[[Category: Structural genomics consortium]]
			[[Category: Ubiquitin]]

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

2011-02-23T09:58:49Z

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

← Older revision	Revision as of 09:58, 23 February 2011
(No difference)