3phd: Difference between revisions

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-[[Image:3phd.jpg|left|200px]]
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+==Crystal structure of human HDAC6 in complex with ubiquitin==
-The line below this paragraph, containing "STRUCTURE_3phd", creates the "Structure Box" on the page.
+<StructureSection load='3phd' size='340' side='right'caption='[[3phd]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<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>
-or leave the SCENE parameter empty for the default display.
+</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&#8491;</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>
-{{STRUCTURE_3phd|  PDB=3phd  |  SCENE=  }}
+<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>
+== 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>
+<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.
-===Crystal structure of human HDAC6 in complex with ubiquitin===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3phd" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[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].
+*[[Histone deacetylase 3D structures|Histone deacetylase 3D structures]]
-[[Category: Histone deacetylase]]
+*[[3D structures of ubiquitin|3D structures of ubiquitin]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Dong, A.]]
+[[Category: Large Structures]]
-[[Category: Kozieradzki, I.]]
+[[Category: Dong A]]
-[[Category: Li, F.]]
+[[Category: Kozieradzki I]]
-[[Category: Loppnau, P.]]
+[[Category: Li F]]
-[[Category: Mackenzie, F.]]
+[[Category: Loppnau P]]
-[[Category: Ouyang, H.]]
+[[Category: Mackenzie F]]
-[[Category: Qui, W.]]
+[[Category: Ouyang H]]
-[[Category: Ravichandran, M.]]
+[[Category: Qui W]]
-[[Category: SGC, Structural Genomics Consortium.]]
+[[Category: Ravichandran M]]
-[[Category: Schuetz, A.]]
+[[Category: Schuetz A]]