3c5k: Difference between revisions

Latest revision as of 09:33, 21 February 2024

Crystal structure of human HDAC6 zinc finger domain

Structural highlights

3c5k is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.55Å
Ligands:	ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1] ^[2] 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.^[3] ^[4]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

↑ Hubbert C, Guardiola A, Shao R, Kawaguchi Y, Ito A, Nixon A, Yoshida M, Wang XF, Yao TP. HDAC6 is a microtubule-associated deacetylase. Nature. 2002 May 23;417(6887):455-8. PMID:12024216 doi:https://dx.doi.org/10.1038/417455a
↑ Olzmann JA, Li L, Chudaev MV, Chen J, Perez FA, Palmiter RD, Chin LS. Parkin-mediated K63-linked polyubiquitination targets misfolded DJ-1 to aggresomes via binding to HDAC6. J Cell Biol. 2007 Sep 10;178(6):1025-38. PMID:17846173 doi:10.1083/jcb.200611128
↑ Hubbert C, Guardiola A, Shao R, Kawaguchi Y, Ito A, Nixon A, Yoshida M, Wang XF, Yao TP. HDAC6 is a microtubule-associated deacetylase. Nature. 2002 May 23;417(6887):455-8. PMID:12024216 doi:https://dx.doi.org/10.1038/417455a
↑ Olzmann JA, Li L, Chudaev MV, Chen J, Perez FA, Palmiter RD, Chin LS. Parkin-mediated K63-linked polyubiquitination targets misfolded DJ-1 to aggresomes via binding to HDAC6. J Cell Biol. 2007 Sep 10;178(6):1025-38. PMID:17846173 doi:10.1083/jcb.200611128

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Hubbert C, Guardiola A, Shao R, Kawaguchi Y, Ito A, Nixon A, Yoshida M, Wang XF, Yao TP. HDAC6 is a microtubule-associated deacetylase. Nature. 2002 May 23;417(6887):455-8. PMID:12024216 doi:https://dx.doi.org/10.1038/417455a

[2] Olzmann JA, Li L, Chudaev MV, Chen J, Perez FA, Palmiter RD, Chin LS. Parkin-mediated K63-linked polyubiquitination targets misfolded DJ-1 to aggresomes via binding to HDAC6. J Cell Biol. 2007 Sep 10;178(6):1025-38. PMID:17846173 doi:10.1083/jcb.200611128

[3] Hubbert C, Guardiola A, Shao R, Kawaguchi Y, Ito A, Nixon A, Yoshida M, Wang XF, Yao TP. HDAC6 is a microtubule-associated deacetylase. Nature. 2002 May 23;417(6887):455-8. PMID:12024216 doi:https://dx.doi.org/10.1038/417455a

[4] Olzmann JA, Li L, Chudaev MV, Chen J, Perez FA, Palmiter RD, Chin LS. Parkin-mediated K63-linked polyubiquitination targets misfolded DJ-1 to aggresomes via binding to HDAC6. J Cell Biol. 2007 Sep 10;178(6):1025-38. PMID:17846173 doi:10.1083/jcb.200611128

[1]

[2]

[3]

[4]

@@ Line 1: / Line 1: @@
-[[Image:3c5k.jpg|left|200px]]
-<!--
+==Crystal structure of human HDAC6 zinc finger domain==
-The line below this paragraph, containing "STRUCTURE_3c5k", creates the "Structure Box" on the page.
+<StructureSection load='3c5k' size='340' side='right'caption='[[3c5k]], [[Resolution|resolution]] 1.55&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'>[[3c5k]] is a 1 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=3C5K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C5K 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]] 1.55&#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_3c5k|  PDB=3c5k  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3c5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c5k OCA], [https://pdbe.org/3c5k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c5k RCSB], [https://www.ebi.ac.uk/pdbsum/3c5k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c5k 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>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c5/3c5k_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3c5k ConSurf].
+<div style="clear:both"></div>
-'''Crystal structure of human HDAC6 zinc finger domain'''
+==See Also==
+*[[Histone deacetylase 3D structures|Histone deacetylase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-C5K is a [[Single protein]] structure of 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=3C5K OCA].
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Arrowsmith, C H.]]
+[[Category: Arrowsmith CH]]
-[[Category: Bochkarev, A.]]
+[[Category: Bochkarev A]]
-[[Category: Bountra, C.]]
+[[Category: Bountra C]]
-[[Category: Dhe-Paganon, S.]]
+[[Category: Dhe-Paganon S]]
-[[Category: Dong, A.]]
+[[Category: Dong A]]
-[[Category: Edwards, A M.]]
+[[Category: Edwards AM]]
-[[Category: Kozieradzki, I.]]
+[[Category: Kozieradzki I]]
-[[Category: Li, Y.]]
+[[Category: Li Y]]
-[[Category: Loppnau, P.]]
+[[Category: Loppnau P]]
-[[Category: MacKenzie, F.]]
+[[Category: MacKenzie F]]
-[[Category: Min, J.]]
+[[Category: Min J]]
-[[Category: Ouyang, H.]]
+[[Category: Ouyang H]]
-[[Category: Ravichandran, M.]]
+[[Category: Ravichandran M]]
-[[Category: SGC, Structural Genomics Consortium.]]
+[[Category: Schuetz A]]
-[[Category: Schuetz, A.]]
+[[Category: Weigelt J]]
-[[Category: Weigelt, J.]]
-[[Category: Actin-binding]]
-[[Category: Chromatin regulator]]
-[[Category: Cytoplasm]]
-[[Category: Hdac6]]
-[[Category: Hydrolase]]
-[[Category: Metal-binding]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Repressor]]
-[[Category: Sgc]]
-[[Category: Structural genomic]]
-[[Category: Structural genomics consortium]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-[[Category: Ubl conjugation]]
-[[Category: Zinc finger]]
-[[Category: Zinc-finger]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 21:22:11 2008''

3c5k: Difference between revisions

Latest revision as of 09:33, 21 February 2024

Crystal structure of human HDAC6 zinc finger domain

Structural highlights

Function

Evolutionary Conservation

See Also

References

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