5g0f: Difference between revisions
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<StructureSection load='5g0f' size='340' side='right'caption='[[5g0f]], [[Resolution|resolution]] 1.90Å' scene=''> | <StructureSection load='5g0f' size='340' side='right'caption='[[5g0f]], [[Resolution|resolution]] 1.90Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5g0f]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[5g0f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5G0F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5G0F FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5g0f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g0f OCA], [https://pdbe.org/5g0f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5g0f RCSB], [https://www.ebi.ac.uk/pdbsum/5g0f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5g0f ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/F8W4B7_DANRE F8W4B7_DANRE] | |||
<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: | [[Category: Danio rerio]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Gut | [[Category: Gut H]] | ||
[[Category: Helquist | [[Category: Helquist P]] | ||
[[Category: Hess | [[Category: Hess D]] | ||
[[Category: Keusch | [[Category: Keusch JJ]] | ||
[[Category: Matthias | [[Category: Matthias P]] | ||
[[Category: Melancon | [[Category: Melancon BJ]] | ||
[[Category: Miyake | [[Category: Miyake Y]] | ||
[[Category: Saito | [[Category: Saito M]] | ||
[[Category: Wang | [[Category: Wang L]] | ||
[[Category: Wang | [[Category: Wang X]] | ||
Latest revision as of 16:34, 26 July 2023
Crystal structure of Danio rerio HDAC6 ZnF-UBP domainCrystal structure of Danio rerio HDAC6 ZnF-UBP domain
Structural highlights
FunctionPublication Abstract from PubMedWe report crystal structures of zebrafish histone deacetylase 6 (HDAC6) catalytic domains in tandem or as single domains in complex with the (R) and (S) enantiomers of trichostatin A (TSA) or with the HDAC6-specific inhibitor nexturastat A. The tandem domains formed, together with the inter-domain linker, an ellipsoid-shaped complex with pseudo-twofold symmetry. We identified important active site differences between both catalytic domains and revealed the binding mode of HDAC6 selective inhibitors. HDAC inhibition assays with (R)- and (S)-TSA showed that (R)-TSA was a broad-range inhibitor, whereas (S)-TSA had moderate selectivity for HDAC6. We identified a uniquely positioned alpha-helix and a flexible tryptophan residue in the loop joining alpha-helices H20 to H21 as critical for deacetylation of the physiologic substrate tubulin. Using single-molecule measurements and biochemical assays we demonstrated that HDAC6 catalytic domain 2 deacetylated alpha-tubulin lysine 40 in the lumen of microtubules, but that its preferred substrate was unpolymerized tubulin. Structural insights into HDAC6 tubulin deacetylation and its selective inhibition.,Miyake Y, Keusch JJ, Wang L, Saito M, Hess D, Wang X, Melancon BJ, Helquist P, Gut H, Matthias P Nat Chem Biol. 2016 Jul 25. doi: 10.1038/nchembio.2140. PMID:27454931[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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