5g0i: Difference between revisions
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New page: '''Unreleased structure''' The entry 5g0i is ON HOLD Authors: Miyake, Y., Keusch, J.J., Wang, L., Saito, M., Hess, D., Gut, H., Matthias, P. Description: Crystal structure of Danio rer... |
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==Crystal structure of Danio rerio HDAC6 CD1 and CD2 (linker cleaved) in complex with Nexturastat A== | |||
<StructureSection load='5g0i' size='340' side='right'caption='[[5g0i]], [[Resolution|resolution]] 1.99Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5g0i]] is a 2 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=5G0I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5G0I FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.99Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=N4R:NEXTURASTAT+A'>N4R</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'>[https://proteopedia.org/fgij/fg.htm?mol=5g0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g0i OCA], [https://pdbe.org/5g0i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5g0i RCSB], [https://www.ebi.ac.uk/pdbsum/5g0i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5g0i ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/F8W4B7_DANRE F8W4B7_DANRE] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
We 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<ref>PMID:27454931</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: Hess | <div class="pdbe-citations 5g0i" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: | ==See Also== | ||
[[Category: Miyake | *[[Histone deacetylase 3D structures|Histone deacetylase 3D structures]] | ||
[[Category: Saito | == References == | ||
[[Category: | <references/> | ||
[[Category: | __TOC__ | ||
</StructureSection> | |||
[[Category: Danio rerio]] | |||
[[Category: Large Structures]] | |||
[[Category: Gut H]] | |||
[[Category: Helquist P]] | |||
[[Category: Hess D]] | |||
[[Category: Keusch JJ]] | |||
[[Category: Matthias P]] | |||
[[Category: Melancon BJ]] | |||
[[Category: Miyake Y]] | |||
[[Category: Saito M]] | |||
[[Category: Wang L]] | |||
[[Category: Wang X]] | |||
Latest revision as of 13:34, 26 July 2023
Crystal structure of Danio rerio HDAC6 CD1 and CD2 (linker cleaved) in complex with Nexturastat A
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