5g0g: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 3: / Line 3: @@
 <StructureSection load='5g0g' size='340' side='right'caption='[[5g0g]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5g0g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5G0G OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5G0G FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5g0g]] 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=5G0G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5G0G FirstGlance]. <br>
-</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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TSN:TRICHOSTATIN+A'>TSN</scene>, <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]] 1.499&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5g0f|5g0f]], [[5g0h|5g0h]], [[5g0i|5g0i]], [[5g0j|5g0j]]</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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TSN:TRICHOSTATIN+A'>TSN</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'>[http://proteopedia.org/fgij/fg.htm?mol=5g0g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g0g OCA], [http://pdbe.org/5g0g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5g0g RCSB], [http://www.ebi.ac.uk/pdbsum/5g0g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5g0g 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=5g0g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g0g OCA], [https://pdbe.org/5g0g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5g0g RCSB], [https://www.ebi.ac.uk/pdbsum/5g0g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5g0g ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/F8W4B7_DANRE F8W4B7_DANRE]
-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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5g0g" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Histone deacetylase 3D structures|Histone deacetylase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Brachidanio rerio]]
+[[Category: Danio rerio]]
 [[Category: Large Structures]]
-[[Category: Gut, H]]
+[[Category: Gut H]]
-[[Category: Helquist, P]]
+[[Category: Helquist P]]
-[[Category: Hess, D]]
+[[Category: Hess D]]
-[[Category: Keusch, J J]]
+[[Category: Keusch JJ]]
-[[Category: Matthias, P]]
+[[Category: Matthias P]]
-[[Category: Melancon, B J]]
+[[Category: Melancon BJ]]
-[[Category: Miyake, Y]]
+[[Category: Miyake Y]]
-[[Category: Saito, M]]
+[[Category: Saito M]]
-[[Category: Wang, L]]
+[[Category: Wang L]]
-[[Category: Wang, X]]
+[[Category: Wang X]]
-[[Category: Cell cycle]]
-[[Category: Histone]]
-[[Category: Histone deacetylase]]