5G0G

Crystal structure of Danio rerio HDAC6 CD1 in complex with trichostatin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.499 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Insights Into Hdac6 Tubulin Deacetylation and its Selective Inhibition

Miyake, Y.Keusch, J.J.Wang, L.Saito, M.Hess, D.Wang, X.Melancon, B.J.Helquist, P.Gut, H.Matthias, P.

(2016) Nat.Chem.Biol. 12: 748

  • DOI: 10.1038/nchembio.2140
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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 tande ...

    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 α-helix and a flexible tryptophan residue in the loop joining α-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 α-tubulin lysine 40 in the lumen of microtubules, but that its preferred substrate was unpolymerized tubulin.


    Organizational Affiliation

    Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HDAC6
A
380Danio rerioMutation(s): 0 
Gene Names: hdac6
Find proteins for F8W4B7 (Danio rerio)
Go to UniProtKB:  F8W4B7
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TSN
Query on TSN

Download SDF File 
Download CCD File 
A
TRICHOSTATIN A
7-[4-(DIMETHYLAMINO)PHENYL]-N-HYDROXY-4,6-DIMETHYL-7-OXO-2,4-HEPTADIENAMIDE
C17 H22 N2 O3
RTKIYFITIVXBLE-QEQCGCAPSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.499 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.139 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 68.470α = 90.00
b = 93.010β = 90.00
c = 118.470γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-08-10
    Type: Database references
  • Version 1.2: 2016-09-28
    Type: Database references