5WGI | pdb_00005wgi

Ultrahigh resolution crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with TSA

• PDB DOI: https://doi.org/10.2210/pdb5WGI/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Danio rerio
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-07-14 Released: 2017-12-06 
• Deposition Author(s): Porter, N.J., Christianson, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 
  0.126 (Depositor), 0.119 (DCC) 
• R-Value Work: 
  0.106 (Depositor) 
• R-Value Observed: 
  0.107 (Depositor) 

Starting Model: experimental

Literature

Unusual zinc-binding mode of HDAC6-selective hydroxamate inhibitors.

Porter, N.J., Mahendran, A., Breslow, R., Christianson, D.W.

(2017) Proc Natl Acad Sci U S A 114: 13459-13464

• PubMed: 29203661 
• DOI: https://doi.org/10.1073/pnas.1718823114
• Primary Citation Related Structures: 
  5WGI, 5WGK, 5WGL, 5WGM


• PubMed Abstract: 
  

  Histone deacetylases (HDACs) regulate myriad cellular processes by catalyzing the hydrolysis of acetyl-l-lysine residues in histone and nonhistone proteins. The Zn ²⁺ -dependent class IIb enzyme HDAC6 regulates microtubule function by deacetylating α-tubulin, which suppresses microtubule dynamics and leads to cell cycle arrest and apoptosis. Accordingly, HDAC6 is a target for the development of selective inhibitors that might be useful in new therapeutic approaches for the treatment of cancer, neurodegenerative diseases, and other disorders. Here, we present high-resolution structures of catalytic domain 2 from Danio rerio HDAC6 (henceforth simply "HDAC6") complexed with compounds that selectively inhibit HDAC6 while maintaining nanomolar inhibitory potency: N -hydroxy-4-[( N (2-hydroxyethyl)-2-phenylacetamido)methyl)-benzamide)] (HPB), ACY-1215 (Ricolinostat), and ACY-1083. These structures reveal that an unusual monodentate Zn ²⁺ coordination mode is exploited by sterically bulky HDAC6-selective phenylhydroxamate inhibitors. We additionally report the ultrahigh-resolution structure of the HDAC6-trichostatin A complex, which reveals two Zn ²⁺ -binding conformers for the inhibitor: a major conformer (70%) with canonical bidentate hydroxamate-Zn ²⁺ coordination geometry and a minor conformer (30%) with monodentate hydroxamate-Zn ²⁺ coordination geometry, reflecting a free energy difference of only 0.5 kcal/mol. The minor conformer is not visible in lower resolution structure determinations. Structural comparisons of HDAC6-inhibitor complexes with class I HDACs suggest active site features that contribute to the isozyme selectivity observed in biochemical assays.

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Organizational Affiliation: 
• Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323.
Department of Chemistry, Columbia University, New York, NY 10027.
Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323; [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: immunoprecipitation

Macromolecule Content 

• Total Structure Weight: 41.91 kDa 
• Atom Count: 3,560 
• Modeled Residue Count: 360 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hdac6 protein	A	364	Danio rerio	Mutation(s): 0  Gene Names: hdac6
UniProt
Find proteins for F8W4B7 (Danio rerio) Explore F8W4B7  Go to UniProtKB:  F8W4B7

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TSN	C [auth A]	TRICHOSTATIN A C17 H22 N2 O3 RTKIYFITIVXBLE-QEQCGCAPSA-N
PEG	U [auth A], V [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	R [auth A], S [auth A], T [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	D [auth A], E [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	F [auth A], G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	W [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free:  0.126 (Depositor), 0.119 (DCC) 
• R-Value Work:  0.106 (Depositor) 
• R-Value Observed: 0.107 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.439	α = 90
b = 69.639	β = 110.42
c = 50.193	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-06 
Deposition Author(s): Porter, N.J., Christianson, D.W.

Revision History  

• Version 1.0: 2017-12-06
  Type: Initial release
  
• Version 1.1: 2017-12-20
  Changes: Database references
• Version 1.2: 2018-01-03
  Changes: Database references
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description