5EDU | pdb_00005edu

Crystal structure of human histone deacetylase 6 catalytic domain 2 in complex with trichostatin A

• PDB DOI: https://doi.org/10.2210/pdb5EDU/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Escherichia coli, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-10-22 Released: 2016-07-27 
• Deposition Author(s): Hai, Y., Christianson, D.W.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 
  0.275 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Histone deacetylase 6 structure and molecular basis of catalysis and inhibition.

Hai, Y., Christianson, D.W.

(2016) Nat Chem Biol 12: 741-747

• PubMed: 27454933 
• DOI: https://doi.org/10.1038/nchembio.2134
• Primary Citation Related Structures: 
  5EDU, 5EEF, 5EEI, 5EEK, 5EEM, 5EEN, 5EF7, 5EF8, 5EFB, 5EFG, 5EFH, 5EFJ, 5EFK, 5EFN


• PubMed Abstract: 
  

  Histone deacetylase 6 (HDAC6) is a critical target for drug design because of its role in oncogenic transformation and cancer metastasis, and is unique among all histone deacetylases in that it contains tandem catalytic domains designated CD1 and CD2. We now report the crystal structures of CD2 from Homo sapiens HDAC6 and of CD1 and CD2 from Danio rerio HDAC6. We correlated these structures with activity measurements using 13 different substrates. The catalytic activity of CD2 from both species exhibited broad substrate specificity, whereas that of CD1 was highly specific for substrates bearing C-terminal acetyllysine residues. Crystal structures of substrate complexes yielded unprecedented snapshots of the catalytic mechanism. Additionally, crystal structures of complexes with eight different inhibitors, including belinostat and panobinostat (currently used in cancer chemotherapy), the macrocyclic tetrapeptide HC toxin, and the HDAC6-specific inhibitor N-hydroxy-4-(2-((2-hydroxyethyl)(phenyl)amino)-2-oxoethyl)benzamide, revealed surprising new insight regarding changes in Zn(2+) coordination and isozyme-specific inhibition.

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Organizational Affiliation: 
• Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
Radcliffe Institute for Advanced Study and Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 164.62 kDa 
• Atom Count: 11,179 
• Modeled Residue Count: 1,443 
• Deposited Residue Count: 1,490 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein, Histone deacetylase 6 chimera	A [auth B], B [auth A]	745	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: malE, Z5632, ECs5017, HDAC6, KIAA0901, JM21 EC: 3.5.1.98 (PDB Primary Data), 2.3.2 (UniProt), 3.5.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for Q9UBN7 (Homo sapiens) Explore Q9UBN7  Go to UniProtKB:  Q9UBN7
PHAROS:  Q9UBN7 GTEx:  ENSG00000094631
UniProt Groups	Q9UBN7P0AEX9

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TSN	E [auth B], L [auth A]	TRICHOSTATIN A C17 H22 N2 O3 RTKIYFITIVXBLE-QEQCGCAPSA-N
ZN	F [auth B], I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	G [auth B], H [auth B], J [auth A], K [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	C, D	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free:  0.275 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.262	α = 90
b = 149.032	β = 90
c = 216.333	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-07-27 
Deposition Author(s): Hai, Y., Christianson, D.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM 49758

Revision History  

• Version 1.0: 2016-07-27
  Type: Initial release
  
• Version 1.1: 2016-08-10
  Changes: Database references
• Version 1.2: 2016-09-07
  Changes: Database references
• Version 1.3: 2017-09-13
  Changes: Author supporting evidence, Derived calculations
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2020-12-30
  Changes: Structure summary
• Version 2.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description