5VI6 | pdb_00005vi6

Crystal structure of histone deacetylase 8 in complex with trapoxin A

• PDB DOI: https://doi.org/10.2210/pdb5VI6/pdb

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


• Deposited: 2017-04-14 Released: 2017-09-06 
• Deposition Author(s): Porter, N.J., 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: 1.24 Å
• R-Value Free: 
  0.143 (Depositor), 0.144 (DCC) 
• R-Value Work: 
  0.121 (Depositor), 0.123 (DCC) 
• R-Value Observed: 
  0.122 (Depositor) 

Starting Model: experimental

Literature

Binding of the Microbial Cyclic Tetrapeptide Trapoxin A to the Class I Histone Deacetylase HDAC8.

Porter, N.J., Christianson, D.W.

(2017) ACS Chem Biol 12: 2281-2286

• PubMed: 28846375 
• DOI: https://doi.org/10.1021/acschembio.7b00330
• Primary Citation Related Structures: 
  5VI6


• PubMed Abstract: 
  

  Trapoxin A is a microbial cyclic tetrapeptide that is an essentially irreversible inhibitor of class I histone deacetylases (HDACs). The inhibitory warhead is the α,β-epoxyketone side-chain of (2S,9S)-2-amino-8-oxo-9,10-epoxydecanoic acid (l-Aoe), which mimics the side-chain of the HDAC substrate acetyl-l-lysine. We now report the crystal structure of the HDAC8-trapoxin A complex at 1.24 Å resolution, revealing that the ketone moiety of l-Aoe undergoes nucleophilic attack to form a zinc-bound tetrahedral gem-diolate that mimics the tetrahedral intermediate and its flanking transition states in catalysis. Mass spectrometry, activity measurements, and isothermal titration calorimetry confirm that trapoxin A binds tightly (K _d = 3 ± 1 nM) and does not covalently modify the enzyme, so the epoxide moiety of l-Aoe remains intact. Comparison of the HDAC8-trapoxin A complex with the HDAC6-HC toxin complex provides new insight regarding the inhibitory potency of l-Aoe-containing natural products against class I and class II HDACs.

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Organizational Affiliation: 
• Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104-6323, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 42.74 kDa 
• Atom Count: 3,402 
• Modeled Residue Count: 357 
• Deposited Residue Count: 376 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase 8	A	372	Homo sapiens	Mutation(s): 0  Gene Names: HDAC8, HDACL1, CDA07 EC: 3.5.1.98 (PDB Primary Data), 3.5.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BY41 (Homo sapiens) Explore Q9BY41  Go to UniProtKB:  Q9BY41
PHAROS:  Q9BY41 GTEx:  ENSG00000147099

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Trapoxin A	B	4	Helicoma ambiens	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DIO	P [auth A], Q [auth A]	1,4-DIETHYLENE DIOXIDE C4 H8 O2 RYHBNJHYFVUHQT-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	D [auth A], E [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_002282	B	Trapoxin A	Cyclic peptide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free:  0.143 (Depositor), 0.144 (DCC) 
• R-Value Work:  0.121 (Depositor), 0.123 (DCC) 
• R-Value Observed: 0.122 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.98	α = 90
b = 50.98	β = 90
c = 116.517	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-09-06 
Deposition Author(s): Porter, N.J., 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	GM49758

Revision History  

• Version 1.0: 2017-09-06
  Type: Initial release
  
• Version 2.0: 2017-09-13
  Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2017-09-27
  Changes: Author supporting evidence, Database references
• Version 2.2: 2020-01-01
  Changes: Author supporting evidence
• Version 2.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 3.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations