Biological Assembly 1  

 3D View: Structure | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 42.73 kDa 
• Atom Count: 3213 
• Modelled Residue Count: 372 
• Deposited Residue Count: 375 
• Unique protein chains: 1

1C3P

CRYSTAL STRUCTURE OF AN HDAC HOMOLOG FROM AQUIFEX AEOLICUS

• DOI: 10.2210/pdb1C3P/pdb

• Classification: LYASE
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-07-28 Released: 1999-09-15 
• Deposition Author(s): Finnin, M.S., Donigian, J.R., Pavletich, N.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.240 
• R-Value Work: 0.198 
• R-Value Observed: 0.198 

Literature

Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors.

Finnin, M.S., Donigian, J.R., Cohen, A., Richon, V.M., Rifkind, R.A., Marks, P.A., Breslow, R., Pavletich, N.P.

(1999) Nature 401: 188-193

• PubMed: 10490031 
• DOI: 10.1038/43710
• Primary Citation of Related Structures:  
  1C3P, 1C3R, 1C3S


• PubMed Abstract: 
  

Histone deacetylases (HDACs) mediate changes in nucleosome conformation and are important in the regulation of gene expression. HDACs are involved in cell-cycle progression and differentiation, and their deregulation is associated with several cancers. HDAC inhibitors, such as trichostatin A (TSA) and suberoylanilide hydroxamic acid (SAHA), have anti-tumour effects, as they can inhibit cell growth, induce terminal differentiation and prevent the formation of tumours in mice models, and they are effective in the treatment of promyelocytic leukemia. Here we describe the structure of the histone deacetylase catalytic core, as revealed by the crystal structure of a homologue from the hyperthermophilic bacterium Aquifex aeolicus, that shares 35.2% identity with human HDAC1 over 375 residues, deacetylates histones in vitro and is inhibited by TSA and SAHA. The deacetylase, deacetylase-TSA and deacetylase-SAHA structures reveal an active site consisting of a tubular pocket, a zinc-binding site and two Asp-His charge-relay systems, and establish the mechanism of HDAC inhibition. The residues that make up the active site and contact the inhibitors are conserved across the HDAC family. These structures also suggest a mechanism for the deacetylation reaction and provide a framework for the further development of HDAC inhibitors as antitumour agents.

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Organizational Affiliation: 

Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (HDLP (HISTONE DEACETYLASE-LIKE PROTEIN))	A	375	Aquifex aeolicus	Mutation(s): 0
UniProt
Find proteins for O67135 (Aquifex aeolicus (strain VF5)) Explore O67135  Go to UniProtKB:  O67135

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.240 
• R-Value Work: 0.198 
• R-Value Observed: 0.198 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.4	α = 90
b = 93.8	β = 96.9
c = 78.7	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-07-28 
• Released Date: 1999-09-15 
Deposition Author(s): Finnin, M.S., Donigian, J.R., Pavletich, N.P.

Revision History  

• Version 1.0: 1999-09-15
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance