› 2vqv

X-ray diffraction
3.3Å resolution

Structure of HDAC4 catalytic domain with a gain-of-function mutation bound to a hydroxamic acid inhibitor

Released:
DOI: 10.2210/pdb2vqv/pdb
PDB entry 2vqv coloured by chain, front view.
PDB entry 2vqv coloured by chain, side view.
PDB entry 2vqv coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural and functional analysis of the human HDAC4 catalytic domain reveals a regulatory structural zinc-binding domain.
Bottomley MJ, Lo Surdo P, Di Giovine P, Cirillo A, Scarpelli R, Ferrigno F, Jones P, Neddermann P, De Francesco R, Steinkühler C, Gallinari P, Carfí A
J Biol Chem 283 26694-704 (2008)
PMID: 18614528

Function and Biology Details

Reaction catalysed: 
Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-157479 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone deacetylase 4 Chains: A, B
Molecule details ›
Chains: A, B
Length: 413 amino acids
Theoretical weight: 44.44 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P56524 (Residues: 648-1057; Coverage: 38%)
Gene names: HDAC4, KIAA0288
Sequence domains: Histone deacetylase domain
Structure domains: Histone deacetylase domain

Ligands and Environments

4 bound ligands:
Ligand SO4 4 x SO4
Ligand K 4 x K
Ligand HA3 2 x HA3
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: P21
Unit cell:
a: 86.524Å b: 70.766Å c: 89.011Å
α: 90° β: 108.57° γ: 90°
R-values:
R R work R free
0.235 0.234 0.265
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

54 review citations

The many roles of histone deacetylases in development and physiology: implications for disease and therapy.
Haberland et al. (2009)
53 more

10 mentions without citation

Modulation of epigenetic targets for anticancer therapy: clinicopathological relevance, structural data and drug discovery perspectives.
Andreoli et al. (2013)
9 more