› 5j8j

X-ray diffraction
2.72Å resolution

A histone deacetylase from Saccharomyces cerevisiae

Released:
DOI: 10.2210/pdb5j8j/pdb
PDB entry 5j8j coloured by chain, front view.
PDB entry 5j8j coloured by chain, side view.
PDB entry 5j8j coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Structural and histone binding ability characterization of the ARB2 domain of a histone deacetylase Hda1 from Saccharomyces cerevisiae.
Shen H, Zhu Y, Wang C, Yan H, Teng M, Li X
Sci Rep 6 33905 (2016)
PMID: 27665728

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 domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-156912 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone deacetylase HDA1 Chain: A
Molecule details ›
Chain: A
Length: 251 amino acids
Theoretical weight: 28.89 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P53973 (Residues: 457-698; Coverage: 34%)
Gene names: HDA1, N2819, YNL021W
Sequence domains: Arb2 domain

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-BM
Spacegroup: P3121
Unit cell:
a: 104.974Å b: 104.974Å c: 86.964Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.192 0.19 0.238
Expression system: Escherichia coli

Quick links

Citations

2 review citations

A short guide to histone deacetylases including recent progress on class II enzymes.
Park et al. (2020)
1 more

3 mentions without citation

Structural and histone binding ability characterization of the ARB2 domain of a histone deacetylase Hda1 from Saccharomyces cerevisiae.
Shen et al. (2016)
2 more