› 2od7

X-ray diffraction
2Å resolution

Crystal Structure of yHst2 bound to the intermediate analogue ADP-HPD, and and aceylated H4 peptide

Released:
DOI: 10.2210/pdb2od7/pdb
PDB entry 2od7 coloured by chain, front view.
PDB entry 2od7 coloured by chain, side view.
PDB entry 2od7 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structural basis for nicotinamide inhibition and base exchange in Sir2 enzymes.
Sanders BD, Zhao K, Slama JT, Marmorstein R
Mol Cell 25 463-72 (2007)
PMID: 17289592

Function and Biology Details

Reaction catalysed: 
(1a) [protein]-N(6)-acetyl-L-lysine + NAD(+) = [protein]-N(6)-(1,1-(5-adenosylyl-alpha-D-ribose-1,2-di-O-yl)ethyl)-L-lysine + nicotinamide
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
hetero tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-156855 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
NAD-dependent protein deacetylase HST2 Chain: A
Molecule details ›
Chain: A
Length: 308 amino acids
Theoretical weight: 34.79 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P53686 (Residues: 1-294; Coverage: 82%)
Gene names: HST2, LPA2C, YPL015C
Sequence domains: Sir2 family
Structure domains:
Acetylated histone H4 peptide Chain: B
Molecule details ›
Chain: B
Length: 14 amino acids
Theoretical weight: 1.61 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 1 x ZN
Ligand A1R 1 x A1R
1 modified residue:
Ligand ALY 1 x ALY

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE A1
Spacegroup: P3221
Unit cell:
a: 106.759Å b: 106.759Å c: 67.689Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.234 0.222 0.234
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

10 review citations

Chemistry of acetyl transfer by histone modifying enzymes: structure, mechanism and implications for effector design.
Hodawadekar et al. (2007)
9 more

2 mentions without citation

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