› 5d7o

X-ray diffraction
1.63Å resolution

Crystal structure of Sirt2-ADPR at an improved resolution

Released:
DOI: 10.2210/pdb5d7o/pdb
PDB entry 5d7o coloured by chain, front view.
PDB entry 5d7o coloured by chain, side view.
PDB entry 5d7o coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Seeding for sirtuins: microseed matrix seeding to obtain crystals of human Sirt3 and Sirt2 suitable for soaking.
Rumpf T, Gerhardt S, Einsle O, Jung M
OpenAccess logo Acta Crystallogr F Struct Biol Commun 71 1498-510 (2015)
PMID: 26625292

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

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184916 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
NAD-dependent protein deacetylase sirtuin-2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 310 amino acids
Theoretical weight: 35.02 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8IXJ6 (Residues: 50-356; Coverage: 79%)
Gene names: SIR2L, SIR2L2, SIRT2
Sequence domains: Sir2 family

Ligands and Environments

3 bound ligands:
Ligand ZN 2 x ZN
Ligand AR6 2 x AR6
Ligand PGE 1 x PGE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 78Å b: 78.17Å c: 114.241Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.172 0.171 0.191
Expression system: Escherichia coli

Quick links

Citations

9 review citations

Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics.
Ali et al. (2018)
8 more

5 mentions without citation

Crystal structures of the mitochondrial deacylase Sirtuin 4 reveal isoform-specific acyl recognition and regulation features.
Pannek et al. (2017)
4 more