› 4y6q

X-ray diffraction
1.9Å resolution

Human SIRT2 in complex with 2-O-myristoyl-ADP-ribose

Released:
DOI: 10.2210/pdb4y6q/pdb
PDB entry 4y6q coloured by chain, front view.
PDB entry 4y6q coloured by chain, side view.
PDB entry 4y6q coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Kinetic and Structural Basis for Acyl-Group Selectivity and NAD(+) Dependence in Sirtuin-Catalyzed Deacylation.
Feldman JL, Dittenhafer-Reed KE, Kudo N, Thelen JN, Ito A, Yoshida M, Denu JM
Biochemistry 54 3037-3050 (2015)
PMID: 25897714

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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184917 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
NAD-dependent protein deacetylase sirtuin-2 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 293 amino acids
Theoretical weight: 33.2 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8IXJ6 (Residues: 52-356; Coverage: 75%)
Gene names: SIR2L, SIR2L2, SIRT2
Sequence domains: Sir2 family
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand ZN 4 x ZN
Ligand OMR 4 x OMR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P21
Unit cell:
a: 61.186Å b: 142.369Å c: 62.626Å
α: 90° β: 94.41° γ: 90°
R-values:
R R work R free
0.233 0.231 0.267
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

42 review citations

Slowing ageing by design: the rise of NAD+ and sirtuin-activating compounds.
Bonkowski et al. (2016)
41 more

3 mentions without citation

Chemical and structural biology of protein lysine deacetylases.
Yoshida et al. (2017)
2 more