› 4y6l

X-ray diffraction
1.6Å resolution

Human SIRT2 in complex with myristoylated peptide (H3K9myr)

Released:
DOI: 10.2210/pdb4y6l/pdb
PDB entry 4y6l coloured by chain, front view.
PDB entry 4y6l coloured by chain, side view.
PDB entry 4y6l 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:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159420 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
NAD-dependent protein deacetylase sirtuin-2 Chains: A, B
Molecule details ›
Chains: A, B
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%)
  • Best match: Q8IXJ6-4 (Residues: 52-270)
Gene names: SIR2L, SIR2L2, SIRT2
Sequence domains: Sir2 family
Structure domains:
Histone H3.1 Chains: C, D
Molecule details ›
Chains: C, D
Length: 7 amino acids
Theoretical weight: 931 Da
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 7-13; Coverage: 5%)
Gene names: H3C1, H3C10, H3C11, H3C12, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3FA, H3FB, H3FC HIST1H3C, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
1 modified residue:
Ligand MYK 2 x MYK

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P1
Unit cell:
a: 37.102Å b: 48.824Å c: 97.147Å
α: 101.05° β: 91.53° γ: 112.07°
R-values:
R R work R free
0.208 0.207 0.232
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

43 review citations

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

8 mentions without citation

Kinetic and Structural Basis for Acyl-Group Selectivity and NAD(+) Dependence in Sirtuin-Catalyzed Deacylation.
Feldman et al. (2015)
7 more