› 5g4c

X-ray diffraction
2.1Å resolution

Human SIRT2 catalyse short chain fatty acyl lysine

Released:
DOI: 10.2210/pdb5g4c/pdb
PDB entry 5g4c coloured by chain, front view.
PDB entry 5g4c coloured by chain, side view.
PDB entry 5g4c coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
SIRT2 Reverses 4-Oxononanoyl Lysine Modification on Histones.
Jin J, He B, Zhang X, Lin H, Wang Y
J Am Chem Soc 138 12304-7 (2016)
PMID: 27610633

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-165681 (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: 323 amino acids
Theoretical weight: 36.53 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8IXJ6 (Residues: 34-356; Coverage: 83%)
Gene names: SIR2L, SIR2L2, SIRT2
Sequence domains: Sir2 family
SIRT2 Chains: E, F
Molecule details ›
Chains: E, F
Length: 5 amino acids
Theoretical weight: 701 Da
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)

Ligands and Environments

2 bound ligands:
Ligand ZN 1 x ZN
Ligand CNA 2 x CNA
1 modified residue:
Ligand 6G4 2 x 6G4

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P21
Unit cell:
a: 37.341Å b: 117.31Å c: 71.346Å
α: 90° β: 92.65° γ: 90°
R-values:
R R work R free
0.183 0.183 0.22
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

16 review citations

Redox Signaling by Reactive Electrophiles and Oxidants.
Parvez et al. (2018)
15 more

4 mentions without citation

SIRT2 Reverses 4-Oxononanoyl Lysine Modification on Histones.
Jin et al. (2016)
3 more