› 5y5n

X-ray diffraction
2.3Å resolution

Crystal structure of human Sirtuin 2 in complex with a selective inhibitor

Released:
DOI: 10.2210/pdb5y5n/pdb
PDB entry 5y5n coloured by chain, front view.
PDB entry 5y5n coloured by chain, side view.
PDB entry 5y5n coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Potent mechanism-based sirtuin-2-selective inhibition by an in situ-generated occupant of the substrate-binding site, "selectivity pocket" and NAD+-binding site.
Mellini P, Itoh Y, Tsumoto H, Li Y, Suzuki M, Tokuda N, Kakizawa T, Miura Y, Takeuchi J, Lahtela-Kakkonen M, Suzuki T
Chem Sci 8 6400-6408 (2017)
PMID: 28989670

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184915 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
NAD-dependent protein deacetylase sirtuin-2 Chain: A
Molecule details ›
Chain: A
Length: 336 amino acids
Theoretical weight: 37.84 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8IXJ6 (Residues: 32-308, 309-356; Coverage: 84%)
Gene names: SIR2L, SIR2L2, SIRT2
Sequence domains: Sir2 family

Ligands and Environments

2 bound ligands:
Ligand ZN 1 x ZN
Ligand 8NO 1 x 8NO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 50.85Å b: 57.98Å c: 124.532Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.256 0.256 0.252
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Chemical Protein Degradation Approach and its Application to Epigenetic Targets.
Itoh Y. (2018)
6 more

4 mentions without citation

SIRT1 and SIRT2 Activity Control in Neurodegenerative Diseases.
Manjula et al. (2020)
3 more