› 4fvt

X-ray diffraction
2.47Å resolution

Human SIRT3 bound to Ac-ACS peptide and Carba-NAD

Released:
DOI: 10.2210/pdb4fvt/pdb
PDB entry 4fvt coloured by chain, front view.
PDB entry 4fvt coloured by chain, side view.
PDB entry 4fvt coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Synthesis of carba-NAD and the structures of its ternary complexes with SIRT3 and SIRT5.
Szczepankiewicz BG, Dai H, Koppetsch KJ, Qian D, Jiang F, Mao C, Perni RB
J Org Chem 77 7319-29 (2012)
PMID: 22849721

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-164476 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
NAD-dependent protein deacetylase sirtuin-3, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 274 amino acids
Theoretical weight: 30.55 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NTG7 (Residues: 122-395; Coverage: 69%)
Gene names: SIR2L3, SIRT3
Sequence domains: Sir2 family
Structure domains:
Acetylated ACS2 peptide Chain: B
Molecule details ›
Chain: B
Length: 5 amino acids
Theoretical weight: 545 Da
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand CNA 1 x CNA
Ligand SO4 3 x SO4
Ligand ZN 1 x ZN
Ligand GOL 1 x GOL
2 modified residues:
Ligand ALY 1 x ALY
Ligand NLE 1 x NLE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: C2221
Unit cell:
a: 77.43Å b: 131.05Å c: 77.32Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.202 0.249
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

9 review citations

Metabolic mechanisms of epigenetic regulation.
Meier JL. (2013)
8 more

11 mentions without citation

Structural biology of the writers, readers, and erasers in mono- and poly(ADP-ribose) mediated signaling.
Karlberg et al. (2013)
10 more