› 1yc2

X-ray diffraction
2.4Å resolution

Sir2Af2-NAD-ADPribose-nicotinamide

Released:
DOI: 10.2210/pdb1yc2/pdb
PDB entry 1yc2 coloured by chain, front view.
PDB entry 1yc2 coloured by chain, side view.
PDB entry 1yc2 coloured by chain, top view.
Source organism: Archaeoglobus fulgidus
Primary publication:
Mechanism of sirtuin inhibition by nicotinamide: altering the NAD(+) cosubstrate specificity of a Sir2 enzyme.
Avalos JL, Bever KM, Wolberger C
Mol Cell 17 855-68 (2005)
PMID: 15780941

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:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assemblies composition:
monomeric
homo dimer
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128215 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
NAD-dependent protein deacylase 2 Chains: A, B, C, D, E
Molecule details ›
Chains: A, B, C, D, E
Length: 253 amino acids
Theoretical weight: 28.54 KDa
Source organism: Archaeoglobus fulgidus
Expression system: Escherichia coli
UniProt:
  • Canonical: O30124 (Residues: 1-253; Coverage: 100%)
Gene names: AF_0112, Sir2Af2, cobB2
Sequence domains: Sir2 family
Structure domains:

Ligands and Environments

9 bound ligands:
Ligand ZN 9 x ZN
Ligand SO4 10 x SO4
Ligand NAD 4 x NAD
Ligand NCA 5 x NCA
Ligand EDO 5 x EDO
Ligand 2PE 2 x 2PE
Ligand PG4 1 x PG4
Ligand PGE 1 x PGE
Ligand APR 1 x APR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P21212
Unit cell:
a: 105.122Å b: 181.562Å c: 79.025Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.209 0.255
Expression system: Escherichia coli

Quick links

Citations

73 review citations

NAD+/NADH and NADP+/NADPH in cellular functions and cell death: regulation and biological consequences.
Ying W. (2008)
72 more

5 mentions without citation

Acylation of Biomolecules in Prokaryotes: a Widespread Strategy for the Control of Biological Function and Metabolic Stress.
Hentchel et al. (2015)
4 more