› 4twi

X-ray diffraction
1.79Å resolution

The structure of Sir2Af1 bound to a succinylated histone peptide

Released:
DOI: 10.2210/pdb4twi/pdb
PDB entry 4twi coloured by chain, front view.
PDB entry 4twi coloured by chain, side view.
PDB entry 4twi coloured by chain, top view.
Source organisms:
Primary publication:
Alternate deacylating specificities of the archaeal sirtuins Sir2Af1 and Sir2Af2.
Ringel AE, Roman C, Wolberger C
Protein Sci 23 1686-97 (2014)
PMID: 25200501

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:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128043 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
NAD-dependent protein deacylase 1 Chain: A
Molecule details ›
Chain: A
Length: 245 amino acids
Theoretical weight: 27.18 KDa
Source organism: Archaeoglobus fulgidus DSM 4304
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O28597 (Residues: 1-245; Coverage: 100%)
Gene names: AF_1676, cobB1
Sequence domains: Sir2 family
Structure domains:
Histone H4 Chain: B
Molecule details ›
Chain: B
Length: 14 amino acids
Theoretical weight: 1.68 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Not provided
UniProt:
  • Canonical: P02309 (Residues: 9-21; Coverage: 13%)
Gene names: HHF1, HHF2, N2752, YBR009C, YBR0122, YNL030W

Ligands and Environments

2 bound ligands:
Ligand ZN 1 x ZN
Ligand GOL 1 x GOL
1 modified residue:
Ligand SLL 1 x SLL

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E SUPERBRIGHT
Spacegroup: P21
Unit cell:
a: 44.61Å b: 51.362Å c: 57.687Å
α: 90° β: 101.85° γ: 90°
R-values:
R R work R free
0.194 0.192 0.221
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

The Substrate Specificity of Sirtuins.
Bheda et al. (2016)
2 more

3 mentions without citation

Crystal structures of the mitochondrial deacylase Sirtuin 4 reveal isoform-specific acyl recognition and regulation features.
Pannek et al. (2017)
2 more