› 1s5p

X-ray diffraction
1.96Å resolution

Structure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase from Eschericia coli.

Released:
DOI: 10.2210/pdb1s5p/pdb
PDB entry 1s5p coloured by chain, front view.
PDB entry 1s5p coloured by chain, side view.
PDB entry 1s5p coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase from Escherichia coli.
Zhao K, Chai X, Marmorstein R
J Mol Biol 337 731-41 (2004)
PMID: 15019790

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 domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-160024 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
NAD-dependent protein deacylase Chain: A
Molecule details ›
Chain: A
Length: 235 amino acids
Theoretical weight: 26.09 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P75960 (Residues: 40-274; Coverage: 84%)
Gene names: JW1106, b1120, cobB, ycfY
Sequence domains: Sir2 family
Structure domains:
HISTONE H4 (RESIDUES 12-19) Chain: B
Molecule details ›
Chain: B
Length: 8 amino acids
Theoretical weight: 955 Da
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
1 modified residue:
Ligand ALY 1 x ALY

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25, APS BEAMLINE 19-ID
Spacegroup: P41212
Unit cell:
a: 93.911Å b: 93.911Å c: 61.488Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.234 0.234 0.27
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

25 review citations

The biochemistry of sirtuins.
Sauve et al. (2006)
24 more

12 mentions without citation

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