› 6rxj

X-ray diffraction
1.6Å resolution

Crystal structure of CobB wt in complex with H4K16-Acetyl peptide

Released:
DOI: 10.2210/pdb6rxj/pdb
PDB entry 6rxj coloured by chain, front view.
PDB entry 6rxj coloured by chain, side view.
PDB entry 6rxj coloured by chain, top view.
Source organisms:
Primary publication:
Evolved, Selective Erasers of Distinct Lysine Acylations.
Spinck M, Neumann-Staubitz P, Ecke M, Gasper R, Neumann H
Angew Chem Int Ed Engl 59 11142-11149 (2020)
PMID: 32187803

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-135459 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
NAD-dependent protein deacylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 254 amino acids
Theoretical weight: 28.11 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P75960 (Residues: 40-254; Coverage: 77%)
Gene names: JW1106, b1120, cobB, ycfY
Sequence domains: Sir2 family
Histone H4 Chains: C, D
Molecule details ›
Chains: C, D
Length: 10 amino acids
Theoretical weight: 1.2 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Not provided
UniProt:
  • Canonical: P02309 (Residues: 13-22; Coverage: 10%)
Gene names: HHF1, HHF2, N2752, YBR009C, YBR0122, YNL030W

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
1 modified residue:
Ligand ALY 2 x ALY

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: C2221
Unit cell:
a: 131.1Å b: 131.26Å c: 58.54Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.173 0.188
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

Protein lysine crotonylation: past, present, perspective.
Jiang et al. (2021)
1 more