› 2ier

X-ray diffraction
2.7Å resolution

Crystal Structure of Aquifex aeolicus LpxC Complexed with Uridine 5'-Diphosphate

Released:
DOI: 10.2210/pdb2ier/pdb
PDB entry 2ier coloured by chain, front view.
PDB entry 2ier coloured by chain, side view.
PDB entry 2ier coloured by chain, top view.
Source organism: Aquifex aeolicus
Primary publication:
Binding of uridine 5'-diphosphate in the "basic patch" of the zinc deacetylase LpxC and implications for substrate binding.
Gennadios HA, Christianson DW
Biochemistry 45 15216-23 (2006)
PMID: 17176043

Function and Biology Details

Reaction catalysed: 
UDP-3-O-((3R)-3-hydroxyacyl)-N-acetyl-alpha-D-glucosamine + H(2)O = UDP-3-O-((3R)-3-hydroxyacyl)-alpha-D-glucosamine + acetate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130527 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
UDP-3-O-acyl-N-acetylglucosamine deacetylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 271 amino acids
Theoretical weight: 30.99 KDa
Source organism: Aquifex aeolicus
Expression system: Escherichia coli
UniProt:
  • Canonical: O67648 (Residues: 1-271; Coverage: 96%)
Gene names: aq_1772, envA, lpxC
Sequence domains: UDP-3-O-acyl N-acetylglycosamine deacetylase
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand ZN 9 x ZN
Ligand UDP 2 x UDP
Ligand PLM 2 x PLM
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12C
Spacegroup: P61
Unit cell:
a: 101.206Å b: 101.206Å c: 122.24Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.213 0.213 0.241
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Lipid A modification systems in gram-negative bacteria.
Raetz et al. (2007)
13 other articles

3 mentions without citation

Structure of the bacterial deacetylase LpxC bound to the nucleotide reaction product reveals mechanisms of oxyanion stabilization and proton transfer.
Clayton et al. (2013)
2 more