› 5k8k

X-ray diffraction
2.55Å resolution

Structure of the Haemophilus influenzae LpxH-lipid X complex

Released:
DOI: 10.2210/pdb5k8k/pdb
PDB entry 5k8k coloured by chain, front view.
PDB entry 5k8k coloured by chain, side view.
PDB entry 5k8k coloured by chain, top view.
Source organism: Haemophilus influenzae Rd KW20
Primary publication:
Structure of the essential Haemophilus influenzae UDP-diacylglucosamine pyrophosphohydrolase LpxH in lipid A biosynthesis.
Cho J, Lee CJ, Zhao J, Young HE, Zhou P
Nat Microbiol 1 16154 (2016)
PMID: 27780190

Function and Biology Details

Reaction catalysed: 
A UDP-2-N,3-O-bis((3R)-3-hydroxyacyl)-alpha-D-glucosamine + H(2)O = a lipid X + UMP
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155167 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
UDP-2,3-diacylglucosamine hydrolase Chain: A
Molecule details ›
Chain: A
Length: 256 amino acids
Theoretical weight: 30.52 KDa
Source organism: Haemophilus influenzae Rd KW20
Expression system: Escherichia coli
UniProt:
  • Canonical: P44046 (Residues: 1-237; Coverage: 100%)
Gene names: HI_0735, lpxH
Sequence domains: Calcineurin-like phosphoesterase

Ligands and Environments

4 bound ligands:
Ligand MN 2 x MN
Ligand LP5 1 x LP5
Ligand ACT 2 x ACT
Ligand GOL 2 x GOL
1 modified residue:
Ligand MSE 4 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: R32
Unit cell:
a: 99.84Å b: 99.84Å c: 200.85Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.195 0.192 0.227
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Structure- and Ligand-Dynamics-Based Design of Novel Antibiotics Targeting Lipid A Enzymes LpxC and LpxH in Gram-Negative Bacteria.
Zhou et al. (2021)
1 more

6 mentions without citation

Structure, inhibition, and regulation of essential lipid A enzymes.
Zhou et al. (2017)
5 more