› 5ze6

X-ray diffraction
2.5Å resolution

CRYSTAL STRUCTURE OF OCTAPRENYL PYROPHOSPHATE SYNTHASE FROM ESCHERICHIA COLI WITH BPH-981

Released:
DOI: 10.2210/pdb5ze6/pdb
PDB entry 5ze6 coloured by chain, front view.
PDB entry 5ze6 coloured by chain, side view.
PDB entry 5ze6 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Discovery of Lipophilic Bisphosphonates That Target Bacterial Cell Wall and Quinone Biosynthesis.
Malwal SR, Chen L, Hicks H, Qu F, Liu W, Shillo A, Law WX, Zhang J, Chandnani N, Han X, Zheng Y, Chen CC, Guo RT, AbdelKhalek A, Seleem MN, Oldfield E
J Med Chem 62 2564-2581 (2019)
PMID: 30730737

Function and Biology Details

Reaction catalysed: 
(2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate = 5 diphosphate + all-trans-octaprenyl diphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-142328 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Octaprenyl diphosphate synthase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 323 amino acids
Theoretical weight: 35.25 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0AD57 (Residues: 1-323; Coverage: 100%)
Gene names: JW3154, b3187, cel, ispB, yhbD
Sequence domains: Polyprenyl synthetase
Structure domains: Farnesyl Diphosphate Synthase

Ligands and Environments

2 bound ligands:
Ligand HJX 2 x HJX
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL13B1
Spacegroup: P212121
Unit cell:
a: 94.032Å b: 111.999Å c: 133.822Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.185 0.264
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

β-Lactams against the Fortress of the Gram-Positive Staphylococcus aureus Bacterium.
Fisher et al. (2021)
1 more

1 mention without citation

Discovery of Lipophilic Bisphosphonates That Target Bacterial Cell Wall and Quinone Biosynthesis.
Malwal et al. (2019)