Structural characterization of substrate and inhibitor binding to farnesyl pyrophosphate synthase from Pseudomonas aeruginosa.

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Schmidberger JW, Schnell R, Schneider G

Acta Crystallogr. D Biol. Crystallogr. 71 (Pt 3) 721-731 [2015-03-00; online 2015-02-26]

Locus PA4043 in the genome of Pseudomonas aeruginosa PAO1 has been annotated as coding for a farnesyl pyrophosphate synthase (FPPS). This open reading frame was cloned and expressed recombinantly in Escherichia coli. The dimeric enzyme shows farnesyl pyrophosphate synthase activity and is strongly inhibited by ibandronate and zoledronate, drugs that are presently in clinical use. The structures of the unliganded enzyme and complexes with the substrate geranyl diphosphate (GPP), the inhibitor ibandronate and two compounds obtained from a differential scanning fluorimetry-based screen of a fragment library were determined by X-ray crystallography to resolutions of better than 2.0 Å. The enzyme shows the typical α-helical fold of farnesyl pyrophosphate synthases. The substrate GPP binds in the S1 substrate site in an open conformation of the enzyme. In the enzyme-ibandronate complex three inhibitor molecules are bound in the active site of the enzyme. One inhibitor molecule occupies the allylic substrate site (S1) of each subunit, as observed in complexes of nitrogen-containing bisphosphonate inhibitors of farnesyl synthases from other species. Two (in subunit A) and one (in subunit B) additional ibandronate molecules are bound in the active site. The structures of the fragment complexes show two molecules bound in a hydrophobic pocket adjacent to the active site. This allosteric pocket, which has previously only been described for FPPS from eukaryotic organisms, is thus also present in enzymes from pathogenic prokaryotes and might be utilized for the design of inhibitors of bacterial FPPS with a different chemical scaffold to the highly charged bisphosphonates, which are less likely to pass bacterial membranes.

Protein Science Facility (PSF)

PubMed 25760619

DOI 10.1107/S1399004715001121

Crossref 10.1107/S1399004715001121

pii: S1399004715001121
pmc: PMC4356374
PDB: 3ZMB Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PA01, with bound fragment SPB02696.
PDB: 3ZL6 Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PAO1, with bound fragment KM10833.
PDB: 3ZMC Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PA01, with bound substrate molecule Geranyl pyrophosphate.
PDB: 3ZOU Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PA01, with bound fragment SPB02696, and substrate geranyl pyrophosphate.
PDB: 4UMJ Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PA01, with bound ibandronic acid molecules.