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FDPS: Human Farnesyl Diphosphate Synthase in Complex with Risedronate

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PDB Code 1YQ7 Target Class
Target
Alias
Disease Area/Function
Date Deposited
Authors

Struc Details Tabs

Structure Details
A key branch point enzyme of the mevalonate pathway is farnesyl diphosphate synthase (FDPS, FPPS, EC 2.5.1.10 ), a Mg2+-dependent homodimeric enzyme localized in peroxisomes. FDPS catalyzes the formation of both geranyl and farnesylpyrophosphate from isopentenylpyrophosphate and dimethylallyl pyrophosphate. Post-translational modification of C-terminal C AAX sequences by covalent attachment of these isoprenyl chains is crucial for intracellular localization and proper function of small GTPases such as Ras, Rac, Rho , and CDC42.

Interest in understanding FDPS activity stems from the recent discovery that FDPS is the molecular target of nitrogen-containing bisphosphonates. These compounds disrupt cell growth through FDPS inhibition in parasitic organisms in vitro. In humans, bisphosphonates are targeted to bone tissue where FDPS inhibition in bone-resorbing osteoclasts is a current therapeutic approach for treating post-menopausal osteoporosis. Because of their bone-targeting properties, bisphosphonates have also found use as agents to treat tumor-induced hypercalcemia, Paget's disease, and osteolytic metastases.

Materials & Methods
StructureFDPS (Farnesyl diphosphate synthase)
PDB Code1YQ7
Entry clone accession gi:41281370
Entry clone source MGC
Tag mgsshhhhhhssgrelyfqghm
Construct sequencemgsshhhhhhssgrelyfqghmNGDQNSDVYAQEKQDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKEVLEYNAIGGKYN
RGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACI
YRLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKTAFYSFYLPIAAAMYMAGI
DGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIGTDIQDNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVA
RVKALYEELDLPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYKRRK
Vector p11
Expression host BL21(DE3)
Growth method Overnight cultures in TB (10 mL with100 µg/mL ampicillin) were used to inoculate 1 litre of TB medium containing 100 µg/mL ampicillin. Cultures were grown at 37oC until they reached an OD600 of 0.65 and then induced with 1 mM IPTG. The temperature was adjusted to 18oC and expression was allowed to continue overnight. The cells were collected by centrifugation, transferred to 50 mL tubes, resuspended in 25 mL binding buffer, and frozen at -80°C.
Extraction procedure The frozen cells were thawed on ice and lysed using a high pressure cell disruptor. The lysate was centrifuged at 17,000 RPM for 30 minutes at 4°C and the supernatant was collected.
Purification procedure Ni-affinity Ni-NTA (Qiagen), 4 mL of 50% slurry in 1.5 x 10 cm column, washed with binding buffer. Binding buffer: 50 mM HEPES pH 7.5, 5 mM imidazole, 500 mM NaCl, 5% glycerol. Wash buffer: 50 mM HEPES pH 7.5, 500 mM NaCl, 30 mM imidazole, 5% glycerol. Elution buffer: 50 mM HEPES pH 7.5, 500 mM NaCl, 250 mM imidazole, 5% glycerol. The supernatant was applied by gravity flow onto the Ni-NTA column. The column was sequentially washed with 30 mL binding buffer and 12.5 mL wash buffer. The protein was eluted by applying 12.5 mL of elution buffer and the eluate was collected in 1.5 mL fractions. The fractions were analyzed by SDS-PAGE gel, pooled and concentrated. FDPS was exchanged into crystallization buffer (10 mM Hepes, 0.5 M NaCl, 5% glycerol, pH 7.5) and concentrated to 13 mg/mL using a Millipore centrifugal concentrator with a 10 kDa MW cutoff.
Crystallization Risedronate and MgCl2 were prepared as 100 mM aqueous stock solutions and added to the protein to a final concentration of 2 mM each.  Crystals were grown at 20oC in 150 nl sitting drops by mixing 100 nl of protein solution and 50 nl of precipitant consisting of 40% PEG 300 and 0.1 M phosphate-citrate buffer pH 4.2.
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