1RQJ

Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Risedronate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural basis for bisphosphonate-mediated inhibition of isoprenoid biosynthesis

Hosfield, D.J.Zhang, Y.Dougan, D.R.Brooun, A.Tari, L.W.Swanson, R.V.Finn, J.

(2004) J.Biol.Chem. 279: 8526-8529

  • DOI: 10.1074/jbc.C300511200
  • Primary Citation of Related Structures:  1RQI, 1RTR

  • PubMed Abstract: 
  • Farnesyl pyrophosphate synthetase (FPPS) synthesizes farnesyl pyrophosphate through successive condensations of isopentyl pyrophosphate with dimethylallyl pyrophosphate and geranyl pyrophosphate. Nitrogen-containing bisphosphonate drugs used to treat ...

    Farnesyl pyrophosphate synthetase (FPPS) synthesizes farnesyl pyrophosphate through successive condensations of isopentyl pyrophosphate with dimethylallyl pyrophosphate and geranyl pyrophosphate. Nitrogen-containing bisphosphonate drugs used to treat osteoclast-mediated bone resorption and tumor-induced hypercalcemia are potent inhibitors of the enzyme. Here we present crystal structures of substrate and bisphosphonate complexes of FPPS. The structures reveal how enzyme conformational changes organize conserved active site residues to exploit metal-induced ionization and substrate positioning for catalysis. The structures further demonstrate how nitrogen-containing bisphosphonates mimic a carbocation intermediate to inhibit the enzyme. Together, these FPPS complexes provide a structural template for the design of novel inhibitors that may prove useful for the treatment of osteoporosis and other clinical indications including cancer.


    Organizational Affiliation

    Syrrx Inc., San Diego, California 92121, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Geranyltranstransferase
A, B
299Escherichia coli (strain K12)Gene Names: ispA
EC: 2.5.1.10
Find proteins for P22939 (Escherichia coli (strain K12))
Go to UniProtKB:  P22939
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPE
Query on IPE

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Download CCD File 
A, B
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
ISOPENTENYL PYROPHOSPHATE
C5 H12 O7 P2
NUHSROFQTUXZQQ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
RIS
Query on RIS

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Download CCD File 
A, B
1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID
Risedronate
C7 H11 N O7 P2
IIDJRNMFWXDHID-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.206 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 88.800α = 90.00
b = 88.800β = 90.00
c = 174.988γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-02
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2013-05-22
    Type: Non-polymer description
  • Version 1.4: 2017-10-04
    Type: Advisory, Refinement description, Structure summary