5JA0

Crystal structure of human FPPS with allosterically bound FPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Human farnesyl pyrophosphate synthase is allosterically inhibited by its own product.

Park, J.Zielinski, M.Magder, A.Tsantrizos, Y.S.Berghuis, A.M.

(2017) Nat Commun 8: 14132-14132

  • DOI: 10.1038/ncomms14132

  • PubMed Abstract: 
  • Farnesyl pyrophosphate synthase (FPPS) is an enzyme of the mevalonate pathway and a well-established therapeutic target. Recent research has focused around a newly identified druggable pocket near the enzyme's active site. Pharmacological exploitatio ...

    Farnesyl pyrophosphate synthase (FPPS) is an enzyme of the mevalonate pathway and a well-established therapeutic target. Recent research has focused around a newly identified druggable pocket near the enzyme's active site. Pharmacological exploitation of this pocket is deemed promising; however, its natural biological function, if any, is yet unknown. Here we report that the product of FPPS, farnesyl pyrophosphate (FPP), can bind to this pocket and lock the enzyme in an inactive state. The Kd for this binding is 5-6 μM, within a catalytically relevant range. These results indicate that FPPS activity is sensitive to the product concentration. Kinetic analysis shows that the enzyme is inhibited through FPP accumulation. Having a specific physiological effector, FPPS is a bona fide allosteric enzyme. This allostery offers an exquisite mechanism for controlling prenyl pyrophosphate levels in vivo and thus contributes an additional layer of regulation to the mevalonate pathway.


    Organizational Affiliation

    Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, Quebec, Canada H3G 0B1.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Farnesyl pyrophosphate synthase
F
375Homo sapiensMutation(s): 0 
Gene Names: FDPS (FPS, KIAA1293)
EC: 2.5.1.10
Find proteins for P14324 (Homo sapiens)
Go to Gene View: FDPS
Go to UniProtKB:  P14324
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
F
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
FPP
Query on FPP

Download SDF File 
Download CCD File 
F
FARNESYL DIPHOSPHATE
C15 H28 O7 P2
VWFJDQUYCIWHTN-YFVJMOTDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.172 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 110.890α = 90.00
b = 110.890β = 90.00
c = 77.480γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACphasing
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-02-01
    Type: Database references