5JA0 | pdb_00005ja0

Crystal structure of human FPPS with allosterically bound FPP

• PDB DOI: https://doi.org/10.2210/pdb5JA0/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-04-11 Released: 2017-01-25 
• Deposition Author(s): Park, J., Zielinski, M., Tsantrizos, Y.S., Berghuis, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.211 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

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

• PubMed: 28098152 
• DOI: https://doi.org/10.1038/ncomms14132
• Primary Citation Related Structures: 
  5JA0


• 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 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 K _d 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.

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Organizational Affiliation: 
• Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, Quebec, Canada H3G 0B1.
Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 43.62 kDa 
• Atom Count: 2,806 
• Modeled Residue Count: 331 
• Deposited Residue Count: 375 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyl pyrophosphate synthase	A [auth F]	375	Homo sapiens	Mutation(s): 0  Gene Names: FDPS, FPS, KIAA1293 EC: 2.5.1.10 (PDB Primary Data), 2.5.1.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P14324 (Homo sapiens) Explore P14324  Go to UniProtKB:  P14324
PHAROS:  P14324 GTEx:  ENSG00000160752

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FPP	C [auth F]	FARNESYL DIPHOSPHATE C15 H28 O7 P2 VWFJDQUYCIWHTN-YFVJMOTDSA-N
PO4	B [auth F]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.211 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.89	α = 90
b = 110.89	β = 90
c = 77.48	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-25 
Deposition Author(s): Park, J., Zielinski, M., Tsantrizos, Y.S., Berghuis, A.M.

Revision History  

• Version 1.0: 2017-01-25
  Type: Initial release
  
• Version 1.1: 2017-02-01
  Changes: Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description