1YHM

Structure of the complex of Trypanosoma cruzi farnesyl disphosphate synthase with alendronate, Isopentenyl diphosphate and mg+2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure and mechanism of the farnesyl diphosphate synthase from Trypanosoma cruzi: Implications for drug design.

Gabelli, S.B.McLellan, J.S.Montalvetti, A.Oldfield, E.Docampo, R.Amzel, L.M.

(2005) Proteins 62: 80-88

  • DOI: 10.1002/prot.20754
  • Primary Citation of Related Structures:  
    1YHM, 1YHL, 1YHK

  • PubMed Abstract: 
  • Typanosoma cruzi, the causative agent of Chagas disease, has recently been shown to be sensitive to the action of the bisphosphonates currently used in bone resorption therapy. These compounds target the mevalonate pathway by inhibiting farnesyl diphosphate synthase (farnesyl pyrophosphate synthase, FPPS), the enzyme that condenses the diphosphates of C5 alcohols (isopentenyl and dimethylallyl) to form C10 and C15 diphosphates (geranyl and farnesyl) ...

    Typanosoma cruzi, the causative agent of Chagas disease, has recently been shown to be sensitive to the action of the bisphosphonates currently used in bone resorption therapy. These compounds target the mevalonate pathway by inhibiting farnesyl diphosphate synthase (farnesyl pyrophosphate synthase, FPPS), the enzyme that condenses the diphosphates of C5 alcohols (isopentenyl and dimethylallyl) to form C10 and C15 diphosphates (geranyl and farnesyl). The structures of the T. cruzi FPPS (TcFPPS) alone and in two complexes with substrates and inhibitors reveal that following binding of the two substrates and three Mg2+ ions, the enzyme undergoes a conformational change consisting of a hinge-like closure of the binding site. In this conformation, it would be possible for the enzyme to bind a bisphosphonate inhibitor that spans the sites usually occupied by dimethylallyl diphosphate (DMAPP) and the homoallyl moiety of isopentenyl diphosphate. This observation may lead to the design of new, more potent anti-trypanosomal bisphosphonates, because existing FPPS inhibitors occupy only the DMAPP site. In addition, the structures provide an important mechanistic insight: after its formation, geranyl diphosphate can swing without leaving the enzyme, from the product site to the substrate site to participate in the synthesis of farnesyl diphosphate.


    Organizational Affiliation

    Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
farnesyl pyrophosphate synthaseA, B, C362Trypanosoma cruziMutation(s): 14 
Gene Names: TcFPPS
EC: 2.5.1.10
UniProt
Find proteins for Q8WS26 (Trypanosoma cruzi)
Explore Q8WS26 
Go to UniProtKB:  Q8WS26
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPE (Subject of Investigation/LOI)
Query on IPE

Download Ideal Coordinates CCD File 
I [auth A], O [auth B], U [auth C]3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
C5 H12 O7 P2
NUHSROFQTUXZQQ-UHFFFAOYSA-N
 Ligand Interaction
AHD (Subject of Investigation/LOI)
Query on AHD

Download Ideal Coordinates CCD File 
H [auth A], N [auth B], T [auth C]4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE
C4 H9 N O7 P2
OGSPWJRAVKPPFI-UHFFFAOYSA-J
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A], J [auth B], P [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A] , E [auth A] , F [auth A] , K [auth B] , L [auth B] , M [auth B] , Q [auth C] , R [auth C] , 
D [auth A],  E [auth A],  F [auth A],  K [auth B],  L [auth B],  M [auth B],  Q [auth C],  R [auth C],  S [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, CL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Binding Affinity Annotations 
IDSourceBinding Affinity
AHD PDBBind:  1YHM IC50: 1.47e+5 (nM) from 1 assay(s)
Binding MOAD:  1YHM IC50: 1.47e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.205α = 90
b = 103.205β = 90
c = 385.236γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
AMoREphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2013-04-17
    Changes: Non-polymer description
  • Version 1.4: 2017-10-11
    Changes: Refinement description