4JZB

Crystal Structure of Leshmaniasis major Farnesyl diphosphate synthase in complex with 1-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)-3-PHENYLPYRIDINIUM, IPP and Ca2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural and thermodynamic basis of the inhibition of Leishmania major farnesyl diphosphate synthase by nitrogen-containing bisphosphonates.

Aripirala, S.Gonzalez-Pacanowska, D.Oldfield, E.Kaiser, M.Amzel, L.M.Gabelli, S.B.

(2014) Acta Crystallogr D Biol Crystallogr 70: 802-810

  • DOI: https://doi.org/10.1107/S1399004713033221
  • Primary Citation of Related Structures:  
    4JZB, 4JZX, 4K10

  • PubMed Abstract: 

    Farnesyl diphosphate synthase (FPPS) is an essential enzyme involved in the biosynthesis of sterols (cholesterol in humans and ergosterol in yeasts, fungi and trypanosomatid parasites) as well as in protein prenylation. It is inhibited by bisphosphonates, a class of drugs used in humans to treat diverse bone-related diseases. The development of bisphosphonates as antiparasitic compounds targeting ergosterol biosynthesis has become an important route for therapeutic intervention. Here, the X-ray crystallographic structures of complexes of FPPS from Leishmania major (the causative agent of cutaneous leishmaniasis) with three bisphosphonates determined at resolutions of 1.8, 1.9 and 2.3 Å are reported. Two of the inhibitors, 1-(2-hydroxy-2,2-diphosphonoethyl)-3-phenylpyridinium (300B) and 3-butyl-1-(2,2-diphosphonoethyl)pyridinium (476A), co-crystallize with the homoallylic substrate isopentenyl diphosphate (IPP) and three Ca(2+) ions. A third inhibitor, 3-fluoro-1-(2-hydroxy-2,2-diphosphonoethyl)pyridinium (46I), was found to bind two Mg(2+) ions but not IPP. Calorimetric studies showed that binding of the inhibitors is entropically driven. Comparison of the structures of L. major FPPS (LmFPPS) and human FPPS provides new information for the design of bisphosphonates that will be more specific for inhibition of LmFPPS. The asymmetric structure of the LmFPPS-46I homodimer indicates that binding of the allylic substrate to both monomers of the dimer results in an asymmetric dimer with one open and one closed homoallylic site. It is proposed that IPP first binds to the open site, which then closes, opening the site on the other monomer, which closes after binding the second IPP, leading to the symmetric fully occupied FPPS dimer observed in other structures.


  • Organizational Affiliation

    Institute for Multiscale Modeling of Biological Interactions and Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, 725 North Wolfe Street WBSB 605, Baltimore, MD 21210, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Farnesyl pyrophosphate synthase
A, B
362Leishmania majorMutation(s): 0 
Gene Names: FPPSLMJF_22_1360
EC: 2.5.1.1 (PDB Primary Data), 2.5.1.10 (PDB Primary Data)
UniProt
Find proteins for Q4QBL1 (Leishmania major)
Explore Q4QBL1 
Go to UniProtKB:  Q4QBL1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4QBL1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P2H
Query on P2H

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
1-(2-hydroxy-2,2-diphosphonoethyl)-3-phenylpyridinium
C13 H16 N O7 P2
ZYEONEYSNIUGRA-UHFFFAOYSA-O
IPE
Query on IPE

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
C5 H12 O7 P2
NUHSROFQTUXZQQ-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
K [auth B]
L [auth B]
C [auth A],
D [auth A],
E [auth A],
K [auth B],
L [auth B],
M [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth A],
N [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A, B
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Binding Affinity Annotations 
IDSourceBinding Affinity
P2H BindingDB:  4JZB Ki: 9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.361α = 90
b = 85.967β = 90
c = 107.074γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2014-03-05
    Changes: Database references
  • Version 1.2: 2014-09-24
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Structure summary