2Q58

Cryptosporidium parvum putative polyprenyl pyrophosphate synthase (cgd4_2550) in complex with zoledronate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.238 
  • R-Value Observed: 0.216 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Targeting a uniquely nonspecific prenyl synthase with bisphosphonates to combat cryptosporidiosis

Artz, J.D.Dunford, J.E.Arrowood, M.J.Dong, A.Chruszcz, M.Kavanagh, K.L.Minor, W.Russell, R.G.Ebetino, F.H.Oppermann, U.Hui, R.

(2008) Chem Biol 15: 1296

  • DOI: https://doi.org/10.1016/j.chembiol.2008.10.017
  • Primary Citation of Related Structures:  
    2O1O, 2Q58

  • PubMed Abstract: 

    Cryptosporidiosis is a neglected disease without a wholly effective drug. We present a study demonstrating nitrogen-containing bisphosphonates (N-BPs) to be capable of inhibiting Cryptosporidium parvum at low micromolar concentrations in infected MDCK cells. Predictably, the mechanism of action is based on inhibition of biosynthesis of isoprenoids but the target enzyme is unexpectedly a distinctive C. parvum enzyme dubbed nonspecific polyprenyl pyrophosphate synthase (CpNPPPS). This enzyme produces various isoprenoid products larger than FPP and is inhibited by N-BPs at subnanomolar concentrations. It is part of an isoprenoid pathway in Cryptosporidium distinctly different from other organisms. The proposed mechanism of action is corroborated by crystal structures of the enzyme with risedronate and zoledronate bound showing how this enzyme's unique chain length determinant region enables it to accommodate larger substrates and products. These results, combined with existing data on their clinical use, demonstrate that N-BPs are very promising anticryptosporidial drug candidates.


  • Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Farnesyl pyrophosphate synthase
A, B
368Cryptosporidium parvum Iowa IIMutation(s): 0 
Gene Names: CGD4_2550
UniProt
Find proteins for Q5CR09 (Cryptosporidium parvum (strain Iowa II))
Explore Q5CR09 
Go to UniProtKB:  Q5CR09
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5CR09
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZOL
Query on ZOL

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
ZOLEDRONIC ACID
C5 H10 N2 O7 P2
XRASPMIURGNCCH-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
G [auth B]
H [auth B]
C [auth A],
D [auth A],
E [auth A],
G [auth B],
H [auth B],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
ZOL BindingDB:  2Q58 Ki: 0.05 (nM) from 1 assay(s)
IC50: 30.1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.238 
  • R-Value Observed: 0.216 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.776α = 90
b = 101.776β = 90
c = 75.275γ = 120
Software Package:
Software NamePurpose
MOLREPphasing
SHELXL-97refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2022-04-13
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-08-30
    Changes: Data collection, Refinement description