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 

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Ligand Structure Quality Assessment 


This is version 1.2 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: 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 ...

    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.


    Related Citations: 
    • Genome-Scale Protein Expression and Structural Biology of Plasmodium Falciparum and Related Apicomplexan Organisms
      Vedadi, M., Lew, J., Artz, J., Amani, M., Zhao, Y., Dong, A., Wasney, G.A., Gao, M., Hills, T., Brokx, S., Qiu, W., Sharma, S., Diassiti, A., Alam, Z., Melone, M., Mulichak, A., Wernimont, A., Bray, J., Loppnau, P., Plotnikova, O., Newberry, K., Sundararajan, E., Houston, S., Walker, J., Tempel, W., Bochkarev, A., Kozieradzki, I., Edwards, A., Arrowsmith, C., Roos, D., Kain, K., Hui, R.
      (2007) Mol Biochem Parasitol 151: 100

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Farnesyl pyrophosphate synthaseA, B368Cryptosporidium 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
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

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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