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 

wwPDB Validation 3D Report Full Report


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:  

  • 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 MDC ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Farnesyl pyrophosphate synthase
A, B
368Cryptosporidium parvum (strain Iowa II)Mutation(s): 0 
Find proteins for Q5CR09 (Cryptosporidium parvum (strain Iowa II))
Go to UniProtKB:  Q5CR09
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
ZOL
Query on ZOL

Download SDF File 
Download CCD File 
A, B
ZOLEDRONIC ACID
(1-HYDROXY-2-IMIDAZOL-1-YLETHYLIDENE)DIPHOSPHONIC ACID
C5 H10 N2 O7 P2
XRASPMIURGNCCH-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZOLKi: 0.1 nM (99) BINDINGDB
ZOLIC50: 30.1 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.238 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 101.776α = 90.00
b = 101.776β = 90.00
c = 75.275γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
RESOLVEphasing
SHELXL-97refinement
CrystalCleardata collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance