5CS2

Crystal structure of Plasmodium falciparum diadenosine triphosphate hydrolase in complex with Cyclomarin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Gift from Nature: Cyclomarin A Kills Mycobacteria and Malaria Parasites by Distinct Modes of Action.

Burstner, N.Roggo, S.Ostermann, N.Blank, J.Delmas, C.Freuler, F.Gerhartz, B.Hinniger, A.Hoepfner, D.Liechty, B.Mihalic, M.Murphy, J.Pistorius, D.Rottmann, M.Thomas, J.R.Schirle, M.Schmitt, E.K.

(2015) Chembiochem 16: 2433-2436

  • DOI: 10.1002/cbic.201500472
  • Primary Citation of Related Structures:  
    5CS2

  • PubMed Abstract: 
  • Malaria continues to be one of the most devastating human diseases despite many efforts to limit its spread by prevention of infection or by pharmaceutical treatment of patients. We have conducted a screen for antiplasmodial compounds by using a natural product library ...

    Malaria continues to be one of the most devastating human diseases despite many efforts to limit its spread by prevention of infection or by pharmaceutical treatment of patients. We have conducted a screen for antiplasmodial compounds by using a natural product library. Here we report on cyclomarin A as a potent growth inhibitor of Plasmodium falciparum and the identification of its molecular target, diadenosine triphosphate hydrolase (PfAp3Aase), by chemical proteomics. Using a biochemical assay, we could show that cyclomarin A is a specific inhibitor of the plasmodial enzyme but not of the closest human homologue hFHIT. Co-crystallisation experiments demonstrate a unique binding mode of the inhibitor. One molecule of cyclomarin A binds a dimeric PfAp3Aase and prevents the formation of the enzyme⋅substrate complex. These results validate PfAp3Aase as a new drug target for the treatment of malaria. We have previously elucidated the structurally unrelated regulatory subunit ClpC1 of the ClpP protease as the molecular target of cyclomarin A in Mycobacterium tuberculosis. Thus, cyclomarin A is a rare example of a natural product with two distinct and specific modes of action.


    Organizational Affiliation

    Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland. esther.schmitt@novartis.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histidine triad proteinA201Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF14_0349PF3D7_1436900
EC: 3.6.1.29
UniProt
Find proteins for Q8IL97 (Plasmodium falciparum (isolate 3D7))
Explore Q8IL97 
Go to UniProtKB:  Q8IL97
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclomarin AB7StreptomycesMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
54C
Query on 54C
BL-PEPTIDE LINKINGC16 H20 N2 O4TRP
MLE
Query on MLE
BL-PEPTIDE LINKINGC7 H15 N O2LEU
WLU
Query on WLU
BL-PEPTIDE LINKINGC7 H15 N O3LEU
WPA
Query on WPA
BL-PEPTIDE LINKINGC10 H13 N O3PHE
WVL
Query on WVL
BL-PEPTIDE LINKINGC8 H15 N O2VAL
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.953α = 90
b = 45.953β = 90
c = 138.44γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-28
    Type: Initial release
  • Version 1.1: 2016-01-27
    Changes: Database references
  • Version 2.0: 2019-05-15
    Changes: Data collection, Polymer sequence