2I7C

The crystal structure of spermidine synthase from p. falciparum in complex with AdoDATO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of Plasmodium falciparum spermidine synthase in complex with the substrate decarboxylated S-adenosylmethionine and the potent inhibitors 4MCHA and AdoDATO.

Dufe, V.T.Qiu, W.Muller, I.B.Hui, R.Walter, R.D.Al-Karadaghi, S.

(2007) J Mol Biol 373: 167-177

  • DOI: 10.1016/j.jmb.2007.07.053
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Plasmodium falciparum is the causative agent of the most severe type of malaria, a life-threatening disease affecting the lives of over three billion people. Factors like widespread resistance against available drugs and absence of an effective vaccine are seriously compounding control of the malaria parasite ...

    Plasmodium falciparum is the causative agent of the most severe type of malaria, a life-threatening disease affecting the lives of over three billion people. Factors like widespread resistance against available drugs and absence of an effective vaccine are seriously compounding control of the malaria parasite. Thus, there is an urgent need for the identification and validation of new drug targets. The enzymes of the polyamine biosynthesis pathway have been suggested as possible targets for the treatment of malaria. One of these enzymes is spermidine synthase (SPDS, putrescine aminopropyltransferase), which catalyzes the transfer of an aminopropyl moiety from decarboxylated S-adenosylmethionine (dcAdoMet) to putrescine, leading to the formation of spermidine and 5'-methylthioadenosine. Here we present the three-dimensional structure of P. falciparum spermidine synthase (pfSPDS) in apo form, in complex with dcAdoMet and two inhibitors, S-adenosyl-1,8-diamino-3-thio-octane (AdoDATO) and trans-4-methylcyclohexylamine (4MCHA). The results show that binding of dcAdoMet to pfSPDS stabilizes the conformation of the flexible gatekeeper loop of the enzyme and affects the conformation of the active-site amino acid residues, preparing the protein for binding of the second substrate. The complexes of AdoDATO and 4MCHA with pfSPDS reveal the mode of interactions of these compounds with the enzyme. While AdoDATO essentially fills the entire active-site pocket, 4MCHA only occupies part of it, which suggests that simple modifications of this compound may yield more potent inhibitors of pfSPDS.


    Organizational Affiliation

    Department of Molecular Biophysics, Center for Molecular Protein Science, Lund University, S-221 00 Lund, Sweden.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Spermidine synthaseA, B, C283Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1129000
EC: 2.5.1.16
Find proteins for Q8II73 (Plasmodium falciparum (isolate 3D7))
Explore Q8II73 
Go to UniProtKB:  Q8II73
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AAT
Query on AAT

Download CCD File 
A, B, C
S-ADENOSYL-1,8-DIAMINO-3-THIOOCTANE
C18 H29 N7 O3 S
SUUGLGYBZXSJAA-SCFUHWHPSA-N
 Ligand Interaction
1PG
Query on 1PG

Download CCD File 
A, B
2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
C11 H24 O6
SLNYBUIEAMRFSZ-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B, C
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AATIC50:  8500   nM  Binding MOAD
AATIC50 :  8500   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 198.168α = 90
b = 134.685β = 95.44
c = 48.5γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2006-09-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance