Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 97.99 kDa 
• Atom Count: 7336 
• Modelled Residue Count: 842 
• Deposited Residue Count: 849 
• Unique protein chains: 1

4CXM

Crystal Structure of Plasmodium Falciparum Spermidine Synthase in Complex with METHYLTHIOADENOSIN AND SPERMIDINE after catalysis in crystal

• PDB DOI: 10.2210/pdb4CXM/pdb

• Classification: TRANSFERASE
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-04-07 Released: 2014-10-08 
• Deposition Author(s): Sprenger, J., Svensson, B., Al-Karadaghi, S., Persson, L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.216 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Literature

Three-Dimensional Structures of Plasmodium Falciparum Spermidine Synthase with Bound Inhibitors Suggest New Strategies for Drug Design.

Sprenger, J., Svensson, B., Halander, J., Carey, J., Persson, L., Al-Karadaghi, S.

(2015) Acta Crystallogr D Biol Crystallogr 71: 484

• PubMed: 25760598 
• DOI: 10.1107/S1399004714027011
• Primary Citation of Related Structures:  
  4BP1, 4BP3, 4CWA, 4CXM, 4UOE


• PubMed Abstract: 
  

The enzymes of the polyamine-biosynthesis pathway have been proposed to be promising drug targets in the treatment of malaria. Spermidine synthase (SpdS; putrescine aminopropyltransferase) catalyzes the transfer of the aminopropyl moiety from decarboxylated S-adenosylmethionine to putrescine, leading to the formation of spermidine and 5'-methylthioadenosine (MTA). In this work, X-ray crystallography was used to examine ligand complexes of SpdS from the malaria parasite Plasmodium falciparum (PfSpdS). Five crystal structures were determined of PfSpdS in complex with MTA and the substrate putrescine, with MTA and spermidine, which was obtained as a result of the enzymatic reaction taking place within the crystals, with dcAdoMet and the inhibitor 4-methylaniline, with MTA and 4-aminomethylaniline, and with a compound predicted in earlier in silico screening to bind to the active site of the enzyme, benzimidazol-(2-yl)pentan-1-amine (BIPA). In contrast to the other inhibitors tested, the complex with BIPA was obtained without any ligand bound to the dcAdoMet-binding site of the enzyme. The complexes with the aniline compounds and BIPA revealed a new mode of ligand binding to PfSpdS. The observed binding mode of the ligands, and the interplay between the two substrate-binding sites and the flexible gatekeeper loop, can be used in the design of new approaches in the search for new inhibitors of SpdS.

---

Organizational Affiliation: 

Center for Molecular Protein Science, Lund University, SE-221 00 Lund, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPERMIDINE SYNTHASE	A, B, C	283	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PF3D7_1129000 EC: 2.5.1.16
UniProt
Find proteins for Q8II73 (Plasmodium falciparum (isolate 3D7)) Explore Q8II73  Go to UniProtKB:  Q8II73

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTA	D [auth A], F [auth B], H [auth C]	5'-DEOXY-5'-METHYLTHIOADENOSINE C11 H15 N5 O3 S WUUGFSXJNOTRMR-IOSLPCCCSA-N
SPD	E [auth A], G [auth B], I [auth C]	SPERMIDINE C7 H19 N3 ATHGHQPFGPMSJY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MTA	BindingDB:  4CXM	IC50: 1.59e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.216 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 197.9	α = 90
b = 134.4	β = 95.5
c = 48.3	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-04-07 
• Released Date: 2014-10-08 
Deposition Author(s): Sprenger, J., Svensson, B., Al-Karadaghi, S., Persson, L.

Revision History  

• Version 1.0: 2014-10-08
  Type: Initial release
  
• Version 1.1: 2015-01-14
  Changes: Database references
• Version 1.2: 2015-03-11
  Changes: Database references
• Version 1.3: 2015-03-25
  Changes: Database references
• Version 1.4: 2018-01-17
  Changes: Data collection