4FGZ

Crystal Structure of Phosphoethanolamine Methyltransferase from Plasmodium falciparum in Complex with Amodiaquine

• PDB DOI: https://doi.org/10.2210/pdb4FGZ/pdb

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


• Deposited: 2012-06-05 Released: 2012-07-25 
• Deposition Author(s): Lee, S.G., Alpert, T.D., Jez, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.227 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Crystal structure of phosphoethanolamine methyltransferase from Plasmodium falciparum in complex with amodiaquine.

Lee, S.G., Alpert, T.D., Jez, J.M.

(2012) Bioorg Med Chem Lett 22: 4990-4993

• PubMed: 22771008 
• DOI: https://doi.org/10.1016/j.bmcl.2012.06.032
• Primary Citation of Related Structures:  
  4FGZ


• PubMed Abstract: 
  

  Phosphoethanolamine N-methyltransferase (PMT) is essential for phospholipid biogenesis in the malarial parasite Plasmodium falciparum. PfPMT catalyzes the triple methylation of phosphoethanolamine to produce phosphocholine, which is then used for phosphatidylcholine synthesis. Here we describe the 2.0Å resolution X-ray crystal structure of PfPMT in complex with amodiaquine. To better characterize inhibition of PfPMT by amodiaquine, we determined the IC(50) values of a series of aminoquinolines using a direct radiochemical assay. Both structural and functional analyses provide a possible approach for the development of new small molecule inhibitors of PfPMT.

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Organizational Affiliation: 

Department of Biology, Washington University, St. Louis, MO 63130, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 64.55 kDa 
• Atom Count: 4,610 
• Modelled Residue Count: 516 
• Deposited Residue Count: 532 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoethanolamine N-methyltransferase	A, B	266	Plasmodium falciparum	Mutation(s): 0  Gene Names: PMT EC: 2.1.1.103
UniProt
Find proteins for Q8IDQ9 (Plasmodium falciparum (isolate 3D7)) Explore Q8IDQ9  Go to UniProtKB:  Q8IDQ9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	E [auth A], I [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
CQA	C [auth A], D [auth A], G [auth B], H [auth B]	4-[(7-CHLOROQUINOLIN-4-YL)AMINO]-2-[(DIETHYLAMINO)METHYL]PHENOL C20 H22 Cl N3 O OVCDSSHSILBFBN-UHFFFAOYSA-N
PO4	F [auth A], J [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
CQA	PDBBind:  4FGZ	IC50: 1.35e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.227 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.051	α = 90
b = 60.639	β = 90.008
c = 68.151	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-25 
Deposition Author(s): Lee, S.G., Alpert, T.D., Jez, J.M.

Revision History  

• Version 1.0: 2012-07-25
  Type: Initial release
  
• Version 1.1: 2012-08-01
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations, Structure summary