Biological Assembly 1  

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

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

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

Macromolecule Content

• Total Structure Weight: 31.20 kDa 
• Atom Count: 2737 
• Modelled Residue Count: 258 
• Deposited Residue Count: 266 
• Unique protein chains: 1

3UJC

Phosphoethanolamine methyltransferase mutant (H132A) from Plasmodium falciparum in complex with phosphocholine

• PDB DOI: 10.2210/pdb3UJC/pdb

• Classification: TRANSFERASE
• Organism(s): Plasmodium falciparum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-11-07 Released: 2011-11-30 
• Deposition Author(s): Lee, S.G., Kim, Y., Alpert, T.D., Nagata, A., Jez, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 0.167 
• R-Value Work: 0.145 
• R-Value Observed: 0.146 

Literature

Structure and reaction mechanism of phosphoethanolamine methyltransferase from the malaria parasite Plasmodium falciparum: an antiparasitic drug target.

Lee, S.G., Kim, Y., Alpert, T.D., Nagata, A., Jez, J.M.

(2012) J Biol Chem 287: 1426-1434

• PubMed: 22117061 
• DOI: 10.1074/jbc.M111.315267
• Primary Citation of Related Structures:  
  3UJ6, 3UJ7, 3UJ8, 3UJ9, 3UJA, 3UJB, 3UJC, 3UJD


• PubMed Abstract: 
  

In the malarial parasite Plasmodium falciparum, a multifunctional phosphoethanolamine methyltransferase (PfPMT) catalyzes the methylation of phosphoethanolamine (pEA) to phosphocholine for membrane biogenesis. This pathway is also found in plant and nematodes, but PMT from these organisms use multiple methyltransferase domains for the S-adenosylmethionine (AdoMet) reactions. Because PfPMT is essential for normal growth and survival of Plasmodium and is not found in humans, it is an antiparasitic target. Here we describe the 1.55 Å resolution crystal structure of PfPMT in complex with AdoMet by single-wavelength anomalous dispersion phasing. In addition, 1.19-1.52 Å resolution structures of PfPMT with pEA (substrate), phosphocholine (product), sinefungin (inhibitor), and both pEA and S-adenosylhomocysteine bound were determined. These structures suggest that domain rearrangements occur upon ligand binding and provide insight on active site architecture defining the AdoMet and phosphobase binding sites. Functional characterization of 27 site-directed mutants identifies critical active site residues and suggests that Tyr-19 and His-132 form a catalytic dyad. Kinetic analysis, isothermal titration calorimetry, and protein crystallography of the Y19F and H132A mutants suggest a reaction mechanism for the PMT. Not only are Tyr-19 and His-132 required for phosphobase methylation, but they also form a "catalytic" latch that locks ligands in the active site and orders the site for catalysis. This study provides the first insight on this antiparasitic target enzyme essential for survival of the malaria parasite; however, further studies of the multidomain PMT from plants and nematodes are needed to understand the evolutionary division of metabolic function in the phosphobase pathway of these organisms.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoethanolamine N-methyltransferase	A	266	Plasmodium falciparum	Mutation(s): 1  Gene Names: PMT
UniProt
Find proteins for Q6T755 (Plasmodium falciparum) Explore Q6T755  Go to UniProtKB:  Q6T755

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PC	B [auth A]	PHOSPHOCHOLINE C5 H15 N O4 P YHHSONZFOIEMCP-UHFFFAOYSA-O

Binding Affinity Annotations
ID	Source	Binding Affinity
PC	PDBBind:  3UJC	Kd: 2.60e+4 (nM) from 1 assay(s)
	Binding MOAD:  3UJC	Kd: 2.60e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 0.167 
• R-Value Work: 0.145 
• R-Value Observed: 0.146 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.302	α = 90
b = 44.193	β = 108.8
c = 76.949	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

• Deposited Date: 2011-11-07 
• Released Date: 2011-11-30 
Deposition Author(s): Lee, S.G., Kim, Y., Alpert, T.D., Nagata, A., Jez, J.M.

Revision History  

• Version 1.0: 2011-11-30
  Type: Initial release
  
• Version 1.1: 2011-12-07
  Changes: Atomic model, Other
• Version 1.2: 2012-03-21
  Changes: Database references