4KRG | pdb_00004krg

SeMet Haemonchus contortus Phosphoethanolamine N-methyltransferase 1 in complex with phosphoethanolamine and S-adenosylhomocysteine

• PDB DOI: https://doi.org/10.2210/pdb4KRG/pdb

• Classification: TRANSFERASE
• Organism(s): Haemonchus contortus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-05-16 Released: 2013-09-25 
• Deposition Author(s): Lee, S.G., Jez, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.140 (Depositor), 0.134 (DCC) 
• R-Value Work: 
  0.121 (Depositor), 0.115 (DCC) 
• R-Value Observed: 
  0.123 (Depositor) 

Literature

Evolution of structure and mechanistic divergence in di-domain methyltransferases from nematode phosphocholine biosynthesis.

Lee, S.G., Jez, J.M.

(2013) Structure 21: 1778-1787

• PubMed: 24012478 
• DOI: https://doi.org/10.1016/j.str.2013.07.023
• Primary Citation Related Structures: 
  4KRG, 4KRH, 4KRI


• PubMed Abstract: 
  

  The phosphobase methylation pathway is the major route for supplying phosphocholine to phospholipid biosynthesis in plants, nematodes, and Plasmodium. In this pathway, phosphoethanolamine N-methyltransferase (PMT) catalyzes the sequential methylation of phosphoethanolamine to phosphocholine. In the PMT, one domain (MT1) catalyzes methylation of phosphoethanolamine to phosphomonomethylethanolamine and a second domain (MT2) completes the synthesis of phosphocholine. The X-ray crystal structures of the di-domain PMT from the parasitic nematode Haemonchus contortus (HcPMT1 and HcPMT2) reveal that the catalytic domains of these proteins are structurally distinct and allow for selective methylation of phosphobase substrates using different active site architectures. These structures also reveal changes leading to loss of function in the vestigial domains of the nematode PMT. Divergence of function in the two nematode PMTs provides two distinct antiparasitic inhibitor targets within the same essential metabolic pathway. The PMTs from nematodes, plants, and Plasmodium also highlight adaptable metabolic modularity in evolutionarily diverse organisms.

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Organizational Affiliation: 
• Department of Biology, Washington University in St. Louis, One Brookings Drive, Campus Box 1137, 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: 111.23 kDa 
• Atom Count: 9,786 
• Modeled Residue Count: 932 
• Deposited Residue Count: 932 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoethanolamine N-methyltransferase 1	A, B	466	Haemonchus contortus	Mutation(s): 0  EC: 2.1.1.103
UniProt
Find proteins for U5HK46 (Haemonchus contortus) Explore U5HK46  Go to UniProtKB:  U5HK46

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	D [auth A], I [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
BOG	E [auth A], F [auth A], J [auth B], K [auth B]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
OPE	C [auth A], H [auth B]	PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER C2 H8 N O4 P SUHOOTKUPISOBE-UHFFFAOYSA-N
NA	G [auth A], L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.140 (Depositor), 0.134 (DCC) 
• R-Value Work:  0.121 (Depositor), 0.115 (DCC) 
• R-Value Observed: 0.123 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.998	α = 90
b = 72.998	β = 90
c = 360.62	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-25 
Deposition Author(s): Lee, S.G., Jez, J.M.

Revision History  

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 1.1: 2013-10-30
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2025-03-26
  Changes: Data collection, Database references, Structure summary