6WLF

Phosphoethanolamine Methyltransferase from the Pine Wilt Nematode Bursaphelenchus xylophilus

  • Classification: TRANSFERASE
  • Organism(s): Bursaphelenchus xylophilus
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2020-04-20 Released: 2020-06-17 
  • Deposition Author(s): Lee, S.G., Jez, J.M.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Department of Energy (DOE, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural and biochemical analysis of phosphoethanolamine methyltransferase from the pine wilt nematode Bursaphelenchus xylophilus.

Lee, S.G.Chung, M.S.DeMarsilis, A.J.Holland, C.K.Jaswaney, R.V.Jiang, C.Kroboth, J.H.P.Kulshrestha, K.Marcelo, R.Z.W.Meyyappa, V.M.Nelson, G.B.Patel, J.K.Petronio, A.J.Powers, S.K.Qin, P.R.Ramachandran, M.Rayapati, D.Rincon, J.A.Rocha, A.Ferreira, J.G.R.N.Steinbrecher, M.K.Yao, K.Zhang, E.J.Zou, A.J.Gang, M.Sparks, M.Cascella, B.Cruz, W.Jez, J.M.

(2020) Mol Biochem Parasitol 238: 111291-111291

  • DOI: https://doi.org/10.1016/j.molbiopara.2020.111291
  • Primary Citation of Related Structures:  
    6WLF

  • PubMed Abstract: 

    In free-living and parasitic nematodes, the methylation of phosphoethanolamine to phosphocholine provides a key metabolite to sustain phospholipid biosynthesis for growth and development. Because the phosphoethanolamine methyltransferases (PMT) of nematodes are essential for normal growth and development, these enzymes are potential targets of inhibitor design. The pine wilt nematode (Bursaphelenchus xylophilus) causes extensive damage to trees used for lumber and paper in Asia. As a first step toward testing BxPMT1 as a potential nematicide target, we determined the 2.05 Å resolution x-ray crystal structure of the enzyme as a dead-end complex with phosphoethanolamine and S-adenosylhomocysteine. The three-dimensional structure of BxPMT1 served as a template for site-directed mutagenesis to probe the contribution of active site residues to catalysis and phosphoethanolamine binding using steady-state kinetic analysis. Biochemical analysis of the mutants identifies key residues on the β1d-α6 loop (W123F, M126I, and Y127F) and β1e-α7 loop (S155A, S160A, H170A, T178V, and Y180F) that form the phosphobase binding site and suggest that Tyr127 facilitates the methylation reaction in BxPMT1.


  • Organizational Affiliation

    Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoethanolamine N-methyltransferase 1
A, B
446Bursaphelenchus xylophilusMutation(s): 0 
UniProt
Find proteins for A0A1I7RPU0 (Bursaphelenchus xylophilus)
Explore A0A1I7RPU0 
Go to UniProtKB:  A0A1I7RPU0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1I7RPU0
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.948α = 90
b = 98.259β = 90
c = 164.954γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)NIH-AI-097119
Department of Energy (DOE, United States)DE-AC02-06CH11357

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-17
    Type: Initial release
  • Version 1.1: 2020-06-24
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description