5WP4

Arabidopsis thaliana phosphoethanolamine N-methyltransferase 1 (AtPMT1, XIOPTL) in complex with SAH and phosphocholine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.341 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Conformational changes in the di-domain structure of Arabidopsis phosphoethanolamine methyltransferase leads to active-site formation.

Lee, S.G.Jez, J.M.

(2017) J. Biol. Chem. 292: 21690-21702

  • DOI: 10.1074/jbc.RA117.000106
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Phosphocholine (pCho) is a precursor for phosphatidylcholine and osmoprotectants in plants. In plants, <i>de novo </i> synthesis of pCho relies on the phosphobase methylation pathway. Phosphoethanolamine methyltransferase (PMT) catalyzes the triple ...

    Phosphocholine (pCho) is a precursor for phosphatidylcholine and osmoprotectants in plants. In plants, de novo synthesis of pCho relies on the phosphobase methylation pathway. Phosphoethanolamine methyltransferase (PMT) catalyzes the triple methylation of phosphoethanolamine (pEA) to pCho. The plant PMTs are di-domain methyltransferases that divide the methylation of pEA in one domain from subsequent methylations in the second domain. To understand the molecular basis of this architecture, we examined the biochemical properties of three Arabidopsis thaliana PMTs (AtPMT1-3) and determined the X-ray crystal structures of AtPMT1 and AtPMT2. Although each isoform synthesizes pCho from pEA, their physiological roles differ with AtPMT1 essential for normal growth and salt tolerance, whereas AtPMT2 and AtPMT3 overlap functionally. The structures of AtPMT1 and AtPMT2 reveal unique features in each methyltransferase domain, including active sites that use different chemical mechanisms for phosphobase methylation. These structures also show how rearrangements in both the active sites and the di-domain linker form catalytically competent active sites and provide insight on the evolution of the PMTs in plants, nematodes, and apicomplexans. Connecting conformational changes with catalysis in modular enzymes, like the PMT, provides new insights on interdomain communication in biosynthetic systems.


    Organizational Affiliation

    From the Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130 jjez@wustl.edu.,From the Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphoethanolamine N-methyltransferase 1
A
491Arabidopsis thalianaMutation(s): 0 
Gene Names: NMT1 (PEAMT, XPL1)
EC: 2.1.1.103
Find proteins for Q9FR44 (Arabidopsis thaliana)
Go to Gene View: NMT1
Go to UniProtKB:  Q9FR44
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PC
Query on PC

Download SDF File 
Download CCD File 
A
PHOSPHOCHOLINE
C5 H15 N O4 P
YHHSONZFOIEMCP-UHFFFAOYSA-O
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.341 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.152 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 49.261α = 90.00
b = 86.032β = 106.15
c = 68.242γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
Cootmodel building
HKL-3000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-08-03 
  • Released Date: 2017-11-15 
  • Deposition Author(s): Lee, S.G., Jez, J.M.

Funding OrganizationLocationGrant Number
the National Institutes of HealthUnited StatesAI-097119
the Department of Energy Office of Biological and Environmental ResearchUnited StatesDE-AC02-06CH11357

Revision History 

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2018-01-10
    Type: Database references