8YS9 | pdb_00008ys9

Crystal structure of Phosphatidylethanolamine N-methyltransferase from R. thermophilum complexed with DMPE and SAH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 
    0.197 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.152 (Depositor), 0.165 (DCC) 

Starting Model: experimental
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Literature

Structural insights into phosphatidylethanolamine N -methyltransferase PmtA mediating bacterial phosphatidylcholine synthesis.

Salsabila, S.D.Kim, J.

(2024) Sci Adv 10: eadr0122-eadr0122

  • DOI: https://doi.org/10.1126/sciadv.adr0122
  • Primary Citation of Related Structures:  
    8YS9

  • PubMed Abstract: 

    Phosphatidylethanolamine N -methyltransferase (PmtA) catalyzes the biosynthesis of phosphatidylcholine (PC) from phosphatidylethanolamine (PE). Although PC is one of the major phospholipids constituting bilayer membranes in eukaryotes, certain bacterial species encode PmtA, a membrane-associated methyltransferase, to produce PC, which is correlated with cellular stress responses, adaptability to environmental changes, and symbiosis or virulence with eukaryotic hosts. Depending on the organism, multiple PmtAs may be required for producing monomethyl- and dimethyl-PE derivatives along with PC, whereas in organisms such as Rubellimicrobium thermophilum , a single enzyme is sufficient to direct all three methylation steps. In this study, we present the x-ray crystal structures of PmtA from R. thermophilum in complex with dimethyl-PE and S -adenosyl-l-homocysteine, as well as in its lipid-free form. Moreover, we demonstrate that the enzyme associates with the cellular membrane via electrostatic interactions facilitated by a group of critical basic residues and can successively methylate PE and its methylated derivatives, culminating in the production of PC.


  • Organizational Affiliation
    • Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylethanolamine N-methyltransferase/phosphatidyl-N-methylethanolamine N-methyltransferase
A, B
217Rubellimicrobium thermophilum DSM 16684Mutation(s): 0 
Gene Names: ruthe_01610
EC: 2.1.1.17 (PDB Primary Data), 2.1.1.71 (PDB Primary Data)
UniProt
Find proteins for S9SHS0 (Rubellimicrobium thermophilum DSM 16684)
Explore S9SHS0 
Go to UniProtKB:  S9SHS0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS9SHS0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L1H (Subject of Investigation/LOI)
Query on A1L1H

Download Ideal Coordinates CCD File 
D [auth A][(2~{R})-3-[2-(dimethylamino)ethoxy-oxidanyl-phosphoryl]oxy-2-[(~{Z})-octadec-9-enoyl]oxy-propyl] (~{Z})-octadec-9-enoate
C43 H82 N O8 P
XHPZRQBHFOVLEJ-UNUIOPIBSA-N
LMT
Query on LMT

Download Ideal Coordinates CCD File 
H [auth B]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
TLA
Query on TLA

Download Ideal Coordinates CCD File 
G [auth B]L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free:  0.197 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.152 (Depositor), 0.165 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.042α = 90
b = 77.681β = 90
c = 83.159γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata processing
MOLREPphasing
Cootmodel building
MxDCdata collection
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release