8YS9 | pdb_00008ys9

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

PDB DOI: https://doi.org/10.2210/pdb8YS9/pdb

Classification: TRANSFERASE
Organism(s): Rubellimicrobium thermophilum DSM 16684
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-03-22 Released: 2024-10-16
Deposition Author(s): Kim, J., Salsabila, S.D.
Funding Organization(s): National Research Foundation (NRF, Korea)

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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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

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

Salsabila, S.D., Kim, J.

(2024) Sci Adv 10: eadr0122-eadr0122

PubMed: 39356767 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.adr0122
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 50.7 kDa
Atom Count: 3,735
Modeled Residue Count: 416
Deposited Residue Count: 434
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylethanolamine N-methyltransferase/phosphatidyl-N-methylethanolamine N-methyltransferase	A, B	217	Rubellimicrobium thermophilum DSM 16684	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	S9SHS0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1L1H (Subject of Investigation/LOI) Query on A1L1H Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	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		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
SAH (Subject of Investigation/LOI) Query on SAH Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
TLA Query on TLA Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]