9VUQ | pdb_00009vuq

Structure of glycerol-3-phosphate acyltransferase PlsB from Themomonas haemolytica in complex with Palmitoyl-CoA and DOPA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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Literature

The phospholipid biosynthesis enzyme PlsB contains three distinct domains for membrane association, lysophosphatidic acid synthesis, and dimerization.

Li, Y.Liu, X.Li, A.Liu, Z.

(2026) Protein Sci 35

  • DOI: https://doi.org/10.1002/pro.70685
  • Primary Citation Related Structures: 
    9VUQ

  • PubMed Abstract: 

    Biosynthesis of phospholipids is fundamental for membrane biogenesis in all living organisms. As a member of the glycerol-3-phosphate (G3P) acyltransferase family, PlsB is a crucial enzyme catalyzing the first step of phospholipid synthesis by converting G3P and fatty acyl-coenzyme A (CoA)/acyl carrier protein (ACP) into lysophosphatidic acid and free CoA (CoASH)/ACP. In bacterial cells, PlsB participates in the formation of antibiotic-tolerant persister cells related to multidrug tolerance, and is hence considered as a potential target for anti-persister therapy. By using the single-particle cryo-electron microscopy method, we have solved the structure of full-length PlsB from Thermomonas haemolytica (ThPlsB) at 2.79 Å resolution. The ThPlsB protein forms a homodimer with C2 symmetry and each monomer contains three distinct domains, namely the amino-terminal domain (NTD), the middle catalytic domain (MCD), and the carboxy-terminal domain. In the MCD, a fatty acyl-CoA binds in a membrane-facing surface groove enclosed by a lipid molecule 1,2-dioleoyl-sn-glycero-3-phosphate (DOPA) on one side. The interactions between ThPlsB and the membrane involve four surface-exposed amphipathic regions located in the NTD and MCD, respectively. Our structural and biochemical analysis results suggest a membrane surface association-catalysis coupling model for the PlsB-mediated biosynthesis of lysophosphatidic acid occurring at the membrane-cytosol interface.


  • Organizational Affiliation
    • State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P. R. China.

Macromolecule Content 

  • Total Structure Weight: 203.15 kDa 
  • Atom Count: 11,860 
  • Modeled Residue Count: 1,466 
  • Deposited Residue Count: 1,802 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycerol-3-phosphate acyltransferaseA [auth E],
B [auth C]
901Thermomonas haemolyticaMutation(s): 0 
Gene Names: plsBEDC34_102210
EC: 2.3.1.15
UniProt
Find proteins for A0A4R3N9S6 (Thermomonas haemolytica)
Explore A0A4R3N9S6 
Go to UniProtKB:  A0A4R3N9S6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4R3N9S6
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158
RECONSTRUCTIONRELION3.1

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDB37020101
Chinese Academy of SciencesChinaYSBR-015
National Natural Science Foundation of China (NSFC)China32430053
National Natural Science Foundation of China (NSFC)China32000852

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-01
    Type: Initial release
  • Version 1.1: 2026-07-08
    Changes: Data collection, Database references