9VK1 | pdb_00009vk1

Structure of the plant diacylglycerol O-acyltransferase 1 in complex with oleoyl-CoA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural mechanisms underlying the free fatty acid-mediated regulation of DIACYLGLYCEROL O-ACYLTRANSFERASE 1 in Arabidopsis.

Liu, X.Li, J.Song, D.Liu, Z.

(2025) Plant Cell 37

  • DOI: https://doi.org/10.1093/plcell/koaf239
  • Primary Citation of Related Structures:  
    9VJM, 9VJX, 9VK0, 9VK1

  • PubMed Abstract: 

    Triacylglycerol (TAG) constitutes the primary component of plant oils and is essential for food and biodiesel production. Diacylglycerol O-acyltransferase-1 (DGAT1), the key rate-limiting enzyme in TAG biosynthesis, is an important target for engineering plants with enhanced oil yield and improved fatty acyl composition. Environmental stress triggers the accumulation of toxic lipid intermediates such as free fatty acids (FFAs) and diacylglycerols (DAGs). Plants alleviate lipid toxicity by upregulating DGAT1 to channel the intermediates into TAG. Through biochemical studies, we demonstrate that FFAs directly enhance the activity of Arabidopsis (Arabidopsis thaliana) DGAT1 (AtDGAT1) by ∼3-fold. Cryo-electron microscopy structures of wild-type (WT) AtDGAT1 and a low-activity mutant (H447A) reveal the binding sites for both substrates (DAG and oleoyl-CoA), 2 products (TAG and CoASH), and multiple FFA molecules. Remarkably, mutating a cysteine residue (Cys246) in contact with the FFA head group to Ala, Ser, or Thr increases AtDAGT1 activity significantly. The C246A mutant accommodates the carboxyl group of FFA slightly deeper within the active site, potentially enhancing substrate binding. Furthermore, the FFA molecules orient the acyl-CoA tail at a position favorable for the catalytic reaction. Our integrated biochemical and structural results provide insights into the catalytic mechanism and activity regulation of DGAT1, which will enable the future engineering of oil crops.


  • Organizational Affiliation
    • State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Diacylglycerol O-acyltransferase 1
A, B
528Arabidopsis thalianaMutation(s): 0 
Gene Names: DGAT1ABX45DAGATTAG1At2g19450F3P11.5
EC: 2.3.1.20
UniProt
Find proteins for Q9SLD2 (Arabidopsis thaliana)
Explore Q9SLD2 
Go to UniProtKB:  Q9SLD2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SLD2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3VV (Subject of Investigation/LOI)
Query on 3VV

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate (non-preferred name)
C39 H68 N7 O17 P3 S
XDUHQPOXLUAVEE-BPMMELMSSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARCV3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32000852
National Natural Science Foundation of China (NSFC)China31925024
Chinese Academy of SciencesChinaYSBR-015
Chinese Academy of SciencesChinaXDB37020101
Chinese Academy of SciencesChinaZDBS-LY-SM003

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-05
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Data collection, Database references, Structure summary