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- PDB-9vk0: Structure of plant diacylglycerol O-acyltransferase 1 -

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Basic information

Entry
Database: PDB / ID: 9vk0
TitleStructure of plant diacylglycerol O-acyltransferase 1
ComponentsDiacylglycerol O-acyltransferase 1
KeywordsMEMBRANE PROTEIN / TAG synthysis / activity regulation / FFA / intramembrane enzyme
Function / homology
Function and homology information


positive regulation of seed germination / triglyceride biosynthetic process / diacylglycerol O-acyltransferase / diacylglycerol O-acyltransferase activity / chloroplast membrane / regulation of seed germination / glycerol metabolic process / embryo development ending in seed dormancy / response to abscisic acid / chloroplast envelope ...positive regulation of seed germination / triglyceride biosynthetic process / diacylglycerol O-acyltransferase / diacylglycerol O-acyltransferase activity / chloroplast membrane / regulation of seed germination / glycerol metabolic process / embryo development ending in seed dormancy / response to abscisic acid / chloroplast envelope / regulation of embryonic development / response to glucose / response to salt stress / lipid droplet / response to cold / carbohydrate metabolic process / endoplasmic reticulum membrane / membrane
Similarity search - Function
Diacylglycerol O-acyltransferase 1 / Sterol O-acyltransferase, ACAT/DAG/ARE types / Membrane bound O-acyl transferase, MBOAT / MBOAT, membrane-bound O-acyltransferase family
Similarity search - Domain/homology
: / OLEIC ACID / Diacylglycerol O-acyltransferase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsLiu, X.Y. / Li, J.J. / Song, D.F. / Liu, Z.F.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000852 China
National Natural Science Foundation of China (NSFC)31925024 China
Chinese Academy of SciencesYSBR-015 China
Chinese Academy of SciencesXDB37020101 China
Chinese Academy of SciencesZDBS-LY-SM003 China
CitationJournal: Plant Cell / Year: 2025
Title: Structural mechanisms underlying the free fatty acid-mediated regulation of DIACYLGLYCEROL O-ACYLTRANSFERASE 1 in Arabidopsis.
Authors: Xiuying Liu / Junjie Li / Danfeng Song / Zhenfeng Liu /
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 ...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.
History
DepositionJun 22, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diacylglycerol O-acyltransferase 1
B: Diacylglycerol O-acyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,3956
Polymers120,0592
Non-polymers2,3364
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Diacylglycerol O-acyltransferase 1 / AtDGAT1 / Protein TRIACYLGLYCEROL 1


Mass: 60029.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DGAT1, ABX45, DAGAT, TAG1, At2g19450, F3P11.5 / Production host: Komagataella pastoris (fungus)
References: UniProt: Q9SLD2, diacylglycerol O-acyltransferase
#2: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1LVF / 2,3-bis[[(Z)-octadec-9-enoyl]oxy]propyl (Z)-octadec-9-enoate / Glyceryl trioleate


Mass: 885.432 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C57H104O6 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Dimer of plant diacylglycerol O-acyltransferase 1 with TAG and FFA
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.12 MDa / Experimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Komagataella pastoris (fungus)
Buffer solutionpH: 7.5
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.1particle selection
8PHENIXmodel refinement
13cryoSPARCV3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4524065
3D reconstructionResolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 171030 / Symmetry type: POINT
RefinementHighest resolution: 3.01 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0056268
ELECTRON MICROSCOPYf_angle_d1.048478
ELECTRON MICROSCOPYf_dihedral_angle_d12.664930
ELECTRON MICROSCOPYf_chiral_restr0.058930
ELECTRON MICROSCOPYf_plane_restr0.008998

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