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- PDB-9uet: Cryo-EM structure of human choline-phosphotransferase 1 -

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Basic information

Entry
Database: PDB / ID: 9uet
TitleCryo-EM structure of human choline-phosphotransferase 1
ComponentsCholinephosphotransferase 1
KeywordsMEMBRANE PROTEIN / phosphotransferase
Function / homology
Function and homology information


platelet activating factor biosynthetic process / diacylglycerol cholinephosphotransferase / diacylglycerol cholinephosphotransferase activity / CDP-choline pathway / diacylglycerol binding / phosphatidylcholine biosynthetic process / Synthesis of PC / intracellular membrane-bounded organelle / lipid metabolic process / regulation of cell growth ...platelet activating factor biosynthetic process / diacylglycerol cholinephosphotransferase / diacylglycerol cholinephosphotransferase activity / CDP-choline pathway / diacylglycerol binding / phosphatidylcholine biosynthetic process / Synthesis of PC / intracellular membrane-bounded organelle / lipid metabolic process / regulation of cell growth / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / membrane / metal ion binding
Similarity search - Function
Choline/ethanolamine phosphotransferase / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferase, transmembrane domain / : / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferases signature.
Similarity search - Domain/homology
Chem-POV / Cholinephosphotransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsHe, Y.L. / Qian, H.W.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Biochem Biophys Res Commun / Year: 2025
Title: Structural basis for substrate selectivity and evolutionary insights into human choline phosphotransferase 1.
Authors: Yonglin He / Yufan Yang / Meng Yang / Hongwu Qian /
Abstract: Phosphatidylcholine (PC) and phosphatidylethanolamine (PE), the core phospholipids maintaining eukaryotic membrane structure and function, are predominantly synthesized through the Kennedy pathway. ...Phosphatidylcholine (PC) and phosphatidylethanolamine (PE), the core phospholipids maintaining eukaryotic membrane structure and function, are predominantly synthesized through the Kennedy pathway. The final step of this pathway is catalyzed by choline phosphotransferase 1 (CHPT1) and choline ethanolamine phosphotransferase 1 (CEPT1). Notably, although these enzymes show high sequence homology, CHPT1 specifically synthesizes PC while CEPT1 catalyzes both PC and PE production, and the mechanism of this substrate selectivity remains unclear. Here, we report the 3.7 Å cryo-EM structure of human CHPT1 (hCHPT1), revealing a homodimer in which each monomer consists of an N-terminal domain, a catalytic domain, and a dimerization domain. Through structural and sequence analyses, along with biochemical characterizations, we identified important residues in the catalytic domain that regulate substrate selectivity. Moreover, cross-species sequence alignment showed ovipara CHPT1 conserves important substrate selectivity residues with CEPT1. This residues conservation may endow ovipara CHPT1 with catalytic bifunctionality comparable to CEPT1. These findings not only elucidate the structural basis for substrate selectivity between CHPT1 and CEPT1, but also provide novel evolutionary perspectives on phospholipid synthase adaptation.
History
DepositionApr 9, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cholinephosphotransferase 1
B: Cholinephosphotransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,8818
Polymers90,2632
Non-polymers1,6176
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 Cholinephosphotransferase 1 / human choline-phosphotransferase 1 / hCPT1 / AAPT1-like protein / Diacylglycerol cholinephosphotransferase 1


Mass: 45131.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHPT1, CPT1, MSTP022 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
References: UniProt: Q8WUD6, diacylglycerol cholinephosphotransferase
#2: Chemical ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / 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: Choline-phosphotransferase 1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 45.1 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK 293F / Plasmid: pCAG
Buffer solutionpH: 8
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 295158 / Symmetry type: POINT

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