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- PDB-7f40: Lysophospholipid acyltransferase LPCAT3 in a complex with Arachid... -

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Basic information

Entry
Database: PDB / ID: 7f40
TitleLysophospholipid acyltransferase LPCAT3 in a complex with Arachidonoyl-CoA
ComponentsLPCAT3
KeywordsTRANSFERASE / Lysophospholipid Acyltransferase / LPCAT3 / membrane-bound O-acyltransferase / cryo-EM
Function / homology
Function and homology information


Acyl chain remodelling of PC / Acyl chain remodelling of PS / Acyl chain remodelling of PE / lysophospholipid acyltransferase activity / 1-acylglycerophosphocholine O-acyltransferase activity / lipid modification / phosphatidylcholine biosynthetic process / acyltransferase activity / membrane
Similarity search - Function
Membrane bound O-acyl transferase, MBOAT / MBOAT, membrane-bound O-acyltransferase family
Similarity search - Domain/homology
Chem-3IX / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Lysophosphatidylcholine acyltransferase 3
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsZhang, Q. / Yao, D. / Rao, B. / Li, S. / Jian, L. / Chen, Y. / Hu, K. / Xia, Y. / Shen, Y. / Cao, Y.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFC1004704 China
National Natural Science Foundation of China (NSFC)8212500015 China
CitationJournal: Nat Commun / Year: 2021
Title: The structural basis for the phospholipid remodeling by lysophosphatidylcholine acyltransferase 3.
Authors: Qing Zhang / Deqiang Yao / Bing Rao / Liyan Jian / Yang Chen / Kexin Hu / Ying Xia / Shaobai Li / Yafeng Shen / An Qin / Jie Zhao / Lu Zhou / Ming Lei / Xian-Cheng Jiang / Yu Cao /
Abstract: As the major component of cell membranes, phosphatidylcholine (PC) is synthesized de novo in the Kennedy pathway and then undergoes extensive deacylation-reacylation remodeling via Lands' cycle. The ...As the major component of cell membranes, phosphatidylcholine (PC) is synthesized de novo in the Kennedy pathway and then undergoes extensive deacylation-reacylation remodeling via Lands' cycle. The re-acylation is catalyzed by lysophosphatidylcholine acyltransferase (LPCAT) and among the four LPCAT members in human, the LPCAT3 preferentially introduces polyunsaturated acyl onto the sn-2 position of lysophosphatidylcholine, thereby modulating the membrane fluidity and membrane protein functions therein. Combining the x-ray crystallography and the cryo-electron microscopy, we determined the structures of LPCAT3 in apo-, acyl donor-bound, and acyl receptor-bound states. A reaction chamber was revealed in the LPCAT3 structure where the lysophosphatidylcholine and arachidonoyl-CoA were positioned in two tunnels connected near to the catalytic center. A side pocket was found expanding the tunnel for the arachidonoyl CoA and holding the main body of arachidonoyl. The structural and functional analysis provides the basis for the re-acylation of lysophosphatidylcholine and the substrate preference during the reactions.
History
DepositionJun 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 15, 2021Group: Derived calculations / Structure summary / Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
A: LPCAT3
B: LPCAT3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,2126
Polymers114,5302
Non-polymers3,6824
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2040 Å2
ΔGint-25 kcal/mol
Surface area50360 Å2

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Components

#1: Protein LPCAT3


Mass: 57265.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LPCAT3 / Plasmid: pcDNA3.4 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: A0A1L1RNG8
#2: Chemical ChemComp-3IX / S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenethioate / Arachidonyl-CoA


Mass: 1053.986 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H66N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
Has ligand of interestY

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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: Lysophospholipid acyltransferase 5 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Gallus gallus (chicken)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 292613 / Symmetry type: POINT

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