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- PDB-7ewt: The crystal structure of Lysophospholipid acyltransferase LPCAT3 ... -

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Basic information

Entry
Database: PDB / ID: 7ewt
TitleThe crystal structure of Lysophospholipid acyltransferase LPCAT3 (MOBAT5) in its monomeric and apo form
ComponentsLysophospholipid acyltransferase 5
KeywordsTRANSFERASE / Lysophospholipid Acyltransferase / membrane bound O-acyltransferase / phospholipid remodeling / MEMBRANE PROTEIN
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
Lysophosphatidylcholine acyltransferase 3
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.4 Å
AuthorsZhang, Q. / Yao, D. / Rao, B. / Li, S. / Jian, L. / Chen, Y. / Hu, K. / Xia, 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
DepositionMay 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Structure summary / Category: citation / citation_author / struct
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 / _struct.title
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysophospholipid acyltransferase 5


Theoretical massNumber of molelcules
Total (without water)51,8821
Polymers51,8821
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21890 Å2
Unit cell
Length a, b, c (Å)76.789, 82.261, 116.925
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lysophospholipid acyltransferase 5


Mass: 51881.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LPCAT3 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A1L1RNG8

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 65.8 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 6
Details: PEG 400, 4-Morpholineethanesulfonic acid (MES), Magnesium Acetate, Formamide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.4→47.65 Å / Num. obs: 10597 / % possible obs: 99.3 % / Redundancy: 7.2 % / Biso Wilson estimate: 191.62 Å2 / CC1/2: 0.572 / Net I/σ(I): 21.84
Reflection shellResolution: 3.4→3.45 Å / Num. unique obs: 1663 / CC1/2: 0.572

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→47.65 Å / Cor.coef. Fo:Fc: 0.839 / Cor.coef. Fo:Fc free: 0.854 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.654
RfactorNum. reflection% reflectionSelection details
Rfree0.345 553 5.22 %RANDOM
Rwork0.343 ---
obs0.343 10597 99.8 %-
Displacement parametersBiso max: 257.17 Å2 / Biso mean: 158.01 Å2 / Biso min: 114.84 Å2
Baniso -1Baniso -2Baniso -3
1-6.2078 Å20 Å20 Å2
2--4.9205 Å20 Å2
3----11.1283 Å2
Refine analyzeLuzzati coordinate error obs: 0.82 Å
Refinement stepCycle: final / Resolution: 3.4→47.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3430 0 0 0 3430
Num. residues----417
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1158SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes557HARMONIC5
X-RAY DIFFRACTIONt_it3528HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion442SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4161SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3528HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg4785HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion2.13
X-RAY DIFFRACTIONt_other_torsion23.99
LS refinement shellResolution: 3.4→3.45 Å / Rfactor Rfree error: 0 / Total num. of bins used: 27
RfactorNum. reflection% reflection
Rfree0.3062 21 5.34 %
Rwork0.2428 372 -
all0.2462 393 -
obs--97.52 %
Refinement TLS params.Method: refined / Origin x: 6.8098 Å / Origin y: 8.9243 Å / Origin z: 28.9186 Å
111213212223313233
T-0.1993 Å20.0719 Å2-0.0624 Å2--0.1985 Å2-0.0632 Å2---0.3044 Å2
L2.2319 °21.1687 °2-0.9349 °2-3.0343 °2-0.8427 °2--2.0997 °2
S0.0215 Å °-0.0631 Å °-0.0199 Å °0.0132 Å °-0.0881 Å °-0.1355 Å °0.0122 Å °0.1781 Å °0.0666 Å °
Refinement TLS groupSelection details: { A|* }

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