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- PDB-9j8q: MprF from Pseudomonas aeruginosa in GDN micelle, C2 symmetry -

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Basic information

Entry
Database: PDB / ID: 9j8q
TitleMprF from Pseudomonas aeruginosa in GDN micelle, C2 symmetry
ComponentsPhosphatidylglycerol lysyltransferase
KeywordsMEMBRANE PROTEIN / Multiple peptide resistance factor / Membrane Enzyme / Synthase / Flippase / aminoacylated lipid
Function / homology
Function and homology information


phosphatidylglycerol alanyltransferase activity / lysyltransferase / phosphatidylglycerol lysyltransferase activity / phospholipid homeostasis / lipid metabolic process / response to antibiotic / plasma membrane
Similarity search - Function
Lysylphosphatidylglycerol synthetase/glycosyltransferase AglD / Lysylphosphatidylglycerol synthase TM region / : / Phosphatidylglycerol lysyltransferase, C-terminal / Phosphatidylglycerol lysyltransferase, C-terminal / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
Chem-J4U / Chem-PGT / PHOSPHATIDYLETHANOLAMINE / Phosphatidylglycerol lysyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsJha, S. / Vinothkumar, K.R.
Funding support India, 2items
OrganizationGrant numberCountry
Other governmentDepartment of Atomic Energy, Government of India, RTI 4006
Department of Biotechnology (DBT, India)DBT/PR12422/MED/31/287/2014 India
CitationJournal: FEBS J / Year: 2026
Title: Cryo-EM structures of multiple-peptide resistance factor (MprF) from Pseudomonas aeruginosa.
Authors: Shaileshanand Jha / Kutti R Vinothkumar /
Abstract: Aminoacylation of the lipid head group in many bacteria is carried out by bi-functional enzymes called MprF, which encode a soluble synthase domain that typically transfers lysine or alanine from a ...Aminoacylation of the lipid head group in many bacteria is carried out by bi-functional enzymes called MprF, which encode a soluble synthase domain that typically transfers lysine or alanine from a tRNA to lipid head groups. The modified lipid is subsequently translocated across the leaflets by a transmembrane domain. This modification of lipids probably evolved to adapt to the environment where the microbes reside. Here, we describe the cryo-EM structures of MprF enzyme from Pseudomonas aeruginosa, revealing a dimeric enzyme with a distinct architecture when compared with the homologous Rhizobium enzymes, and validate this arrangement with biochemical analyses. The cryo-EM maps and the models in detergent micelle and nanodisc reveal a conformational change of the terminal helix of the synthase domain, highlighting the dynamic elements in the enzyme that might facilitate catalysis. Several lipid-like densities are observed in the cryo-EM maps, which might indicate the path taken by the lipids, coupling the function of the two domains. The structures allow postulation of the binding modes of tRNA and lipid transport, and suggest that the mobile secondary structural elements in the synthase domain might play a mechanistic role in these functions.
History
DepositionAug 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 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: Phosphatidylglycerol lysyltransferase
B: Phosphatidylglycerol lysyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,32338
Polymers196,6612
Non-polymers27,66236
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-1), (-1), (1)342.4, 342.4

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Components

#1: Protein Phosphatidylglycerol lysyltransferase / Lysylphosphatidylglycerol synthase / phosphatidylglycerol alanyltransferase


Mass: 98330.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 1-9: MWSHPQFEK - (Strep Tag II), 10-13: GGSG - (Linker), 14-894: PaMprF, 895-899 (RNSSS) - additional residues, from fusion protein 900-903 - VDAL - (N terminus of CPD after cleavage), 1-32, ...Details: 1-9: MWSHPQFEK - (Strep Tag II), 10-13: GGSG - (Linker), 14-894: PaMprF, 895-899 (RNSSS) - additional residues, from fusion protein 900-903 - VDAL - (N terminus of CPD after cleavage), 1-32, 713-726, 805-832, 873-881 - Not modelled (numbering based on Uniprot and doesn't include the fusion construct)
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA0920 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I537, lysyltransferase
#2: Chemical ChemComp-J4U / (2~{R},3~{S},4~{S},5~{S},6~{S})-2-(hydroxymethyl)-6-[(2~{R},3~{S},4~{R},5~{R},6~{R})-2-(hydroxymethyl)-6-[2-[[(2~{R},3~{S},4~{R},5~{R},6~{S})-6-(hydroxymethyl)-5-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxymethyl]-4-[(1~{R},2~{R},4~{S},5'~{R},6~{R},7~{R},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxy-butoxy]-4,5-bis(oxidanyl)oxan-3-yl]oxy-oxane-3,4,5-triol


Mass: 1165.315 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C56H92O25
#3: Chemical...
ChemComp-PGT / (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLGLYCEROL / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT)


Mass: 751.023 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C40H79O10P / Comment: phospholipid*YM
#4: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
Has ligand of interestN
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: MprF dimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.18 MDa / Experimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria) / Cellular location: Cell membrane
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 (DE3) C41 / Plasmid: pET22b-CPD
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisC4H11NO31
2200 mMSodium ChlorideNaCl1
35 mM2-mercaptoethanolC2H6OS1
40.006 %GDNC56H92O251
SpecimenConc.: 5.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: The grid was glow discharged at 25 mA with PELCO easyglow
Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 K / Details: Blot force, 0

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Calibrated magnification: 13084 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 60 sec. / Electron dose: 28.75 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 3877
Details: Images were collected in movie-mode at 40 frames per second
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2EPUimage acquisition
4Gctf1.06CTF correction
5RELION4CTF correction
8Coot0.9.8.8model fitting
9UCSF Chimera1.17.3model fitting
11PHENIX1.20.1-4487model refinement
12REFMAC5.8.0411model refinement
13RELION4initial Euler assignment
14cryoSPARC4.3final Euler assignment
15cryoSPARC4.3classification
16cryoSPARC4.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1239668
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109157 / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingB value: 146.5 / Protocol: OTHER / Space: RECIPROCAL
Atomic model building

3D fitting-ID: 1

IDPDB-IDAccession codeChain residue rangeDetails (eV)Initial refinement model-IDPdb chain residue rangeSource nameType
14v35

4v35

4v35574-872ridid body docked and manually adjusted using coot1574-872PDBexperimental model
233-573The initial model was built as polyalanine helices followed by sequence assignmentOtherin silico model
RefinementResolution: 3.3→130.54 Å / Cor.coef. Fo:Fc: 0.89 / SU B: 12.732 / SU ML: 0.213 / ESU R: 0.295
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.32627 --
obs0.32627 112908 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 144.686 Å2
Refinement stepCycle: 1 / Total: 6528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0020.0126657
ELECTRON MICROSCOPYr_bond_other_d00.0166934
ELECTRON MICROSCOPYr_angle_refined_deg0.7461.6358959
ELECTRON MICROSCOPYr_angle_other_deg0.2471.55215938
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.7455796
ELECTRON MICROSCOPYr_dihedral_angle_2_deg3.8394.88268
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.548101008
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0380.21030
ELECTRON MICROSCOPYr_gen_planes_refined0.0030.027393
ELECTRON MICROSCOPYr_gen_planes_other0.0010.021491
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it6.90113.63193
ELECTRON MICROSCOPYr_mcbond_other6.913.63193
ELECTRON MICROSCOPYr_mcangle_it11.86224.4423986
ELECTRON MICROSCOPYr_mcangle_other11.8624.4483987
ELECTRON MICROSCOPYr_scbond_it7.6115.3583464
ELECTRON MICROSCOPYr_scbond_other7.60915.3583465
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other13.74727.614974
ELECTRON MICROSCOPYr_long_range_B_refined20.166125.917113
ELECTRON MICROSCOPYr_long_range_B_other20.164125.917114
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.349 8418 -
obs--100 %

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