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- PDB-7v53: Crystal structure of full-length phospholipase D from Pseudomonas... -

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Basic information

Entry
Database: PDB / ID: 7v53
TitleCrystal structure of full-length phospholipase D from Pseudomonas aeruginosa PAO1
ComponentsPhospholipase D
KeywordsHYDROLASE / phospholipase D / Toxin
Function / homologyPhospholipase D family / Phospholipase D Active site motif / Phospholipase D. Active site motifs. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile. / phospholipid catabolic process / phospholipase D activity / metal ion binding / Phospholipase D
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYang, Y. / Li, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Structural insights into PA3488-mediated inactivation of Pseudomonas aeruginosa PldA.
Authors: Xiaoyun Yang / Zongqiang Li / Liang Zhao / Zhun She / Zengqiang Gao / Sen-Fang Sui / Yuhui Dong / Yanhua Li /
Abstract: PldA, a phospholipase D (PLD) effector, catalyzes hydrolysis of the phosphodiester bonds of glycerophospholipids-the main component of cell membranes-and assists the invasion of the opportunistic ...PldA, a phospholipase D (PLD) effector, catalyzes hydrolysis of the phosphodiester bonds of glycerophospholipids-the main component of cell membranes-and assists the invasion of the opportunistic pathogen Pseudomonas aeruginosa. As a cognate immunity protein, PA3488 can inhibit the activity of PldA to avoid self-toxicity. However, the precise inhibitory mechanism remains elusive. We determine the crystal structures of full-length and truncated PldA and the cryogenic electron microscopy structure of the PldA-PA3488 complex. Structural analysis reveals that there are different intermediates of PldA between the "open" and "closed" states of the catalytic pocket, accompanied by significant conformational changes in the "lid" region and the peripheral helical domain. Through structure-based mutational analysis, we identify the key residues responsible for the enzymatic activity of PldA. Together, these data provide an insight into the molecular mechanisms of PldA invasion and its neutralization by PA3488, aiding future design of PLD-targeted inhibitors and drugs.
History
DepositionAug 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase D


Theoretical massNumber of molelcules
Total (without water)122,4781
Polymers122,4781
Non-polymers00
Water9,656536
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.329, 111.467, 144.758
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 Phospholipase D


Mass: 122478.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Gene: pldA, PA3487 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HYC2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 40.08 %
Crystal growTemperature: 291.1 K / Method: evaporation
Details: 0.2M Potassium Chloride, 0.05M Mg Chloride, 0.05M Tris Hydrochloride, 10% Polyethylene Glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97774 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97774 Å / Relative weight: 1
ReflectionResolution: 2.1→88.32 Å / Num. obs: 57759 / % possible obs: 96.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 28.69 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.037 / Rrim(I) all: 0.093 / Net I/σ(I): 13.7 / Num. measured all: 375158 / Scaling rejects: 25
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.426 / Num. unique obs: 4567 / CC1/2: 0.93 / Rpim(I) all: 0.183 / Rrim(I) all: 0.465 / % possible all: 99.5

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KZ9

6kz9


Resolution: 2.1→55.73 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2152 2970 5.15 %
Rwork0.1772 54653 -
obs0.1792 57623 96.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.1 Å2 / Biso mean: 35.155 Å2 / Biso min: 15.89 Å2
Refinement stepCycle: final / Resolution: 2.1→55.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7162 0 0 536 7698
Biso mean---36.19 -
Num. residues----930
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.130.26791300.18632672280299
2.13-2.170.23411630.185726542817100
2.17-2.210.2511360.186726392775100
2.21-2.240.29921250.25151861198697
2.26-2.30.331220.27622244236698
2.3-2.350.24921490.201126582807100
2.35-2.40.24771480.184926962844100
2.4-2.460.2271320.170626992831100
2.46-2.530.21341420.178126582800100
2.53-2.60.26861220.180627512873100
2.6-2.680.251420.183926712813100
2.68-2.780.24741460.182326862832100
2.78-2.890.26541360.195527012837100
2.89-3.020.27261540.192827022856100
3.02-3.180.22681540.189126992853100
3.18-3.380.21881470.180227162863100
3.38-3.630.2171560.169926312787100
3.69-4.010.16921020.15261861196382
4.01-4.590.1451590.141827402899100
4.59-5.780.18511290.159728172946100
5.78-55.730.18621760.1828973073100

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