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- PDB-8aq3: In surfo structure of the membrane integral lipoprotein N-acyltra... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8aq3 | |||||||||
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Title | In surfo structure of the membrane integral lipoprotein N-acyltransferase Lnt from E. coli in complex with PE | |||||||||
![]() | Apolipoprotein N-acyltransferase | |||||||||
![]() | TRANSFERASE / Lnt / apolipoprotein N-acyltransferase / Bacterial lipoproteins. | |||||||||
Function / homology | ![]() apolipoprotein N-acyltransferase / N-acyltransferase activity / lipoprotein biosynthetic process / outer membrane-bounded periplasmic space / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Huang, C.-Y. / Weichert, D. / Boland, C. / Smithers, L. / Olieric, V. / Wang, M. / Caffrey, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure snapshots reveal the mechanism of a bacterial membrane lipoprotein -acyltransferase. Authors: Luke Smithers / Oksana Degtjarik / Dietmar Weichert / Chia-Ying Huang / Coilín Boland / Katherine Bowen / Abraham Oluwole / Corinne Lutomski / Carol V Robinson / Eoin M Scanlan / Meitian ...Authors: Luke Smithers / Oksana Degtjarik / Dietmar Weichert / Chia-Ying Huang / Coilín Boland / Katherine Bowen / Abraham Oluwole / Corinne Lutomski / Carol V Robinson / Eoin M Scanlan / Meitian Wang / Vincent Olieric / Moran Shalev-Benami / Martin Caffrey / ![]() ![]() ![]() ![]() Abstract: Bacterial lipoproteins (BLPs) decorate the surface of membranes in the cell envelope. They function in membrane assembly and stability, as enzymes, and in transport. The final enzyme in the BLP ...Bacterial lipoproteins (BLPs) decorate the surface of membranes in the cell envelope. They function in membrane assembly and stability, as enzymes, and in transport. The final enzyme in the BLP synthesis pathway is the apolipoprotein -acyltransferase, Lnt, which is proposed to act by a ping-pong mechanism. Here, we use x-ray crystallography and cryo-electron microscopy to chart the structural changes undergone during the progress of the enzyme through the reaction. We identify a single active site that has evolved to bind, individually and sequentially, substrates that satisfy structural and chemical criteria to position reactive parts next to the catalytic triad for reaction. This study validates the ping-pong mechanism, explains the molecular bases for Lnt's substrate promiscuity, and should facilitate the design of antibiotics with minimal off-target effects. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.6 KB | Display | ![]() |
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PDB format | ![]() | 96.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 25.2 KB | Display | |
Data in CIF | ![]() | 33.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8aq2C ![]() 8aq4C ![]() 8b0kC ![]() 8b0lC ![]() 8b0mC ![]() 8b0nC ![]() 8b0oC ![]() 8b0pC ![]() 5n6lS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein / Sugars , 2 types, 6 molecules A![](data/chem/img/LMT.gif)
![](data/chem/img/LMT.gif)
#1: Protein | Mass: 59248.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P23930, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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#8: Sugar | ChemComp-LMT / |
-Non-polymers , 8 types, 75 molecules ![](data/chem/img/6OU.gif)
![](data/chem/img/PG5.gif)
![](data/chem/img/PG6.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG5.gif)
![](data/chem/img/PG6.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-PG5 / #4: Chemical | ChemComp-PG6 / | #5: Chemical | ChemComp-TRS / | #6: Chemical | ChemComp-ACT / | #7: Chemical | ChemComp-GOL / #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.76 Å3/Da / Density % sol: 78.66 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion Details: 50 mM sodium acetate pH 5.0, 50 mM magnesium acetate and 28-36 %(v/v) PEG200 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96861 Å / Relative weight: 1 |
Reflection | Resolution: 2.395→46.48 Å / Num. obs: 53802 / % possible obs: 99.9 % / Redundancy: 11.1 % / CC1/2: 0.99 / Rrim(I) all: 0.14 / Net I/σ(I): 12.46 |
Reflection shell | Resolution: 2.4→2.54 Å / Redundancy: 11.22 % / Mean I/σ(I) obs: 0.88 / Num. unique obs: 8590 / CC1/2: 0.46 / Rrim(I) all: 2.92 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5N6L Resolution: 2.395→43.376 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 237.89 Å2 / Biso mean: 76.696 Å2 / Biso min: 42.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.395→43.376 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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