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Yorodumi- PDB-8b0o: Cryo-EM structure apolipoprotein N-acyltransferase Lnt from E.col... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8b0o | |||||||||
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Title | Cryo-EM structure apolipoprotein N-acyltransferase Lnt from E.coli in complex with FP3 | |||||||||
Components | Apolipoprotein N-acyltransferase | |||||||||
Keywords | TRANSFERASE / Lnt / apolipoprotein N-acyltransferase / bacterial lipoprotein / cryo-EM | |||||||||
Function / homology | Function and homology information apolipoprotein N-acyltransferase / N-acyltransferase activity / lipoprotein biosynthetic process / outer membrane-bounded periplasmic space / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 Å | |||||||||
Authors | Degtjarik, O. / Smithers, L. / Boland, C. / Caffrey, M. / Shalev Benami, M. | |||||||||
Funding support | Ireland, 2items
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Citation | Journal: Sci Adv / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b0o.cif.gz | 152.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b0o.ent.gz | 94.3 KB | Display | PDB format |
PDBx/mmJSON format | 8b0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b0o_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8b0o_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8b0o_validation.xml.gz | 31.2 KB | Display | |
Data in CIF | 8b0o_validation.cif.gz | 43.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/8b0o ftp://data.pdbj.org/pub/pdb/validation_reports/b0/8b0o | HTTPS FTP |
-Related structure data
Related structure data | 15790MC 8aq2C 8aq3C 8aq4C 8b0kC 8b0lC 8b0mC 8b0nC 8b0pC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 59264.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: lnt, cutE, b0657, JW0654 / Production host: Escherichia coli (E. coli) References: UniProt: P23930, apolipoprotein N-acyltransferase |
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#2: Chemical | ChemComp-OJF / [( |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Apolipoprotein N-acyltransferase / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) | ||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||
Buffer solution | pH: 6 | ||||||||||||||||
Buffer component |
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Specimen | Conc.: 14 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 33 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 112304 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.81 Å2 | ||||||||||||||||||||||||
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