+Open data
-Basic information
Entry | Database: PDB / ID: 7qun | ||||||||||||||||||
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Title | CryoEM structure of mammalian AAP in complex with Meropenem | ||||||||||||||||||
Components | Acylamino-acid-releasing enzyme | ||||||||||||||||||
Keywords | HYDROLASE / inhibitor / complex / acylaminoacyl-peptidase / meropenem / carbapenem / acylpeptide hydrolase | ||||||||||||||||||
Function / homology | Function and homology information acylaminoacyl-peptidase / omega peptidase activity / serine-type endopeptidase activity / proteolysis / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Sus scrofa domesticus (domestic pig) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å | ||||||||||||||||||
Authors | Kiss-Szeman, A.J. / Harmat, V. / Straner, P. / Jakli, I. / Menyhard, K.D. / Masiulis, S. / Perczel, A. | ||||||||||||||||||
Funding support | Hungary, 5items
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Citation | Journal: Chem Sci / Year: 2022 Title: A carbapenem antibiotic inhibiting a mammalian serine protease: structure of the acylaminoacyl peptidase-meropenem complex. Authors: Anna J Kiss-Szemán / Luca Takács / Zoltán Orgován / Pál Stráner / Imre Jákli / Gitta Schlosser / Simonas Masiulis / Veronika Harmat / Dóra K Menyhárd / András Perczel / Abstract: The structure of porcine AAP (pAAP) in a covalently bound complex with meropenem was determined by cryo-EM to 2.1 Å resolution, showing the mammalian serine-protease inhibited by a carbapenem ...The structure of porcine AAP (pAAP) in a covalently bound complex with meropenem was determined by cryo-EM to 2.1 Å resolution, showing the mammalian serine-protease inhibited by a carbapenem antibiotic. AAP is a modulator of the ubiquitin-proteasome degradation system and the site of a drug-drug interaction between the widely used antipsychotic, valproate and carbapenems. The active form of pAAP - a toroidal tetramer - binds four meropenem molecules covalently linked to the catalytic Ser587 of the serine-protease triad, in an acyl-enzyme state. AAP is hindered from fully processing the antibiotic by the displacement and protonation of His707 of the catalytic triad. We show that AAP is made susceptible to the association by its unusually sheltered active pockets and flexible catalytic triads, while the carbapenems possess sufficiently small substituents on their β-lactam rings to fit into the shallow substrate-specificity pocket of the enzyme. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qun.cif.gz | 460.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qun.ent.gz | 379.8 KB | Display | PDB format |
PDBx/mmJSON format | 7qun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qun_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7qun_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7qun_validation.xml.gz | 68.8 KB | Display | |
Data in CIF | 7qun_validation.cif.gz | 108.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/7qun ftp://data.pdbj.org/pub/pdb/validation_reports/qu/7qun | HTTPS FTP |
-Related structure data
Related structure data | 14149MC 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: 81324.391 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: P19205 #2: Chemical | ChemComp-DWZ / ( Has ligand of interest | Y | Has protein modification | Y | |
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-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: Homotetramer of aclyaminoacyl-peptidase / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Sus scrofa domesticus (domestic pig) |
Buffer solution | pH: 7.5 |
Buffer component | Conc.: 10 mM / Name: TRIS / Formula: C4H11NO3 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Covalent complex with carbapenem type antibiotic Meropenem |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 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 magnification: 130000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm |
Image recording | Average exposure time: 5.93 sec. / Electron dose: 41 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 4 / Num. of real images: 11625 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 654863 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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