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Yorodumi- PDB-7pk6: Providencia stuartii Arginine decarboxylase (Adc), stack structure -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pk6 | |||||||||
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Title | Providencia stuartii Arginine decarboxylase (Adc), stack structure | |||||||||
Components | Biodegradative arginine decarboxylase | |||||||||
Keywords | LYASE / Decarboxylase / LAOdc / PLP-dependant enzyme / Adc | |||||||||
Function / homology | Function and homology information arginine decarboxylase / arginine decarboxylase activity / amino acid metabolic process / cytoplasm Similarity search - Function | |||||||||
Biological species | Providencia stuartii (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.15 Å | |||||||||
Authors | Jessop, M. / Desfosses, A. / Bacia-Verloop, M. / Gutsche, I. | |||||||||
Funding support | France, 2items
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Citation | Journal: Commun Biol / Year: 2022 Title: Structural and biochemical characterisation of the Providencia stuartii arginine decarboxylase shows distinct polymerisation and regulation. Authors: Matthew Jessop / Karine Huard / Ambroise Desfosses / Guillaume Tetreau / Diego Carriel / Maria Bacia-Verloop / Caroline Mas / Philippe Mas / Angélique Fraudeau / Jacques-Philippe Colletier / Irina Gutsche / Abstract: Bacterial homologous lysine and arginine decarboxylases play major roles in the acid stress response, physiology, antibiotic resistance and virulence. The Escherichia coli enzymes are considered as ...Bacterial homologous lysine and arginine decarboxylases play major roles in the acid stress response, physiology, antibiotic resistance and virulence. The Escherichia coli enzymes are considered as their archetypes. Whereas acid stress triggers polymerisation of the E. coli lysine decarboxylase LdcI, such behaviour has not been observed for the arginine decarboxylase Adc. Here we show that the Adc from a multidrug-resistant human pathogen Providencia stuartii massively polymerises into filaments whose cryo-EM structure reveals pronounced differences between Adc and LdcI assembly mechanisms. While the structural determinants of Adc polymerisation are conserved only in certain Providencia and Burkholderia species, acid stress-induced polymerisation of LdcI appears general for enterobacteria. Analysis of the expression, activity and oligomerisation of the P. stuartii Adc further highlights the distinct properties of this unusual protein and lays a platform for future investigation of the role of supramolecular assembly in the superfamily or arginine and lysine decarboxylases. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pk6.cif.gz | 2.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7pk6.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7pk6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pk6_validation.pdf.gz | 966.1 KB | Display | wwPDB validaton report |
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Full document | 7pk6_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7pk6_validation.xml.gz | 322.8 KB | Display | |
Data in CIF | 7pk6_validation.cif.gz | 462.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/7pk6 ftp://data.pdbj.org/pub/pdb/validation_reports/pk/7pk6 | HTTPS FTP |
-Related structure data
Related structure data | 13466MC 7p9bC C: citing same article (ref.) M: map data used to model this data |
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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: 86150.250 Da / Num. of mol.: 20 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Providencia stuartii (bacteria) / Gene: adiA, NCTC11800_00068, NCTC12257_03729 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A379GV98, arginine decarboxylase Has ligand of interest | 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: Stacked decamer form of P. stuartii Adc / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.858 MDa / Experimental value: YES |
Source (natural) | Organism: Providencia stuartii (bacteria) / Strain: ATCC 29914 |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 6.5 Details: 25 mM MES, 150 mM NaCl, 1 mM DTT, 0.1 mM PLP, pH 6.5 |
Specimen | Conc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-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: 215000 X |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 10023 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 438429 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D5 (2x5 fold dihedral) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 268579 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL |