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- PDB-7pk6: Providencia stuartii Arginine decarboxylase (Adc), stack structure -

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Basic information

Entry
Database: PDB / ID: 7pk6
TitleProvidencia stuartii Arginine decarboxylase (Adc), stack structure
ComponentsBiodegradative arginine decarboxylase
KeywordsLYASE / 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
Orn/Lys/Arg decarboxylase, N-terminal / Ornithine/lysine/arginine decarboxylase / Orn/Lys/Arg decarboxylase, N-terminal domain / Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site. / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal / Orn/Lys/Arg decarboxylase, C-terminal domain superfamily / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal domain / Pyridoxal phosphate-dependent transferase, small domain ...Orn/Lys/Arg decarboxylase, N-terminal / Ornithine/lysine/arginine decarboxylase / Orn/Lys/Arg decarboxylase, N-terminal domain / Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site. / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal / Orn/Lys/Arg decarboxylase, C-terminal domain superfamily / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Biodegradative arginine decarboxylase
Similarity search - Component
Biological speciesProvidencia stuartii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.15 Å
AuthorsJessop, M. / Desfosses, A. / Bacia-Verloop, M. / Gutsche, I.
Funding support France, 2items
OrganizationGrant numberCountry
European Research Council (ERC)647784 France
Agence Nationale de la Recherche (ANR)ANR-2018-CE11-0005-02 France
CitationJournal: 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
DepositionAug 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Biodegradative arginine decarboxylase
B: Biodegradative arginine decarboxylase
K: Biodegradative arginine decarboxylase
P: Biodegradative arginine decarboxylase
L: Biodegradative arginine decarboxylase
Q: Biodegradative arginine decarboxylase
M: Biodegradative arginine decarboxylase
R: Biodegradative arginine decarboxylase
N: Biodegradative arginine decarboxylase
S: Biodegradative arginine decarboxylase
O: Biodegradative arginine decarboxylase
T: Biodegradative arginine decarboxylase
C: Biodegradative arginine decarboxylase
G: Biodegradative arginine decarboxylase
D: Biodegradative arginine decarboxylase
H: Biodegradative arginine decarboxylase
E: Biodegradative arginine decarboxylase
I: Biodegradative arginine decarboxylase
F: Biodegradative arginine decarboxylase
J: Biodegradative arginine decarboxylase


Theoretical massNumber of molelcules
Total (without water)1,723,00520
Polymers1,723,00520
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area157070 Å2
ΔGint-731 kcal/mol
Surface area480680 Å2

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Components

#1: Protein
Biodegradative arginine decarboxylase


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 interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Stacked decamer form of P. stuartii Adc / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.858 MDa / Experimental value: YES
Source (natural)Organism: Providencia stuartii (bacteria) / Strain: ATCC 29914
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 6.5
Details: 25 mM MES, 150 mM NaCl, 1 mM DTT, 0.1 mM PLP, pH 6.5
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 215000 X
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage 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 opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
7Cootmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIX1.13-2998model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 438429
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionResolution: 2.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 268579 / Symmetry type: POINT
Atomic model buildingSpace: REAL

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