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- PDB-6q6i: Lysine decarboxylase A from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6q6i
TitleLysine decarboxylase A from Pseudomonas aeruginosa
ComponentsBiodegradative arginine decarboxylase
KeywordsOXIDOREDUCTASE / bacterial stress response
Function / homology
Function and homology information


arginine decarboxylase / arginine decarboxylase activity / lysine decarboxylase / lysine decarboxylase activity / amino acid metabolic process / : / cytoplasm
Similarity search - Function
Ornithine Decarboxylase; Chain A, domain 4 / Orn/Lys/Arg decarboxylase, C-terminal 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 ...Ornithine Decarboxylase; Chain A, domain 4 / Orn/Lys/Arg decarboxylase, C-terminal 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 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Biodegradative arginine decarboxylase / Lysine decarboxylase LdcA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKandiah, E. / Gutsche, I.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-12-JSV8-0002 France
European Research CouncilERC 647784 France
CitationJournal: Structure / Year: 2019
Title: Structure, Function, and Evolution of the Pseudomonas aeruginosa Lysine Decarboxylase LdcA.
Authors: Eaazhisai Kandiah / Diego Carriel / Pierre Simon Garcia / Jan Felix / Manuel Banzhaf / George Kritikos / Maria Bacia-Verloop / Céline Brochier-Armanet / Sylvie Elsen / Irina Gutsche /
Abstract: The only enzyme responsible for cadaverine production in the major multidrug-resistant human pathogen Pseudomonas aeruginosa is the lysine decarboxylase LdcA. This enzyme modulates the general ...The only enzyme responsible for cadaverine production in the major multidrug-resistant human pathogen Pseudomonas aeruginosa is the lysine decarboxylase LdcA. This enzyme modulates the general polyamine homeostasis, promotes growth, and reduces bacterial persistence during carbenicillin treatment. Here we present a 3.7-Å resolution cryoelectron microscopy structure of LdcA. We introduce an original approach correlating phylogenetic signal with structural information and reveal possible recombination among LdcA and arginine decarboxylase subfamilies within structural domain boundaries. We show that LdcA is involved in full virulence in an insect pathogenesis model. Furthermore, unlike its enterobacterial counterparts, LdcA is regulated neither by the stringent response alarmone ppGpp nor by the AAA+ ATPase RavA. Instead, the P. aeruginosa ravA gene seems to play a defensive role. Altogether, our study identifies LdcA as an important player in P. aeruginosa physiology and virulence and as a potential drug target.
History
DepositionDec 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Data processing / Category: em_3d_reconstruction
Item: _em_3d_reconstruction.num_particles / _em_3d_reconstruction.resolution

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Assembly

Deposited unit
A: Biodegradative arginine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1012
Polymers82,8541
Non-polymers2471
Water0
1
A: Biodegradative arginine decarboxylase
hetero molecules
x 10


Theoretical massNumber of molelcules
Total (without water)831,01320
Polymers828,54110
Non-polymers2,47110
Water0
TypeNameSymmetry operationNumber
identity operation1
point symmetry operation9
Buried area0 Å2
ΔGint0 kcal/mol
Surface area34570 Å2
MethodPISA

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Components

#1: Protein Biodegradative arginine decarboxylase / Lysine decarboxylase


Mass: 82854.148 Da / Num. of mol.: 1 / Mutation: Q31H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: adiA, adiA_2, CAZ10_25795, CGU42_31920, DY979_03865, DZ962_05275, EB236_18185, EGV95_19425, EGY23_25530, IPC3_20945, IPC669_04165, PA34_018150, PAERUG_E15_London_28_01_14_10034, PAMH19_5219, RW109_RW109_04238
Production host: Escherichia coli (E. coli)
References: UniProt: A0A071KXD7, UniProt: Q9I2S7*PLUS, arginine decarboxylase, lysine decarboxylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
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: Lysine decarboxylase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.8 MDa / Experimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategory
4GctfCTF correction
9RELION1.4initial Euler assignment
12RELION1.43D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66193 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00859720
ELECTRON MICROSCOPYf_angle_d1.45781120
ELECTRON MICROSCOPYf_dihedral_angle_d17.83435410
ELECTRON MICROSCOPYf_chiral_restr0.0688950
ELECTRON MICROSCOPYf_plane_restr0.0110570

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