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- EMDB-4468: Lysine decarboxylase A from Pseudomonas aeruginosa -

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Basic information

Entry
Database: EMDB / ID: EMD-4468
TitleLysine decarboxylase A from Pseudomonas aeruginosa
Map data
Sample
  • Complex: Lysine decarboxylase
    • Protein or peptide: Biodegradative arginine decarboxylase
  • Ligand: PYRIDOXAL-5'-PHOSPHATEPyridoxal phosphate
Function / homology
Function and homology information


arginine decarboxylase / arginine decarboxylase activity / lysine decarboxylase / lysine 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 / Lysine decarboxylase LdcA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKandiah E / Gutsche I
Funding support France, 2 items
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, 2018-
Header (metadata) releaseSep 25, 2019-
Map releaseSep 25, 2019-
UpdateOct 23, 2019-
Current statusOct 23, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6q6i
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6q6i
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4468.png

Downloads & links

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Map

FileDownload / File: emd_4468.map.gz / Format: CCP4 / Size: 196.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.81551 Å
Density
Contour LevelBy AUTHOR: 0.007 / Movie #1: 0.007
Minimum - Maximum-0.025253009 - 0.0423207
Average (Standard dev.)0.00010944534 (±0.0014731085)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-186-186-186
Dimensions372372372
Spacing372372372
CellA=B=C: 303.369 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.815508064516130.815508064516130.81550806451613
M x/y/z372372372
origin x/y/z0.0000.0000.000
length x/y/z303.369303.369303.369
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-186-186-186
NC/NR/NS372372372
D min/max/mean-0.0250.0420.000

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Supplemental data

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Sample components

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Entire : Lysine decarboxylase

EntireName: Lysine decarboxylase
Components
  • Complex: Lysine decarboxylase
    • Protein or peptide: Biodegradative arginine decarboxylase
  • Ligand: PYRIDOXAL-5'-PHOSPHATEPyridoxal phosphate

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Supramolecule #1: Lysine decarboxylase

SupramoleculeName: Lysine decarboxylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 800 KDa

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Macromolecule #1: Biodegradative arginine decarboxylase

MacromoleculeName: Biodegradative arginine decarboxylase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: arginine decarboxylase
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 82.854148 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MYKDLKFPVL IVHRDIKADT VAGERVRGIA HELEQDGFSI LSTASSAEGR IVASTHHGLA CILVAAEGAG ENQRLLQDVV ELIRVARVR APQLPIFALG EQVTIENAPA ESMADLHQLR GILYLFEDTV PFLARQVARA ARNYLAGLLP PFFRALVEHT A QSNYSWHT ...String:
MYKDLKFPVL IVHRDIKADT VAGERVRGIA HELEQDGFSI LSTASSAEGR IVASTHHGLA CILVAAEGAG ENQRLLQDVV ELIRVARVR APQLPIFALG EQVTIENAPA ESMADLHQLR GILYLFEDTV PFLARQVARA ARNYLAGLLP PFFRALVEHT A QSNYSWHT PGHGGGVAYR KSPVGQAFHQ FFGENTLRSD LSVSVPELGS LLDHTGPLAE AEDRAARNFG ADHTFFVING TS TANKIVW HSMVGREDLV LVDRNCHKSI LHSIIMTGAI PLYLTPERNE LGIIGPIPLS EFSKESIAAK IAASPLARGR EPK VKLAVV TNSTYDGLCY NAELIKQTLG DSVEVLHFDE AWYAYAAFHE FYDGRYGMGT SRSEEGPLVF ATHSTHKMLA AFSQ ASMIH VQDGGTRKLD VARFNEAFMM HISTSPQYGI IASLDVASAM MEGPAGRSLI QETFDEALSF RRALANVRQN LDRND WWFG VWQPEQVEGT DQVGTHDWVL EPSADWHGFG DIAEDYVLLD PIKVTLTTPG LSAGGKLSEQ GIPAAIVSRF LWERGL VVE KTGLYSFLVL FSMGITKGKW STLVTELLEF KRCYDANLPL LDVLPSVAQA GGKRYNGVGL RDLSDAMHAS YRDNATA KA MKRMYTVLPE VAMRPSEAYD KLVRGEVEAV PIARLEGRIA AVMLVPYPPG IPLIMPGERF TEATRSILDY LEFARTFE R AFPGFDSDVH GLQHQDGPSG RCYTVECIKE

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Macromolecule #2: PYRIDOXAL-5'-PHOSPHATE

MacromoleculeName: PYRIDOXAL-5'-PHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: PLP
Molecular weightTheoretical: 247.142 Da
Chemical component information

ChemComp-PLP:
PYRIDOXAL-5'-PHOSPHATE / Pyridoxal phosphate

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: EMDB MAP
EMDB ID:

3205

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 66193

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6q6i:
Lysine decarboxylase A from Pseudomonas aeruginosa

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