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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3205 | |||||||||
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Title | Structure of E.coli Constitutive lysine decarboxylase | |||||||||
![]() | Reconstruction of E.coli Constitutive lysine decarboxylase | |||||||||
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![]() | acid-stress / lysine decarboxylase / RavA / cage | |||||||||
Function / homology | ![]() lysine decarboxylase / lysine catabolic process / lysine decarboxylase activity / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.1 Å | |||||||||
![]() | Kandiah E / Carriel D / Perard J / Malet H / Bacia M / Liu K / Chan WSS / Houry AW / Ollagnier de Choudens S / Elsen S / Gutsche I | |||||||||
![]() | ![]() Title: Structural insights into the Escherichia coli lysine decarboxylases and molecular determinants of interaction with the AAA+ ATPase RavA. Authors: Eaazhisai Kandiah / Diego Carriel / Julien Perard / Hélène Malet / Maria Bacia / Kaiyin Liu / Sze W S Chan / Walid A Houry / Sandrine Ollagnier de Choudens / Sylvie Elsen / Irina Gutsche / ![]() ![]() Abstract: The inducible lysine decarboxylase LdcI is an important enterobacterial acid stress response enzyme whereas LdcC is its close paralogue thought to play mainly a metabolic role. A unique ...The inducible lysine decarboxylase LdcI is an important enterobacterial acid stress response enzyme whereas LdcC is its close paralogue thought to play mainly a metabolic role. A unique macromolecular cage formed by two decamers of the Escherichia coli LdcI and five hexamers of the AAA+ ATPase RavA was shown to counteract acid stress under starvation. Previously, we proposed a pseudoatomic model of the LdcI-RavA cage based on its cryo-electron microscopy map and crystal structures of an inactive LdcI decamer and a RavA monomer. We now present cryo-electron microscopy 3D reconstructions of the E. coli LdcI and LdcC, and an improved map of the LdcI bound to the LARA domain of RavA, at pH optimal for their enzymatic activity. Comparison with each other and with available structures uncovers differences between LdcI and LdcC explaining why only the acid stress response enzyme is capable of binding RavA. We identify interdomain movements associated with the pH-dependent enzyme activation and with the RavA binding. Multiple sequence alignment coupled to a phylogenetic analysis reveals that certain enterobacteria exert evolutionary pressure on the lysine decarboxylase towards the cage-like assembly with RavA, implying that this complex may have an important function under particular stress conditions. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 8.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.5 KB 11.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.7 KB | Display | ![]() |
Images | ![]() | 1.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 261.7 KB | Display | ![]() |
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Full document | ![]() | 260.8 KB | Display | |
Data in XML | ![]() | 10.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fkzMC ![]() 3204C ![]() 3206C ![]() 5fkxC ![]() 5fl2C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Reconstruction of E.coli Constitutive lysine decarboxylase | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.186 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : E.coli Constitutive Lysine Decarboxylase
Entire | Name: E.coli Constitutive Lysine Decarboxylase |
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Components |
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-Supramolecule #1000: E.coli Constitutive Lysine Decarboxylase
Supramolecule | Name: E.coli Constitutive Lysine Decarboxylase / type: sample / ID: 1000 / Oligomeric state: Homodecamer / Number unique components: 1 |
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Molecular weight | Experimental: 80 KDa / Theoretical: 80 KDa / Method: Size exclusion |
-Macromolecule #1: Constitutive Lysine decarboxylase
Macromolecule | Name: Constitutive Lysine decarboxylase / type: protein_or_peptide / ID: 1 / Name.synonym: LdcI / Number of copies: 10 / Oligomeric state: Homodecamer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 80 KDa / Theoretical: 80 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | UniProtKB: Constitutive lysine decarboxylase GO: cytoplasm, lysine decarboxylase activity, lysine catabolic process InterPro: Orn/Lys/Arg decarboxylase, N-terminal, Ornithine/lysine/arginine decarboxylase, Orn/Lys/Arg decarboxylase, major domain, Orn/Lys/Arg decarboxylase, C-terminal, Pyridoxal phosphate-dependent ...InterPro: Orn/Lys/Arg decarboxylase, N-terminal, Ornithine/lysine/arginine decarboxylase, Orn/Lys/Arg decarboxylase, major domain, Orn/Lys/Arg decarboxylase, C-terminal, Pyridoxal phosphate-dependent transferase, Pyridoxal phosphate-dependent transferase, major domain, Pyridoxal phosphate-dependent transferase, small domain |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.2 Details: 25 mM HEPES, 100 mM NaCl, 0.2 mM PLP, 1 mM DTT, pH 7.2 |
Grid | Details: glow-discharged quantifoil grids 300 mesh 2/1 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 91 K / Instrument: FEI VITROBOT MARK III / Method: Blot for 2.5 seconds before plunging |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 90 K / Max: 92 K / Average: 91 K |
Alignment procedure | Legacy - Electron beam tilt params: 0 |
Date | Jul 17, 2014 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 206 / Average electron dose: 25 e/Å2 / Bits/pixel: 8 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 59000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.29 µm / Nominal defocus min: 0.54 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder: Nitrogen cooled / Specimen holder model: GATAN HELIUM |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |