+Open data
-Basic information
Entry | Database: PDB / ID: 5fkz | ||||||
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Title | Structure of E.coli Constitutive lysine decarboxylase | ||||||
Components | LYSINE DECARBOXYLASE, CONSTITUTIVE | ||||||
Keywords | LYASE / ACID-STRESS / LYSINE DECARBOXYLASE / RAVA / CAGE | ||||||
Function / homology | Function and homology information lysine decarboxylase / lysine catabolic process / lysine decarboxylase activity / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.5 Å | ||||||
Authors | Kandiah, E. / Carriel, D. / Perard, J. / Malet, H. / Bacia, M. / Liu, K. / Chan, S.W.S. / Houry, W.A. / Ollagnier de Choudens, S. / Elsen, S. / Gutsche, I. | ||||||
Citation | Journal: Sci Rep / Year: 2016 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5fkz.cif.gz | 109.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fkz.ent.gz | 67.5 KB | Display | PDB format |
PDBx/mmJSON format | 5fkz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fkz_validation.pdf.gz | 727.4 KB | Display | wwPDB validaton report |
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Full document | 5fkz_full_validation.pdf.gz | 727 KB | Display | |
Data in XML | 5fkz_validation.xml.gz | 27.1 KB | Display | |
Data in CIF | 5fkz_validation.cif.gz | 40.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/5fkz ftp://data.pdbj.org/pub/pdb/validation_reports/fk/5fkz | HTTPS FTP |
-Related structure data
Related structure data | 3205MC 3204C 3206C 5fkxC 5fl2C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 80417.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): MG1655 / References: UniProt: P52095, lysine decarboxylase |
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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: E.coli Constitutive Lysine Decarboxylase / Type: COMPLEX |
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Buffer solution | Name: 25 MM HEPES, 100 MM NACL, 0.2 MM PLP, 1 MM DTT, PH 7.2 pH: 7.2 |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 91, INSTRUMENT- FEI VITROBOT MARK III, METHOD- BLOT FOR 2.5 SECONDS BEFORE PLUNGING, |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 / Date: Jul 17, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 59000 X / Nominal defocus max: 4290 nm / Nominal defocus min: 540 nm / Cs: 2 mm |
Specimen holder | Temperature: 91 K |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 206 |
-Processing
CTF correction | Details: INDIVIDUAL PARTICLE WAS APPLIED FULL CTF CORRECTION AFTER FIRST PEAK | ||||||||||||
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Symmetry | Point symmetry: D5 (2x5 fold dihedral) | ||||||||||||
3D reconstruction | Method: PROJECTION MATCHING / Resolution: 5.5 Å / Nominal pixel size: 1.186 Å / Actual pixel size: 1.186 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3205. (DEPOSITION ID: 13909). | ||||||||||||
Atomic model building | Method: CROSS-CORRELATION, ENERGY / Space: REAL / Target criteria: Cross-correlation coefficient / Details: X-ray | ||||||||||||
Refinement | Highest resolution: 5.5 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 5.5 Å
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