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- PDB-5fkz: Structure of E.coli Constitutive lysine decarboxylase -

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Entry
Database: PDB / ID: 5fkz
TitleStructure of E.coli Constitutive lysine decarboxylase
ComponentsLYSINE DECARBOXYLASE, CONSTITUTIVE
KeywordsLYASE / ACID-STRESS / LYSINE DECARBOXYLASE / RAVA / CAGE
Function / homology
Function and homology information


lysine catabolic process / lysine decarboxylase / lysine decarboxylase activity / identical protein binding / 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
Constitutive lysine decarboxylase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsKandiah, 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.
CitationJournal: 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
DepositionOct 20, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Refinement description / Category: em_3d_fitting / Item: _em_3d_fitting.target_criteria

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Assembly

Deposited unit
E: LYSINE DECARBOXYLASE, CONSTITUTIVE


Theoretical massNumber of molelcules
Total (without water)80,4181
Polymers80,4181
Non-polymers00
Water0
1
E: LYSINE DECARBOXYLASE, CONSTITUTIVE
x 10


Theoretical massNumber of molelcules
Total (without water)804,17810
Polymers804,17810
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation9
MethodPISA

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Components

#1: Protein LYSINE DECARBOXYLASE, CONSTITUTIVE / / LDC / CONSTITUTIVE LYSINE DECARBOXYLASE


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

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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: E.coli Constitutive Lysine Decarboxylase / Type: COMPLEX
Buffer solutionName: 25 MM HEPES, 100 MM NACL, 0.2 MM PLP, 1 MM DTT, PH 7.2
pH: 7.2
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationDetails: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 91, INSTRUMENT- FEI VITROBOT MARK III, METHOD- BLOT FOR 2.5 SECONDS BEFORE PLUNGING,

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Jul 17, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Calibrated magnification: 59000 X / Nominal defocus max: 4290 nm / Nominal defocus min: 540 nm / Cs: 2 mm
Specimen holderTemperature: 91 K
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 206

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Processing

CTF correctionDetails: INDIVIDUAL PARTICLE WAS APPLIED FULL CTF CORRECTION AFTER FIRST PEAK
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionMethod: 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 buildingMethod: CROSS-CORRELATION, ENERGY / Space: REAL / Target criteria: Cross-correlation coefficient / Details: X-ray
RefinementHighest resolution: 5.5 Å
Refinement stepCycle: LAST / Highest resolution: 5.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3501 0 0 0 3501

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