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- PDB-5fl2: Revisited cryo-EM structure of Inducible lysine decarboxylase com... -

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Basic information

Entry
Database: PDB / ID: 5fl2
TitleRevisited cryo-EM structure of Inducible lysine decarboxylase complexed with LARA domain of RavA ATPase
Components
  • ATPASE RAVA
  • LYSINE DECARBOXYLASE, INDUCIBLE
KeywordsHYDROLASE/ISOMERASE / HYDROLASE-ISOMERASE COMPLEX / ACID-STRESS / ATPASE / RAVA
Function / homology
Function and homology information


lysine decarboxylase / lysine catabolic process / lysine decarboxylase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / guanosine tetraphosphate binding / ATP hydrolysis activity / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
: / ATPase, RavA, C-terminal / ATPase RavA / ATPase RavA-like, AAA lid domain / MoxR domain / ATPase RavA, LARA domain / ATPase RavA, LARA domain superfamily / ATPase, RavA, C-terminal / AAA lid domain / MoxR domain in the MoxR-vWA-beta-propeller ternary systems ...: / ATPase, RavA, C-terminal / ATPase RavA / ATPase RavA-like, AAA lid domain / MoxR domain / ATPase RavA, LARA domain / ATPase RavA, LARA domain superfamily / ATPase, RavA, C-terminal / AAA lid domain / MoxR domain in the MoxR-vWA-beta-propeller ternary systems / ATPase, RavA, LARA 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Inducible lysine decarboxylase / ATPase RavA
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.2 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.
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.
#1: Journal: Elife / Year: 2014
Title: Assembly principles of a unique cage formed by hexameric and decameric E. coli proteins.
Authors: Hélène Malet / Kaiyin Liu / Majida El Bakkouri / Sze Wah Samuel Chan / Gregory Effantin / Maria Bacia / Walid A Houry / Irina Gutsche /
Abstract: A 3.3 MDa macromolecular cage between two Escherichia coli proteins with seemingly incompatible symmetries-the hexameric AAA+ ATPase RavA and the decameric inducible lysine decarboxylase LdcI-is ...A 3.3 MDa macromolecular cage between two Escherichia coli proteins with seemingly incompatible symmetries-the hexameric AAA+ ATPase RavA and the decameric inducible lysine decarboxylase LdcI-is reconstructed by cryo-electron microscopy to 11 Å resolution. Combined with a 7.5 Å resolution reconstruction of the minimal complex between LdcI and the LdcI-binding domain of RavA, and the previously solved crystal structures of the individual components, this work enables to build a reliable pseudoatomic model of this unusual architecture and to identify conformational rearrangements and specific elements essential for complex formation. The design of the cage created via lateral interactions between five RavA rings is unique for the diverse AAA+ ATPase superfamily.
History
DepositionOct 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Other
Revision 1.2Aug 30, 2017Group: Refinement description / Category: em_3d_fitting / Item: _em_3d_fitting.target_criteria
Revision 1.3May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Assembly

Deposited unit
A: LYSINE DECARBOXYLASE, INDUCIBLE
K: ATPASE RAVA


Theoretical massNumber of molelcules
Total (without water)92,5452
Polymers92,5452
Non-polymers00
Water00
1
A: LYSINE DECARBOXYLASE, INDUCIBLE
K: ATPASE RAVA
x 10


Theoretical massNumber of molelcules
Total (without water)925,44920
Polymers925,44920
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation9
MethodPISA

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Components

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


Mass: 80882.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria)
Production host: ESCHERICHIA COLI STR. K-12 SUBSTR. MG1655 (bacteria)
References: UniProt: P0A9H3, lysine decarboxylase
#2: Protein ATPASE RAVA / REGULATORY ATPASE VARIANT A / REGULATORY ATPASE VARIANT A / R AVA ATPASE


Mass: 11662.463 Da / Num. of mol.: 1 / Fragment: LARA DOMAIN OF RAVA ATPASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)
References: UniProt: P31473, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances

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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: Complex between a decamer of inducible lysine decarboxylase LdcI and ten LARA domains of the AAA+ ATPase RavA
Type: COMPLEX
Buffer solutionName: 50MM MES PH 6.5, 100MM NACL, 0.2MM PLP, 1MM DTT, 0.01% GLUTARALDEHYDE
pH: 6.5
SpecimenConc.: 0.6 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 SECONDS BEFORE PLUNGING,

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Sep 14, 2012 / Details: AUTOMATIC DATA ACQUISITION WITH FEI EPU SOFTWARE
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 51660 X / Calibrated magnification: 51660 X / Nominal defocus max: 2700 nm / Nominal defocus min: 1500 nm / Cs: 2 mm
Specimen holderTemperature: 91 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNum. digital images: 911

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Processing

CTF correctionDetails: INDIVIDUAL PARTICLE WITH FULL CTF CORRECTION AFTER FIRST PEAK
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 6.2 Å / Nominal pixel size: 1.46466 Å / Actual pixel size: 1.46466 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3206.(DEPOSITION ID: 13911).
Atomic model buildingMethod: FLEXIBLE / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: X-RAY
Atomic model buildingPDB-ID: 3N75

3n75


Accession code: 3N75 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 6.2 Å
Refinement stepCycle: LAST / Highest resolution: 6.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4027 0 0 0 4027

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