Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Dihedral - D5  (3D View)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 assigned by authors and generated by UCSF CHIMERA 1.8_B38824. (software)

Macromolecule Content

• Total Structure Weight: 80.88 kDa 
• Atom Count: 3506 
• Modelled Residue Count: 710 
• Deposited Residue Count: 711 
• Unique protein chains: 1

5FKX

Structure of E.coli inducible lysine decarboxylase at active pH

• PDB DOI: 10.2210/pdb5FKX/pdb
• EM Map EMD-3204:EMDBEMDataResource

• Classification: LYASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli str. K-12 substr. MG1655
• Mutation(s): No 


• Deposited: 2015-10-20 Released: 2016-09-21 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural Insights Into the Escherichia Coli Lysine Decarboxylases and Molecular Determinants of Interaction with the Aaa+ ATPase Rava.

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.

(2016) Sci Rep 6: 24601

• PubMed: 27080013 
• DOI: 10.1038/srep24601
• Primary Citation of Related Structures:  
  5FKX, 5FKZ, 5FL2


• PubMed 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 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.

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Organizational Affiliation: 

CEA, IBS, F-38044 Grenoble, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSINE DECARBOXYLASE, INDUCIBLE	A	711	Escherichia coli K-12	Mutation(s): 0  Gene Names: cadA, ldcI, b4131, JW4092 EC: 4.1.1.18
UniProt
Find proteins for P0A9H3 (Escherichia coli (strain K12)) Explore P0A9H3  Go to UniProtKB:  P0A9H3

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-10-20 
• Released Date: 2016-09-21 
Deposition Author(s): 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.

Revision History  

• Version 1.0: 2016-09-21
  Type: Initial release
  
• Version 1.1: 2016-12-14
  Changes: Other
• Version 1.2: 2017-08-30
  Changes: Refinement description
• Version 1.3: 2019-10-23
  Changes: Data collection, Other