5FL2

Revisited cryo-EM structure of Inducible lysine decarboxylase complexed with LARA domain of RavA ATPase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • 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 ...

    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.


    Related Citations: 
    • Assembly Principles of a Unique Cage Formed by Hexameric and Decameric E. Coli Proteins.
      Malet, H., Liu, K., El Bakkouri, M., Chan, S.W.S., Effantin, G., Bacia, M., Houry, W.A., Gutsche, I.
      (2014) Elife 3: 03653

    Organizational Affiliation

    CEA, IBS, F-38044 Grenoble, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LYSINE DECARBOXYLASE, INDUCIBLEA711Escherichia coli K-12Mutation(s): 0 
Gene Names: cadAldcIb4131JW4092
EC: 4.1.1.18
UniProt
Find proteins for P0A9H3 (Escherichia coli (strain K12))
Explore P0A9H3 
Go to UniProtKB:  P0A9H3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A9H3
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATPASE RAVAB [auth K]106Escherichia coli K-12Mutation(s): 0 
Gene Names: ravAyieNb3746JW3725
EC: 3.6.3
UniProt
Find proteins for P31473 (Escherichia coli (strain K12))
Explore P31473 
Go to UniProtKB:  P31473
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31473
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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