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TitleStructural insights into the Escherichia coli lysine decarboxylases and molecular determinants of interaction with the AAA+ ATPase RavA.
Journal, issue, pagesSci Rep, Vol. 6, Page 24601, Year 2016
Publish dateApr 15, 2016
AuthorsEaazhisai 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 /
PubMed AbstractThe 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.
External linksSci Rep / PubMed:27080013 / PubMed Central
MethodsEM (single particle)
Resolution5.5 - 6.2 Å
Structure data

3204

5fkx

EMDB-3204: Structures of E.coli lysine decarboxylases
PDB-5fkx: Structure of E.coli inducible lysine decarboxylase at active pH
Method: EM (single particle) / Resolution: 6.1 Å

3205

5fkz

EMDB-3205, PDB-5fkz:
Structure of E.coli Constitutive lysine decarboxylase
Method: EM (single particle) / Resolution: 6.1 Å

3206

5fl2

EMDB-3206, PDB-5fl2:
Revisited cryo-EM structure of Inducible lysine decarboxylase complexed with LARA domain of RavA ATPase
Method: EM (single particle) / Resolution: 6.2 Å

Source
  • escherichia coli k-12 (bacteria)
  • escherichia coli (E. coli)
KeywordsLYASE / ACID-STRESS / LYSINE DECARBOXYLASE / RAVA / CAGE / HYDROLASE/ISOMERASE / HYDROLASE-ISOMERASE COMPLEX / ATPASE

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