5FKZ

Structure of E.coli Constitutive lysine decarboxylase

Summary for 5FKZ

• Entry DOI: 10.2210/pdb5fkz/pdb
• Related: 5FKX 5FL2
• EMDB information: 3205
• Descriptor: LYSINE DECARBOXYLASE, CONSTITUTIVE (1 entity in total)
• Functional Keywords: lyase, acid-stress, lysine decarboxylase, rava, cage
• Biological source: ESCHERICHIA COLI
• Total number of polymer chains: 1
• Total formula weight: 80417.77

Authors

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. (deposition date: 2015-10-20, release date: 2016-09-21, Last modification date: 2024-05-08)

Primary citation

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.
Structural Insights Into the Escherichia Coli Lysine Decarboxylases and Molecular Determinants of Interaction with the Aaa+ ATPase Rava.
Sci.Rep., 6:24601-, 2016

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.

PubMed: 27080013
DOI: 10.1038/SREP24601

Experimental method

ELECTRON MICROSCOPY (5.5 Å)