title: Structural insights into the Escherichia coli lysine decarboxylases and molecular determinants of interaction with the AAA+ ATPase RavA.
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.
authors.affiliation: University Grenoble Alpes, IBS, F-38044 Grenoble, France.|CNRS, IBS, F-38044 Grenoble, France.|CEA, IBS, F-38044 Grenoble, France.
authors.forename: Eaazhisai
authors.initials: E
authors.lastname: Kandiah
authors.affiliation: University Grenoble Alpes, IBS, F-38044 Grenoble, France.|CNRS, IBS, F-38044 Grenoble, France.|CEA, IBS, F-38044 Grenoble, France.|INSERM, Biologie du Cancer et de l'Infection (UMR-S1036), F-38054 Grenoble, France.|Centre National de la Recherche Scientifique (CNRS), ERL5261 F-38054 Grenoble, France.|University Grenoble Alpes, BIG, Grenoble, F-38041, France.|CEA, BIG, Grenoble, France.
authors.forename: Diego
authors.initials: D
authors.lastname: Carriel
authors.affiliation: University Grenoble Alpes, BIG, Grenoble, F-38041, France.|CEA, BIG, Grenoble, France.|CNRS, LCMB, BIG, Grenoble, France.
authors.forename: Julien
authors.initials: J
authors.lastname: Perard
authors.affiliation: University Grenoble Alpes, IBS, F-38044 Grenoble, France.|CNRS, IBS, F-38044 Grenoble, France.|CEA, IBS, F-38044 Grenoble, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Malet
authors.affiliation: University Grenoble Alpes, IBS, F-38044 Grenoble, France.|CNRS, IBS, F-38044 Grenoble, France.|CEA, IBS, F-38044 Grenoble, France.
authors.forename: Maria
authors.initials: M
authors.lastname: Bacia
authors.affiliation: Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
authors.forename: Kaiyin
authors.initials: K
authors.lastname: Liu
authors.affiliation: Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
authors.forename: Sze W S
authors.initials: SW
authors.lastname: Chan
authors.affiliation: Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
authors.forename: Walid A
authors.initials: WA
authors.lastname: Houry
authors.affiliation: University Grenoble Alpes, BIG, Grenoble, F-38041, France.|CEA, BIG, Grenoble, France.|CNRS, LCMB, BIG, Grenoble, France.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Ollagnier de Choudens
authors.affiliation: INSERM, Biologie du Cancer et de l'Infection (UMR-S1036), F-38054 Grenoble, France.|Centre National de la Recherche Scientifique (CNRS), ERL5261 F-38054 Grenoble, France.|University Grenoble Alpes, BIG, Grenoble, F-38041, France.|CEA, BIG, Grenoble, France.
authors.forename: Sylvie
authors.initials: S
authors.lastname: Elsen
authors.affiliation: University Grenoble Alpes, IBS, F-38044 Grenoble, France.|CNRS, IBS, F-38044 Grenoble, France.|CEA, IBS, F-38044 Grenoble, France.
authors.forename: Irina
authors.initials: I
authors.lastname: Gutsche
mesh_terms: D000251:Adenosine Triphosphatases / Q000737:chemistry / Q000378:metabolism*; D000595:Amino Acid Sequence; D002262:Carboxy-Lyases / Q000737:chemistry / Q000378:metabolism*; D020134:Catalytic Domain; D020285:Cryoelectron Microscopy; D004789:Enzyme Activation; D004926:Escherichia coli / Q000201:enzymology*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism*; D006863:Hydrogen-Ion Concentration; D008958:Models, Molecular; D011485:Protein Binding
chemical_list: D029968:Escherichia coli Proteins; D000251:Adenosine Triphosphatases; C508688:RavA protein, E coli; D002262:Carboxy-Lyases; C021520:lysine decarboxylase