title: Structural basis for Rab1 de-AMPylation by the Legionella pneumophila effector SidD.
abstract: The covalent attachment of adenosine monophosphate (AMP) to proteins, a process called AMPylation (adenylylation), has recently emerged as a novel theme in microbial pathogenesis. Although several AMPylating enzymes have been characterized, the only known virulence protein with de-AMPylation activity is SidD from the human pathogen Legionella pneumophila. SidD de-AMPylates mammalian Rab1, a small GTPase involved in secretory vesicle transport, thereby targeting the host protein for inactivation. The molecular mechanisms underlying Rab1 recognition and de-AMPylation by SidD are unclear. Here, we report the crystal structure of the catalytic region of SidD at 1.6 Å resolution. The structure reveals a phosphatase-like fold with additional structural elements not present in generic PP2C-type phosphatases. The catalytic pocket contains a binuclear metal-binding site characteristic of hydrolytic metalloenzymes, with strong dependency on magnesium ions. Subsequent docking and molecular dynamics simulations between SidD and Rab1 revealed the interface contacts and the energetic contribution of key residues to the interaction. In conjunction with an extensive structure-based mutational analysis, we provide in vivo and in vitro evidence for a remarkable adaptation of SidD to its host cell target Rab1 which explains how this effector confers specificity to the reaction it catalyses.
authors.affiliation: Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America.
authors.forename: Yang
authors.initials: Y
authors.lastname: Chen
authors.forename: Igor
authors.initials: I
authors.lastname: Tascón
authors.forename: M Ramona
authors.initials: MR
authors.lastname: Neunuebel
authors.forename: Chiara
authors.initials: C
authors.lastname: Pallara
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Brady
authors.forename: Lisa N
authors.initials: LN
authors.lastname: Kinch
authors.forename: Juan
authors.initials: J
authors.lastname: Fernández-Recio
authors.forename: Adriana L
authors.initials: AL
authors.lastname: Rojas
authors.forename: Matthias P
authors.initials: MP
authors.lastname: Machner
authors.forename: Aitor
authors.initials: A
authors.lastname: Hierro
mesh_terms: D000249:Adenosine Monophosphate / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D018360:Crystallography, X-Ray; D006801:Humans; D016952:Legionella pneumophila / Q000201:enzymology* / Q000235:genetics; D062105:Molecular Docking Simulation; D010749:Phosphoprotein Phosphatases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D000071636:Protein Phosphatase 2C; D020836:Protein Structure, Quaternary; D013329:Structure-Activity Relationship; D020761:rab1 GTP-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; C559758:SidD protein, Legionella pneumophila; D000249:Adenosine Monophosphate; D010749:Phosphoprotein Phosphatases; D000071636:Protein Phosphatase 2C; D020761:rab1 GTP-Binding Proteins