title: Putative binding mode of Escherichia coli exopolyphosphatase and polyphosphates based on a hybrid in silico/biochemical approach.
abstract: The exopolyphosphatase of Escherichia coli processively and completely hydrolyses long polyphosphate chains to ortho-phosphate. Genetic surveys, based on the analysis of single ppx(-) or ppk(-) mutants and on the double mutant, demonstrate a relationship between these genes and the survival capacity. The exopolyphosphatase belongs to the ASKHA protein superfamily, hence, its active site is well known; however, the knowledge of the way in which this enzyme binds polyP remains incomplete. Here we present different computational approaches, site-direct mutagenesis and kinetic data to understand the relationship between structure and function of exopolyphosphatase. We propose H(378) as a fundamental gatekeeper for the recognition of long chain polyphosphate.
authors.affiliation: Departamento de Biología Molecular, Facultad de Ciencias Exactas Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Argentina.
authors.forename: Cristhian
authors.initials: C
authors.lastname: Boetsch
authors.affiliation: Centro de Bioinformática y Biología Integrativa, Universidad Andres Bello, Santiago, Chile.
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Aguayo-Villegas
authors.affiliation: Centro de Bioinformática y Biología Integrativa, Universidad Andres Bello, Santiago, Chile.
authors.forename: Fernando D
authors.initials: FD
authors.lastname: Gonzalez-Nilo
authors.affiliation: Departamento de Biología Molecular, Facultad de Ciencias Exactas Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Argentina.
authors.forename: Á Teresita
authors.initials: ÁT
authors.lastname: Lisa
authors.affiliation: Departamento de Biología Molecular, Facultad de Ciencias Exactas Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Argentina. Electronic address: pbeassoni@exa.unrc.edu.ar.
authors.forename: Paola R
authors.initials: PR
authors.lastname: Beassoni
mesh_terms: D017766:Acid Anhydride Hydrolases / Q000737:chemistry*; D001426:Bacterial Proteins / Q000737:chemistry*; D001665:Binding Sites; D020134:Catalytic Domain; D004926:Escherichia coli / Q000378:metabolism*; D006859:Hydrogen / Q000737:chemistry; D007700:Kinetics; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D016297:Mutagenesis, Site-Directed; D009154:Mutation; D011122:Polyphosphates / Q000737:chemistry; D011485:Protein Binding; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D011122:Polyphosphates; D006859:Hydrogen; D017766:Acid Anhydride Hydrolases; C022563:endopolyphosphatase; C513394:Ppx protein, Escherichia coli; C020137:exopolyphosphatase
keywords: Binding; Exopolyphosphatase; Molecular dynamics; Polyphosphate; Processivity