Conserved residues of the Pro103-Arg115 loop are involved in triggering the allosteric response of the Escherichia coli ADP-glucose pyrophosphorylase

• Published in: Protein science 2015-05, Vol.24 (5), p.714-728
• Main Authors: Hill, Benjamin L, Wong, Jennifer, May, Brian M, Huerta, Fidel B, Manley, Tara E, Sullivan, Peter R F, Olsen, Kenneth W, Ballicora, Miguel A
• Format: Article
• Language: English
• Subjects: Active sites; Adenosine diphosphate; Adenosine triphosphate; Alanine; Allosteric properties; Allosteric Regulation - genetics; Amino Acid Sequence - genetics; Arginine - chemistry; ATP; Binding; Computer applications; Conserved Sequence - genetics; E coli; Escherichia coli; Escherichia coli - chemistry; Escherichia coli - enzymology; Escherichia coli - genetics; Fructose; Glucose; Glucose-1-Phosphate Adenylyltransferase - chemistry; Glucose-1-Phosphate Adenylyltransferase - genetics; Glucose-1-Phosphate Adenylyltransferase - metabolism; Glycogen; Glycogen - metabolism; Glycogens; Kinetics; Molecular dynamics; Molecular Dynamics Simulation; Mutagenesis; Mutagenesis, Site-Directed; Mutants; Mutation; Network analysis; Nucleotides; Proline - chemistry; Residues; Site-directed mutagenesis; Starch - metabolism
• ISSN: 0961-8368; 1469-896X
• DOI: 10.1002/pro.2644

The synthesis of glycogen in bacteria and starch in plants is allosterically controlled by the production of ADP-glucose by ADP-glucose pyrophosphorylase. Using computational studies, site-directed mutagenesis, and kinetic characterization, we found a critical region for transmitting the allosteric signal in the Escherichia coli ADP-glucose pyrophosphorylase. Molecular dynamics simulations and structural comparisons with other ADP-glucose pyrophosphorylases provided information to hypothesize that a Pro103-Arg115 loop is part of an activation path. It had strongly correlated movements with regions of the enzyme associated with regulation and ATP binding, and a network analysis showed that the optimal network pathways linking ATP and the activator binding Lys39 mainly involved residues of this loop. This hypothesis was biochemically tested by mutagenesis. We found that several alanine mutants of the Pro103-Arg115 loop had altered activation profiles for fructose-1,6-bisphosphate. Mutants P103A, Q106A, R107A, W113A, Y114A, and R115A had the most altered kinetic profiles, primarily characterized by a lack of response to fructose-1,6-bisphosphate. This loop is a distinct insertional element present only in allosterically regulated sugar nucleotide pyrophosphorylases that could have been acquired to build a triggering mechanism to link proto-allosteric and catalytic sites.