Role of glycine 212 in the allosteric behavior of phosphofructokinase from Bacillus stearothermophilus

Improving the thermostability and modulating the inulin profile of inulosucrase through rational glycine-to-proline substitution

The flexibility of protein structure plays a crucial role in enzyme stability and catalysis. Among the amino acids, glycine is particularly important in conferring flexibility to proteins. In this study, the effects of flexible glycine residues in Lactobacillus reuteri 121 inulosucrase (LrInu) on stability and inulin profile were investigated through glycine-to-proline substitutions. Molecular dynamics (MD) simulations were employed to discover the flexible glycine residues, and eight glycine residues, including Gly217, Gly298, Gly330, Gly416, Gly450, Gly624, Gly627, Gly629, were selected for site-directed mutagenesis. The results demonstrated significant changes in both thermostability and inulin profiles of the variants. Particularly, the G624P and G627P variants showed reduced production of long-chain oligosaccharides compared to the WT. This can be ascribed to the increased rigidity of the active site, which is crucial for the induction-fit mechanism. Overall, this study provides valuable insights into the role of flexible glycine residues in the activity, stability, and inulin synthesis of LrInu.

Plant-like phosphofructokinase from Plasmodium falciparum belongs to a novel class of ATP-dependent enzymes

Malaria parasite-infected erythrocytes exhibit enhanced glucose utilisation and 6-phospho-1-fructokinase (PFK) is a key enzyme in glycolysis. Here we present the characterisation of PFK from the human malaria parasite Plasmodium falciparum. Of the two putative PFK genes on chromosome 9 (PfPFK9) and 11 (PfPFK11), only the PfPFK9 gene appeared to possess all the catalytic features appropriate for PFK activity. The deduced PfPFK proteins contain domains homologous to the plant-like pyrophosphate (PPi)-dependent PFK beta and alpha subunits, which are quite different from the human erythrocyte PFK protein. The PfPFK9 gene beta and alpha regions were cloned and expressed as His(6)- and GST-tagged proteins in Escherichia coli. Complementation of PFK-deficient E. coli and activity analysis of purified recombinant proteins confirmed that PfPFK9beta possessed catalytic activity. Monoclonal antibodies against the recombinant beta protein confirmed that the PfPFK9 protein has beta and alpha domains fused into a 200 kDa protein, as opposed to the independent subunits found in plants. Despite an overall structural similarity to plant PPi-PFKs, the recombinant protein and the parasite extract exhibited only ATP-dependent enzyme activity, and none with PPi. Unlike host PFK, the Plasmodium PFK was insensitive to fructose-2,6-bisphosphate (F-2,6-bP), phosphoenolpyruvate (PEP) and citrate. A comparison of the deduced PFK proteins from several protozoan PFK genome databases implicates a unique class of ATP-dependent PFK present amongst the apicomplexan protozoans.

The utility of molecular dynamics simulations for understanding site-directed mutagenesis of glycine residues in biotin carboxylase

Biotin carboxylase from Escherichia coli catalyzes the ATP-dependent carboxylation of biotin and is one component of the multienzyme complex acetyl-CoA carboxylase, which catalyzes the committed step in long-chain fatty acid synthesis. Comparison of the crystal structures of biotin carboxylase in the absence and presence of ATP showed a central B-domain closure when ATP was bound. Peptidic NH groups from two active site glycine residues (Gly165 and Gly166) that form hydrogen bonds to the phosphate oxygens of ATP were postulated to act as a "trigger" for movement of the B-domain. The function of these two glycine residues in the catalytic mechanism was studied by disruption of the hydrogen bonds using site-directed mutagenesis. Both single (G165V) and (G166V) and double mutants (G165V-G166V) were constructed. The mutations did not affect the maximal velocity of a partial reaction, the bicarbonate-dependent ATPase activity. This suggests that the peptidic NH groups of Gly165 and Gly166 are not triggers for domain movement. However, the K(m) values for ATP for each of the mutants was increased over 40-fold when compared with wild-type indicating the peptidic NH groups of Gly165 and Gly166 play a role in binding ATP. Consistent with ATP binding, the maximal velocity for the biotin-dependent ATPase activity (i.e. the complete reaction) was decreased over 100-fold suggesting the mutations have misaligned the reactants for optimal catalysis. Molecular dynamics studies confirm perturbation of the hydrogen bonds from the mutated residues to ATP, whereas the double mutant exhibits antagonistic effects such that hydrogen bonding from residues 165 and 166 to ATP is similar to that in the wild-type. Consistent with the site-directed mutagenesis results the molecular dynamics studies show that ATP is misaligned in the mutants.

Cloning, sequencing and developmental expression of phosphofructokinase from Dictyostelium discoideum

Phosphofructokinase (PFK) from Dictyostelium discoideum is a non-allosteric enzyme that lacks any of the characteristic regulatory mechanisms of PFK from other cells. We have determined the DNA sequence and analyzed the amino acid sequence of D. discoideum PFK, as an initial step toward understanding the peculiar properties of this enzyme. Three overlapping fragments, two of cDNA and one of genomic DNA, were isolated, which together could encode the complete sequence of D. discoideum PFK. The constructed full-length cDNA coded for a protein of 834 amino acids, with a calculated molecular mass of 92.4 kDa, which was similar to other eukaryotic and prokaryotic PFK. Alignments of the amino acid sequence with other isozymes revealed that many of the amino acid residues assigned to binding sites of substrates and allosteric effectors are conserved in this enzyme, but changes were also found that may contribute to the absence of allosteric mechanisms. A phylogenetic tree for the eukaryotic PFK family was constructed and showed that the N-terminal domain clustered with those of yeast subunits, whereas the C-terminal domain was more related to PFK from metazoa. Southern blotting indicated that D. discoideum PFK is encoded by a single gene. The enzyme is present throughout the life cycle of D. discoideum, with a gradual decrease of its expression during development.