Direct Mg2+ Binding Activates Adenylate Kinase from Escherichia coli

We report evidence that adenylate kinase (AK) from Escherichia coli can be activated by the direct binding of a magnesium ion to the enzyme, in addition to ATP-complexed Mg²⁺. By systematically varying the concentrations of AMP, ATP, and magnesium in kinetic experiments, we found that the apparent substrate inhibition of AK, formerly attributed to AMP, was suppressed at low magnesium concentrations and enhanced at high magnesium concentrations. This previously unreported magnesium dependence can be accounted for by a modified random bi-bi model in which Mg²⁺ can bind to AK directly prior to AMP binding. A new kinetic model is proposed to replace the conventional random bi-bi mechanism with substrate inhibition and is able to describe the kinetic data over a physiologically relevant range of magnesium concentrations. According to this model, the magnesium-activated AK exhibits a 23- ± 3-fold increase in its forward reaction rate compared with the unactivated form. The findings imply that Mg²⁺ could be an important affecter in the energy signaling network in cells.Adenylate kinase (AK)² is a ∼24-kDa enzyme involved in cellular metabolism that catalyzes the reversible phosphoryl transfer reaction (1) as in Reaction 1. Mg2+⋅ATP+AMP⇌reverseforwardMg2+⋅ADP+ADPREACTION 1It is recognized to play an important role in cellular energetic signaling networks (2, 3). A deficiency in human AK function may lead to such illness as hemolytic anemia (4–8) and coronary artery disease (9); the latter is thought to be caused by a disruption of the AMP signaling network of AK (10). The ubiquity of AK makes it an ideal candidate for investigating evolutionary divergence and natural adaptation at a molecular level (11, 12). Indeed, extensive structure-function studies have been carried out for AK (reviewed in Ref. 13). Both structural and biophysical studies have suggested that large-amplitude conformational changes in AK are important for catalysis (14–19). More recently, the functional roles of conformational dynamics have been investigated using NMR (20–22), computer simulations (23–27), and single-molecule spectroscopy (28). Given the critical role of AK in regulating cellular energy networks and its use as a model system for understanding the functional roles of conformational changes in enzymes, it is imperative that the enzymatic mechanism of AK be thoroughly characterized and understood.The enzymatic reaction of adenylate kinase has been shown to follow a random bi-bi mechanism using isotope exchange experiments (29). Isoforms of adenylate kinases characterized from a wide range of species have a high degree of sequence, structure, and functional conservation. Although all AKs appear to follow the same random bi-bi mechanistic framework (15, 29–33), a detailed kinetic analysis reveals interesting variations among different isoforms. For example, one of the most puzzling discrepancies is the change in turnover rates with increasing AMP concentration between rabbit muscle AK and Escherichia coli AK. Although the reactivity of rabbit muscle AK is slightly inhibited at higher AMP concentrations (29, 32), E. coli AK exhibits its maximum turnover rate around 0.2 mm AMP followed by a steep drop, which plateaus at still higher AMP concentrations (33–35). This observation has been traditionally attributed to greater substrate inhibition by AMP in E. coli AK compared with the rabbit isoform; yet, the issue of whether the reaction involves competitive or non-competitive inhibition by AMP at the ATP binding site remains unresolved (15, 33, 35–37).Here, we report a comprehensive kinetic study of the forward reaction of AK, exploring concentrations of nucleotides and Mg²⁺ that are comparable to those inside E. coli cells, Mg²⁺] ∼ 1–2 mm (38) and ATP] up to 3 mm (39). We discovered a previously unreported phenomenon: an increase in the forward reaction rate of AK with increasing Mg²⁺ concentrations, where the stoichiometry of Mg²⁺ to the enzyme is greater than one. The new observation leads us to propose an Mg²⁺-activation mechanism augmenting the commonly accepted random bi-bi model for E. coli AK. Our model can fully explain AK’s observed kinetic behavior involving AMP, ATP, and Mg²⁺ as substrates, out-performing the previous model requiring AMP inhibition. The new Mg²⁺-activation model also explains the discrepancies in AMP inhibition behavior and currently available E. coli AK kinetic data. Given the central role of AK in energy regulation and our new experimental evidence, it is possible that Mg²⁺ and its regulation may participate in respiratory network through AK (40–42), an exciting future research direction.