Opportunistic complexes of E. coli L-asparaginases with citrate anions

Towards a dependable data set of structures for L-asparaginase research

The Protein Data Bank (PDB) includes a carefully curated treasury of experimentally derived structural data on biological macromolecules and their various complexes. Such information is fundamental for a multitude of projects that involve large-scale data mining and/or detailed evaluation of individual structures of importance to chemistry, biology and, most of all, to medicine, where it provides the foundation for structure-based drug discovery. However, despite extensive validation mechanisms, it is almost inevitable that among the ∼215 000 entries there will occasionally be suboptimal or incorrect structure models. It is thus vital to apply careful verification procedures to those segments of the PDB that are of direct medicinal interest. Here, such an analysis was carried out for crystallographic models of L-asparaginases, enzymes that include approved drugs for the treatment of certain types of leukemia. The focus was on the adherence of the atomic coordinates to the rules of stereochemistry and their agreement with the experimental electron-density maps. Whereas the current clinical application of L-asparaginases is limited to two bacterial proteins and their chemical modifications, the field of investigations of such enzymes has expanded tremendously in recent years with the discovery of three entirely different structural classes and with numerous reports, not always quite reliable, of the anticancer properties of L-asparaginases of different origins.

The E. coli L-asparaginase V27T mutant: structural and functional characterization and comparison with theoretical predictions

Bacterial L-asparaginases have been used for over 40 years as anticancer drugs. Ardalan et al. (Medical Hypotheses 112, 7-17, 2018) proposed that the V27T mutant of Escherichia coli type II L-asparaginase, EcAII(V27T), should display altered biophysical and catalytic properties compared to the wild-type enzyme, EcAII(wt), rendering it more favourable as a pharmaceutical. They postulated that EcAII(V27T) would exhibit reduced glutaminolytic activity and be more stable compared to EcAII(wt). Their postulates, however, were purely theoretical. Here, we characterized experimentally selected properties of EcAII(V27T). We found asparaginolytic activity of this mutant unchanged, whereas its glutaminolytic activity was fourfold lower compared with EcAII(wt). We did not observe significant differences in stabilities of EcAII(wt) and EcAII(V27T). Crystal structures of the complexes with L-Asp and L-Glu showed considerable differences in binding modes of both substrates.

Biochemical characterization and detection of antitumor activity of l-asparaginase from thermophilic Geobacillus kaustophilus DSM 7263T

L-asparaginases, which are oncolytic enzymes, have been used in clinical applications for many years. These enzymes are also important in food processing industry due to their potential in acrylamide-mitigation. In this study, the gene for l-asparaginase (GkASN) from a thermophilic bacterium, Geobacillus kaustophilus, was cloned and expressed in E. coli Rosetta™2 (DE3) cells utilizing the pET-22b(+) vector. The 6xHis-tag attached enzyme was purified and analyzed both biochemically and structurally. The molecular mass of GkASN was determined as ∼36 kDa by SDS-PAGE, Western Blotting, and MALDI-TOF MS analyses. Optimum temperature and pH for the enzyme was determined as 55 °C and 8.5, respectively. The enzyme retained 89% of its thermal stability at 37 °C and 75% at 55 °C after 6 h of incubation. The enzyme activity was inhibited in the presence of Cu²⁺, Fe³⁺, Zn²⁺, and EDTA, while the activity was enhanced in the presence of Mn²⁺, Mg²⁺, and thiol group protective agents such as 2-mercaptoethanol and DTT. The structural modeling analysis demonstrated that the catalytic residues of the enzyme were partially similar to other asparaginases. The therapeutic potential of GkASN was tested on hepatocellular carcinoma cells, a solid cancer type with high mortality rate and rapidly increasing incidence in recent years. We showed that the GkASN-induced asparagine deficiency effectively reduced the metastatic synergy in HCC SNU387 cells on a xCELLigence system with differentiated epithelial Hep3B and poorly differentiated metastatic mesenchymal HCC SNU387 cells.

Structural and biophysical aspects of l-asparaginases: a growing family with amazing diversity

l-Asparaginases have remained an intriguing research topic since their discovery ∼120 years ago, especially after their introduction in the 1960s as very efficient antileukemic drugs. In addition to bacterial asparaginases, which are still used to treat childhood leukemia, enzymes of plant and mammalian origin are now also known. They have all been structurally characterized by crystallography, in some cases at outstanding resolution. The structural data have also shed light on the mechanistic details of these deceptively simple enzymes. Yet, despite all this progress, no better therapeutic agents have been found to beat bacterial asparaginases. However, a new option might arise with the discovery of yet another type of asparaginase, those from symbiotic nitrogen-fixing Rhizobia, and with progress in the protein engineering of enzymes with desired properties. This review surveys the field of structural biology of l-asparaginases, focusing on the mechanistic aspects of the well established types and speculating about the potential of the new members of this amazingly diversified family.

Structural and biochemical properties of L-asparaginase

l-Asparaginase (a hydrolase converting l-asparagine to l-aspartic acid) was the first enzyme to be used in clinical practice as an anticancer agent after its approval in 1978 as a component of a treatment protocol for childhood acute lymphoblastic leukemia. Structural and biochemical properties of l-asparaginases have been extensively investigated during the last half-century, providing an accurate structural description of the enzyme isolated from a variety of sources, as well as clarifying the mechanism of its activity. This review provides a critical assessment of the current state of knowledge of primarily structural, but also selected biochemical properties of 'bacterial-type' l-asparaginases from different organisms. The most extensively studied members of this enzyme family are l-asparaginases highly homologous to one of the two enzymes from Escherichia coli (usually referred to as EcAI and EcAII). Members of this enzyme family, although often called bacterial-type l-asparaginases, have been also identified in such divergent organisms as archaea or eukarya. Over 100 structural models of l-asparaginases have been deposited in the Protein Data Bank during the last 30 years. One of the prime achievements of structure-centered approaches was the elucidation of the details of the mechanism of enzymatic action of this unique hydrolase that utilizes a side chain of threonine as the primary nucleophile. The molecular basis of other important properties of these enzymes, such as their substrate specificity, is still being evaluated. Results of structural and mechanistic studies of l-asparaginases are being utilized in efforts to improve the clinical properties of this important anticancer drug.

Structural insights into the function of the catalytically active human Taspase1

Taspase1 is an Ntn-hydrolase overexpressed in primary human cancers, coordinating cancer cell proliferation, invasion, and metastasis. Loss of Taspase1 activity disrupts proliferation of human cancer cells in vitro and in mouse models of glioblastoma. Taspase1 is synthesized as an inactive proenzyme, becoming active upon intramolecular cleavage. The activation process changes the conformation of a long fragment at the C-terminus of the α subunit, for which no full-length structural information exists and whose function is poorly understood. We present a cloning strategy to generate a circularly permuted form of Taspase1 to determine the crystallographic structure of active Taspase1. We discovered that this region forms a long helix and is indispensable for the catalytic activity of Taspase1. Our study highlights the importance of this element for the enzymatic activity of Ntn-hydrolases, suggesting that it could be a potential target for the design of inhibitors with potential to be developed into anticancer therapeutics.

Structures of l-asparaginase from Bacillus licheniformis Reveal an Essential Residue for its Substrate Stereoselectivity

l-Asparaginase, which catalyzes the hydrolysis of l-asparagine, is an important enzyme in both the clinical and food industry. Exploration of efficient l-asparaginase with high substrate specificity, especially high chiral selectivity, is essential for extending its use. Herein, various crystal structures of type I l-asparaginase from Bacillus licheniformis (BlAsnase) have been resolved, and we found that there are two additional tyrosines in BlAsnase, contributing to the binding and catalysis of d-asparagine. Strikingly, the substitution of Tyr278 with methionine impaired the interaction with d-asparagine via water molecules due to the small hydrophobic side chain of methionine, which forced the ligand to the deep side of the active site toward the catalytic residues and thus resulted in the loss of hydrolyzing function. Our investigation of the substrate recognition mechanism of BlAsnase is significant for both a better understanding of l-asparaginase and its rational design to achieve high specificity for clinical and industrial applications.

Generalized enzymatic mechanism of catalysis by tetrameric L-asparaginases from mesophilic bacteria

The mechanism of catalysis by the L-glutaminase-asparaginase from Pseudomonas 7A (PGA) was investigated using structural, mass spectrometry, and kinetic data. We had previously proposed mechanism of hydrolysis of L-Asn by the type II L-asparaginase from E. coli (EcAII), but that work was limited to just one enzyme. Based on results presented in this report, we postulate that all homotetrameric L-asparaginases from mesophilic bacteria utilize a common ping-pong mechanism of catalysis consisting of two subsequent nucleophilic substitutions. Several new structures of non-covalent complexes of PGA with different substrates, as well as structures of covalent acyl-enzyme intermediates of PGA with canonical substrates (L-Asp and L-Glu) and an opportunistic ligand, a citrate anion, were determined. The results of kinetic experiments monitored by high-resolution LC/MS, when combined with new structural data, clearly show that the reaction catalyzed by L-glutaminase-asparaginases proceeds through formation of a covalent intermediate, as observed previously for EcAII. Additionally, by showing that the same mechanism applies to L-Asn and L-Gln, we postulate that it is common for all these structurally related enzymes.

Mechanism of Catalysis by l-Asparaginase

Two bacterial type II l-asparaginases, from Escherichia coli and Dickeya chrysanthemi, have played a critical role for more than 40 years as therapeutic agents against juvenile leukemias and lymphomas. Despite a long history of successful pharmacological applications and the apparent simplicity of the catalytic reaction, controversies still exist regarding major steps of the mechanism. In this report, we provide a detailed description of the reaction catalyzed by E. coli type II l-asparaginase (EcAII). Our model was developed on the basis of new structural and biochemical experiments combined with previously published data. The proposed mechanism is supported by quantum chemistry calculations based on density functional theory. We provide strong evidence that EcAII catalyzes the reaction according to the double-displacement (ping-pong) mechanism, with formation of a covalent intermediate. Several steps of catalysis by EcAII are unique when compared to reactions catalyzed by other known hydrolytic enzymes. Here, the reaction is initiated by a weak nucleophile, threonine, without direct assistance of a general base, although a distant general base is identified. Furthermore, tetrahedral intermediates formed during the catalytic process are stabilized by a never previously described motif. Although the scheme of the catalytic mechanism was developed only on the basis of data obtained from EcAII and its variants, this novel mechanism of enzymatic hydrolysis could potentially apply to most (and possibly all) l-asparaginases.

A shared vision for macromolecular crystallography over the next five years

Macromolecular crystallography (MX) is the dominant means of determining the three-dimensional structures of biological macromolecules, but the method has reached a critical juncture. New diffraction-limited storage rings and upgrades to the existing sources will provide beamlines with higher flux and brilliance, and even the largest detectors can collect at rates of several hundred hertz. Electron cryomicroscopy is successfully competing for structural biologists' most exciting projects. As a result, formerly scarce beam time is becoming increasingly abundant, and beamlines must innovate to attract users and ensure continued funding. Here, we will show how data collection has changed over the preceding five years and how alternative methods have emerged. We then explore how MX at synchrotrons might develop over the next five years. We predict that, despite the continued dominance of rotation crystallography, applications previously considered niche or experimental, such as serial crystallography, pink-beam crystallography, and crystallography at energies above 25 keV and below 5 keV, will rise in prominence as beamlines specialize to offer users the best value. Most of these emerging methods will require new hardware and software. With these advances, MX will more efficiently provide the high-resolution structures needed for drug development. MX will also be able to address a broader range of questions than before and contribute to a deeper understanding of biological processes in the context of integrative structural biology.