Comparative studies of the catalytic mechanisms of two chorismatases: CH-fkbo and CH-Hyg5

Exploring the Substrate-Assisted Dehydration of Chorismate Catalyzed by Dehydratase MqnA from QM/MM Calculations: The Role of Pocket Residues and the Hydrolysis Mechanism of N17D Mutant

MqnA is the first enzyme on the futalosine pathway to menaquinone, which catalyzes the dehydration of chorismate to yield 3-enolpyruvyl-benzoate (3-EPB). MqnA is also the only chorismate dehydratase known so far. In this work, based on the recently determined crystal structures, we constructed the enzyme-substrate complex models and conducted quantum mechanics/molecular mechanics (QM/MM) calculations to elucidate the reaction details of MqnA and the critical roles of pocket residues. The calculation results confirm that the MqnA-catalyzed dehydration of chorismate follows the substrate-assisted E1cb mechanism, in which the enol carboxylate in the side chain of the substrate is responsible for deprotonating the C3 of chorismate. This proton transfer process is much slower than C4-OH departure. Calculations on different mutants reveal that S86 and N17 are important for anchoring the enol carboxylate of the substrate in a favorable conformation to extract the C3-proton. The strong H-bonds formed between the enol carboxylate of chorismate and S86/N17 play a key role in stabilizing the reaction intermediate. Consistent with the experimental observations, our calculations demonstrate that the MqnA N17D mutant also shows hydrolase activity and the typical enzyme-catalyzed hydrolysis mechanism is elucidated. The protonated D17 is responsible for saturating the methylene group of chorismate to start the hydrolysis reaction. The orientation of the carboxyl group of D17 is key in determining MqnA to be a dehydratase or hydrolase.

Catalytic Mechanism of Pyridoxal 5'-Phosphate-Dependent Aminodeoxychorismate Lyase: A Computational QM/MM Study

Aminodeoxychorismate lyase (ADCL) is a kind of pyridoxal-5'-phosphate (PLP)-dependent enzyme that catalyzes the conversion of 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate (PABA), which is a key step for the biosynthesis of folate. To illuminate the reaction details at the atomistic level, an enzyme-substrate reactant model has been constructed, and QM/MM calculations have been performed. Our calculation results reveal that the overall catalytic cycle contains 11 elementary steps, which can be described by three stages, including the transamination reaction of PLP, the release of pyruvate and aromatization of ADC, and the recovery to the initial aldimine. During the reaction, a series of intramolecular proton transfer are involved, which are the key for the C-N bond formation and cleavage as well as the aromatization of the ADC ring. In addition to forming the Schiff base with the pocket residue Lys251 and substrate in the internal aldimine and the external aldimine, respectively, the coenzyme PLP also plays a critical role in the intramolecular proton transfer by employing its hydroxyl oxygen anion and phosphate group. These findings may provide useful information for further understanding the catalytic mechanism of other PLP-dependent enzymes.

Chorismate- and isochorismate converting enzymes: versatile catalysts acting on an important metabolic node

Chorismate and isochorismate represent an important branching point connecting primary and secondary metabolism in bacteria, fungi, archaea and plants. Chorismate- and isochorismate-converting enzymes are potential targets for new bioactive compounds, as well as valuable biocatalysts for the in vivo and in vitro synthesis of fine chemicals. The diversity of the products of chorismate- and isochorismate-converting enzymes is reflected in the enzymatic three-dimensional structures and molecular mechanisms. Due to the high reactivity of chorismate and its derivatives, these enzymes have evolved to be accurately tailored to their respective reaction; at the same time, many of them exhibit a fascinating flexibility regarding side reactions and acceptance of alternative substrates. Here, we give an overview of the different (sub)families of chorismate- and isochorismate-converting enzymes, their molecular mechanisms, and three-dimensional structures. In addition, we highlight important results of mutagenetic approaches that generate a broader understanding of the influence of distinct active site residues for product formation and the conversion of one subfamily into another. Based on this, we discuss to what extent the recent advances in the field might influence the general mechanistic understanding of chorismate- and isochorismate-converting enzymes. Recent discoveries of new chorismate-derived products and pathways, as well as biocatalytic conversions of non-physiological substrates, highlight how this vast field is expected to continue developing in the future.

Engineering a Synthetic Pathway for Gentisate in Pseudomonas Chlororaphis P3

Pseudomonas chlororaphis P3 has been well-engineered as a platform organism for biologicals production due to enhanced shikimate pathway and excellent physiological and genetic characteristics. Gentisate displays high antiradical and antioxidant activities and is an important intermediate that can be used as a precursor for drugs. Herein, a plasmid-free biosynthetic pathway of gentisate was constructed by connecting the endogenous degradation pathway from 3-hydroxybenzoate in Pseudomonas for the first time. As a result, the production of gentisate reached 365 mg/L from 3-HBA via blocking gentisate conversion and enhancing the gentisate precursors supply through the overexpression of the rate-limiting step. With a close-up at the future perspectives, a series of bioactive compounds could be achieved by constructing synthetic pathways in conventional Pseudomonas to establish a cell factory.

Exploring the Mechanism of Catalysis with the Unified Reaction Valley Approach (URVA)—A Review

The unified reaction valley approach (URVA) differs from mainstream mechanistic studies, as it describes a chemical reaction via the reaction path and the surrounding reaction valley on the potential energy surface from the van der Waals region to the transition state and far out into the exit channel, where the products are located. The key feature of URVA is the focus on the curving of the reaction path. Moving along the reaction path, any electronic structure change of the reacting molecules is registered by a change in their normal vibrational modes and their coupling with the path, which recovers the curvature of the reaction path. This leads to a unique curvature profile for each chemical reaction with curvature minima reflecting minimal change and curvature maxima, the location of important chemical events such as bond breaking/forming, charge polarization and transfer, rehybridization, etc. A unique decomposition of the path curvature into internal coordinate components provides comprehensive insights into the origins of the chemical changes taking place. After presenting the theoretical background of URVA, we discuss its application to four diverse catalytic processes: (i) the Rh catalyzed methanol carbonylation—the Monsanto process; (ii) the Sharpless epoxidation of allylic alcohols—transition to heterogenous catalysis; (iii) Au(I) assisted [3,3]-sigmatropic rearrangement of allyl acetate; and (iv) the Bacillus subtilis chorismate mutase catalyzed Claisen rearrangement—and show how URVA leads to a new protocol for fine-tuning of existing catalysts and the design of new efficient and eco-friendly catalysts. At the end of this article the pURVA software is introduced. The overall goal of this article is to introduce to the chemical community a new protocol for fine-tuning existing catalytic reactions while aiding in the design of modern and environmentally friendly catalysts.

How Chorismatases Regulate Distinct Reaction Channels in a Single Conserved Active Pocket: Mechanistic Analysis with QM/MM (ONIOM) Investigations

The FkbO and Hyg5 subfamilies of chorismatases share the same active-site architectures, but perform distinct reaction mechanisms, that is, FkbO employs a hydrolysis reaction whereas Hyg5 proceeds through an intramolecular mechanism. Despite extensive research efforts, the detailed mechanism of the product selectivity in chorismatases need to be further unmasked. In this study, the effects of the A/G residue group (A244^FkbO /G240^Hyg5 ) and the V/Q residue group (V209^FkbO /Q201^Hyg5 ) on the catalytic mechanisms are investigated by employing molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations of the two wild-type models (FkbO/CHO and Hyg5/CHO; CHO=chorismate) and four mutants models (A244G-FkbO/CHO and G240A-Hyg5/CHO; V209Q-FkbO/CHO and Q201V-Hyg5/CHO). Our results showed that the A/G residue group mentioned by previous works would cause changes in the binding states of the substrate and the orientation of the catalytic glutamate, but only these changes affect the product selectivity in chorismatases limitedly. Interestingly, the distal V/Q residue group, which determines the internal water self-regulating ability at the active site, has significant impact on the selectivity of the catalytic mechanisms. The V/Q residue group is suggested to be an important factor to control the catalytic activities in chorismatases. The results are consistent with biochemical and structural experiments, providing novel insight into the mechanism of product selectivity in chorismatases.

Chorismatases – the family is growing

A newly discovered subfamily of chorismatases catalyses the same reaction as chorismate lyases (cleavage of chorismate to 4-hydroxybenzoate), but does not suffer from product inhibition.