Structure-guided insights into heterocyclic ring-cleavage catalysis of the non-heme Fe (II) dioxygenase NicX

Ligand-field-controlled catalysis: Enzymatic hydrolysis of N, N-dimethylformamide

N, N-dimethylformamide (DMF) is a widely used polar aprotic solvent as well as a troublesome toxic pollutant, removal of which has attracted increasing attention. Certain organisms encode N, N-dimethylformamidase (DMFase) to metabolize DMF. In the present work, molecular dynamics and quantum mechanics/molecular mechanics were adopted to explore the mechanism of DMF in DMFase. The calculations show that the structure that N atom of DMF coordinated with Fe3+ is the preferred initial conformation (N-pathway), compared with the structure in which O atom coordinated with Fe3+ (O-pathway). In the N-pathway, the coordination of N and Fe3+ disables the conjugation effect of the amide bond in the substrate and ligand field is highly flexible. By contrast, the conjugated structure of DMF is maintained well in the O-pathway, and ligand field is highly rigid with conserved electronic states during the water attack step. These two factors lead to the higher energy barrier in the O-pathway, while N-pathway is the preferred mechanism for DMF degradation. In addition, we displayed that Glu657 is involved in the catalytic process as a proton transfer mediator. Our work sheds light on the metabolic mechanism of DMF in DMFase, revealing the important role of ligand field in the catalytic process.

Three distinct strategies lead to programmable aliphatic C-H oxidation in bicyclomycin biosynthesis

The C-H bond functionalization has been widely used in chemical synthesis over the past decade. However, regio- and stereoselectivity still remain a significant challenge, especially for inert aliphatic C-H bonds. Here we report the mechanism of three Fe(II)/α-ketoglutarate-dependent dioxygenases in bicyclomycin synthesis, which depicts the natural tactic to sequentially hydroxylate specific C-H bonds of similar substrates (cyclodipeptides). Molecular basis by crystallographic studies, computational simulations, and site-directed mutagenesis reveals the exquisite arrangement of three enzymes using mutually orthogonal strategies to realize three different regio-selectivities. Moreover, this programmable selective hydroxylation can be extended to other cyclodipeptides. This evidence not only provides a naturally occurring showcase corresponding to the widely used methods in chemical catalysis but also expands the toolbox of biocatalysts to address the regioselective functionalization of C-H bonds.

Semirational Design of 4-Hydroxyphenylpyruvate Dioxygenase for Efficient and Regioselective Production of 3-Hydroxy-3-methylbutyrate

3-Hydroxy-3-methylbutyrate (HMB), an important dietary supplement, can enhance the quality of life for sedentary and elderly people. However, the catalytic efficiency of the pathway enzymes limited the biosynthesis of HMB. Here, we identified an efficient 4-hydroxyphenylpyruvate dioxygenase (4-HPPD) from Bacteroides barnesiae (BbHPPD) that converted l-Leucine (l-Leu) to HMB together with an efficient L-amino acid deaminase (L-AAD) in lab-preserved Proteus mirabilis (PmL-AADQ92A). The regioselective hydroxylation mechanism of the decarboxylated intermediate of 4-methyl-2-oxopentanoic acid (α-KIC) catalyzed by BbHPPD was elucidated for the first time. Structure-guided semirational design of BbHPPD generated a mutant M4. Compared to the wild type, the titer of mutant M4 increased by 254% when using α-KIC as a substrate. Finally, the engineered Escherichia coli 06 strain achieved the HMB titer of 11.6 g/L, a molar conversion of 65%, and a space-time yield of 0.64 g/(L·h) (the highest to date) in 18 h. This study lays the foundation for industrial-scale biosynthesis of HMB.

Expression, purification, kinetics, and crystallization of non-heme mononuclear iron enzymes: Biphenyl, Phthalate, and Terephthalate dioxygenases

Non-heme iron oxygenases constitute a versatile enzyme family that is crucial for incorporating molecular oxygen into diverse biomolecules. Despite their importance, only a limited number of these enzymes have been structurally and functionally characterized. Surprisingly, there remains a significant gap in understanding how these enzymes utilize a typical architecture and reaction mechanism to catalyze a wide range of reactions. Improving our understanding of these catalysts holds promise for advancing both fundamental enzymology and practical applications. This chapter aims to outline methods for heterologous expression, enzyme preparation, in vitro enzyme assays, and crystallization of biphenyl dioxygenase, phthalate dioxygenase and terephthalate dioxygenase. These enzymes catalyze the dihydroxylation of biphenyl, phthalate and terephthalate molecules, serving as a model for functional and structural analysis of other non-heme iron oxygenases.

Engineering a Carotenoid Cleavage Oxygenase for Coenzyme-Free Synthesis of Vanillin from Ferulic Acid

One-pot biosynthesis of vanillin from ferulic acid without providing energy and cofactors adds significant value to lignin waste streams. However, naturally evolved carotenoid cleavage oxygenase (CCO) with extreme catalytic conditions greatly limited the above pathway for vanillin bioproduction. Herein, CCO from Thermothelomyces thermophilus (TtCCO) was rationally engineered for achieving high catalytic activity under neutral pH conditions and was further utilized for constructing a one-pot synthesis system of vanillin with Bacillus pumilus ferulic acid decarboxylase. TtCCO with the K192N-V310G-A311T-R404N-D407F-N556A mutation (TtCCOM3) was gradually obtained using substrate access channel engineering, catalytic pocket engineering, and pocket charge engineering. Molecular dynamics simulations revealed that reducing the site-blocking effect in the substrate access channel, enhancing affinity for substrates in the catalytic pocket, and eliminating the pocket's alkaline charge contributed to the high catalytic activity of TtCCOM3 under neutral pH conditions. Finally, the one-pot synthesis of vanillin in our study could achieve a maximum rate of up to 6.89 ± 0.3 mM h-1. Therefore, our study paves the way for a one-pot biosynthetic process of transforming renewable lignin-related aromatics into valuable chemicals.

Characterization of the Pro101Gln mutation that enhances the catalytic performance of T. indicus NADH-dependent d-lactate dehydrogenase

NADH-dependent d-lactate dehydrogenases (d-LDH) are important for the industrial production of d-lactic acid. Here, we identify and characterize an improved d-lactate dehydrogenase mutant (d-LDH1) that contains the Pro101Gln mutation. The specific enzyme activities of d-LDH1 toward pyruvate and NADH are 21.8- and 11.0-fold greater compared to the wild-type enzyme. We determined the crystal structure of Apo-d-LDH1 at 2.65 Å resolution. Based on our structural analysis and docking studies, we explain the differences in activity with an altered binding conformation of NADH in d-LDH1. The role of the conserved residue Pro101 in d-LDH was further probed in site-directed mutagenesis experiments. We introduced d-LDH1 into Bacillus licheniformis yielding a d-lactic acid production of 145.9 g L-1 within 60 h at 50°C, which was three times higher than that of the wild-type enzyme. The discovery of d-LDH1 will pave the way for the efficient production of d-lactic acid by thermophilic bacteria.

Mechanistic Insights into Pyridine Ring Degradation Catalyzed by 2,5-Dihydroxypyridine Dioxygenase NicX

2,5-Dihydroxypyridine dioxygenase (NicX) from Pseudomonas putida KT2440 is a mononuclear non-heme iron oxygenase that can catalyze the oxidative pyridine ring cleavage. Recently, the reported crystal structure of NicX has lent support to an apical dioxygen catalytic mechanism, while the mechanistic details remain unclear. In this work, we constructed a Fe(II)-O2-substrate complex model and performed a series of combined quantum mechanics/molecular mechanics (QM/MM) calculations to illuminate the catalysis of NicX. Our results reveal that although the substrate does not directly coordinate with the central iron ion, there is an electron transfer from the substrate to the Fe-coordinated dioxygen, and the active form of the reactant complex can be described as DHP•+-Fe(II)-O2•-, which is different from other similar mononuclear non-heme iron. The NicX-catalyzed pyridine ring degradation contains three parts, including the attack of Fe(II)-superoxo on the activated pyridine ring, the dissociation of the Op-Od bond, and the ring-opening of the seven-membered-ring lactone. Owing to the radical characteristic of the pyridine ring, the first attack of Fe(II)-superoxo on the C6 of the pyridine ring was calculated to be quite easy. In the second step of the reaction, the dissociation of the Op-Od bond leads to the incorporation of the first oxygen atom into the substrate, which is the rate-limiting step of the overall reaction with an energy barrier of 18.0 kcal/mol. The resultant intermediate then undergoes an arrangement by the intramolecular attack of Od• on the carbonyl C5, forming the seven-membered-ring lactone. Finally, the Fe(III)-oxo attacks the carbonyl C5 of lactone, accompanied by the ring-opening to generate N-formylmaleamic acid. His105 can promote reactivity by donating a proton to Fe(III)-oxo, but it is not a necessary residue. In addition to the ligated residues of iron, other pocket residues such as Glu177, His189, and His105 mainly play roles in anchoring the substrate.