Dihydrofolate reductase-like protein inactivates hemiaminal pharmacophore for self-resistance in safracin biosynthesis

Dihydrofolate reductase (DHFR), a housekeeping enzyme in primary metabolism, has been extensively studied as a model of acid-base catalysis and a clinic drug target. Herein, we investigated the enzymology of a DHFR-like protein SacH in safracin (SAC) biosynthesis, which reductively inactivates hemiaminal pharmacophore-containing biosynthetic intermediates and antibiotics for self-resistance. Furthermore, based on the crystal structure of SacH-NADPH-SAC-A ternary complexes and mutagenesis, we proposed a catalytic mechanism that is distinct from the previously characterized short-chain dehydrogenases/reductases-mediated inactivation of hemiaminal pharmacophore. These findings expand the functions of DHFR family proteins, reveal that the common reaction can be catalyzed by distinct family of enzymes, and imply the possibility for the discovery of novel antibiotics with hemiaminal pharmacophore.

Insights into the biosynthesis of septacidin l-heptosamine moiety unveils a VOC family sugar epimerase

l-Heptopyranoses are important components of bacterial polysaccharides and biological active secondary metabolites like septacidin (SEP), which represents a group of nucleoside antibiotics with antitumor, antifungal, and pain-relief activities. However, little is known about the formation mechanisms of those l-heptose moieties. In this study, we deciphered the biosynthetic pathway of the l,l-gluco-heptosamine moiety in SEPs by functional characterizing four genes and proposed that SepI initiates the process by oxidizing the 4'-hydroxyl of l-glycero-α-d-manno-heptose moiety of SEP-328 ( 2) to a keto group. Subsequently, SepJ (C5 epimerase) and SepA (C3 epimerase) shape the 4'-keto-l-heptopyranose moiety by sequential epimerization reactions. At the last step, an aminotransferase SepG installs the 4'-amino group of the l,l-gluco-heptosamine moiety to generate SEP-327 ( 3). An interesting phenomenon is that the SEP intermediates with 4'-keto-l-heptopyranose moieties exist as special bicyclic sugars with hemiacetal-hemiketal structures. Notably, l-pyranose is usually converted from d-pyranose by bifunctional C3/C5 epimerase. SepA is an unprecedented monofunctional l-pyranose C3 epimerase. Further in silico and experimental studies revealed that it represents an overlooked metal dependent-sugar epimerase family bearing vicinal oxygen chelate (VOC) architecture.

Advances in the structure and function of chitosanase / 生物工程学报

Chitosanases represent a class of glycoside hydrolases with high catalytic activity on chitosan but nearly no activity on chitin. Chitosanases can convert high molecular weight chitosan into functional chitooligosaccharides with low molecular weight. In recent years, remarkable progress has been made in the research on chitosanases. This review summarizes and discusses its biochemical properties, crystal structures, catalytic mechanisms, and protein engineering, highlighting the preparation of pure chitooligosaccharides by enzymatic hydrolysis. This review may advance the understandings on the mechanism of chitosanases and promote its industrial applications.

Advances in poly(ethylene terephthalate) hydrolases / 生物工程学报

Plastics have brought invaluable convenience to human life since it was firstly synthesized in the last century. However, the stable polymer structure of plastics led to the continuous accumulation of plastic wastes, which poses serious threats to the ecological environment and human health. Poly(ethylene terephthalate) (PET) is the most widely produced polyester plastics. Recent researches on PET hydrolases have shown great potential of enzymatic degradation and recycling of plastics. Meanwhile, the biodegradation pathway of PET has become a reference model for the biodegradation of other plastics. This review summarizes the sources of PET hydrolases and their degradation capacity, degradation mechanism of PET by the most representative PET hydrolase-IsPETase, and recently reported highly efficient degrading enzymes through enzyme engineering. The advances of PET hydrolases may facilitate the research on the degradation mechanism of PET and further exploration and engineering of efficient PET degradation enzymes.

Oxidosqualene cyclases in triterpenoids biosynthesis: a review / 生物工程学报

Triterpenoids are one of the most diverse compounds in plant metabolites, and they have a wide variety of physiological activities and are of important economic value. Oxidosqualene cyclases catalyze the cyclization of 2, 3-oxidosqualene to generate different types of sterols and plant triterpenoids, which is of great significance to the structural diversity of natural products. However, the mechanism of the diversified cyclization of 2, 3-oxidosqualene catalyzed by oxidosqualene cyclases remains unclear. This review summarized the research progress of oxidosqualene cyclases from the aspects of catalytic function, molecular evolutionary relationship between genes and proteins, protein structure, molecular simulation and molecular calculations, which may provide a reference for protein engineering and metabolic engineering of triterpene cyclase.

Catalytic mechanism, molecular engineering and applications of threonine aldolases / 生物工程学报

Threonine aldolases catalyze the aldol condensation of aldehydes with glycine to furnish β-hydroxy-α-amino acid with two stereogenic centers in a single reaction. This is one of the most promising green methods for the synthesis of optically pure β-hydroxy-α-amino acid with high atomic economy and less negative environmental impact. Several threonine aldolases from different origins have been identified and characterized. The insufficient -carbon stereoselectivity and the challenges of balancing kinetic versus thermodynamic control to achieve the optimal optical purity and yield hampered the application of threonine aldolases. This review summarizes the recent advances in discovery, catalytic mechanism, high-throughput screening, molecular engineering and applications of threonine aldolases, with the aim to provide some insights for further research in this field.

Advances of structure, function, and catalytic mechanism of methyl-coenzyme M reductase / 生物工程学报

Methanogens are unique microorganisms for methane production and the main contributor of the biogenic methane in atmosphere. Methyl-coenzyme M reductase (Mcr) catalyzes the last step of methane production in methanogenesis and the first step of methane activation in anaerobic oxidation of methane. The genes encoding this enzyme are highly conserved and are widely used as a marker in the identification and phylogenetic study of archaea. There has been a longstanding interest in its unique cofactor F430 and the underpinning mechanisms of enzymatic cleavage of alkane C-H bond. The recent breakthroughs of high-resolution protein and catalytic-transition-state structures further advanced the structure-function study of Mcr. In particular, the recent discovery of methyl-coenzyme M reductase-like (Mcr-like) enzymes that activates the anaerobic degradation of non-methane alkanes has attracted much interest in the molecular mechanisms of C-H activation without oxygen. This review summarized the advances on function-structure-mechanism study of Mcr/Mcr-like enzymes. Additionally, future directions in anaerobic oxidation of alkanes and greenhouse-gas control using Mcr/Mcr-like enzymes were proposed.

Enzymatic properties of α-L-rhamnosidase and the factors affecting its activity: a review / 生物工程学报

α-L-rhamnosidase is a very important industrial enzyme that is widely distributed in a variety of organisms. α-L-rhamnosidase of different origins show functional diversity. For example, the optimal pH of α-L-rhamnosidase from bacteria is close to neutral or alkaline, while the optimal pH of α-L-rhamnosidase from fungi is in the acidic range. Furthermore, the enzymatic properties of α-L-rhamnosidases of different origins differ in terms of the optimal temperature, the thermal stability, and the substrate specificity, which determine the different applications of these enzymes. In this connection, it is crucial to elucidate the similarities and differences in the catalytic mechanism and substrate specificity of α-L-rhamnosidase of different origins through analyzing its enzymatic properties. Moreover, it is important to explore and understand the effects of aglycon and metal cations on enzyme activity and the competitive inhibition of L-rhamnose and glucose on enzymes. These knowledge can help discover α-L-rhamnosidase of industrial significance and promote its industrial application.

Function, structure and catalytic mechanism of sucrose phosphate synthase: a review / 生物工程学报

Sucrose is a natural product occurs widely in nature. In living organisms such as plants, sucrose phosphate synthase (SPS) is the key rate-limiting enzyme for sucrose synthesis. SPS catalyzes the synthesis of sucrose-6-phosphate, which is further hydrolyzed by sucrose phosphatase to form sucrose. Researches on SPS in recent decades have been focused on the determination of enzymatic activity of SPS, the identification of the inhibitors and activators of SPS, the covalent modification of SPS, the carbohydrate distribution in plants regulated by SPS, the mechanism for promoting plant growth by SPS, the sweetness of fruit controlled by SPS, and many others. A systematic review of these aspects as well as the crystal structure and catalytic mechanism of SPS are presented.

Recent progress in 2-haloacid dehalogenases / 生物工程学报

2-Haloacid dehalogenases (EC 3.8.1.X) catalyze the hydrolytic dehalogenation of 2-haloacids, releasing halogen ions and producing corresponding 2-hydroxyacids. The enzymes not only degrade xenobiotic halogenated pollutants, but also show wide substrate profile and astonishing efficiency for enantiomer resolution, making them valuable in environmental protection and the green synthesis of optically pure chiral compounds. A variety of 2-haloacid dehalogenases have been biochemically characterized so far. Further studies have been made in protein crystal structures and catalytic mechanisms. Here, we review the recent progresses of 2-haloacid dehalogenases in their source, protein structures, reaction mechanisms, catalytic properties and application. We also suggest further research directions for 2-haloacid dehalogenase.

Research progress in structure and function of pectin methylesterase / 生物工程学报

Pectin methylesterase (PME) is an important pectinase that hydrolyzes methyl esters in pectin to release methanol and reduce the degree of methylation of pectin. At present, it has broad application prospects in food processing, tea beverage, paper making and other production processes. With the in-depth study of PME, the crystal structures with different sources have been reported. Analysis of these resolved crystal structures reveals that PME belongs to the right-hand parallel β-helix structure, and its catalytic residues are two aspartic acids and a glutamine, which play the role of general acid-base, nucleophile and stable intermediate, in the catalytic process. At the same time, the substrate specificity is analyzed to understand the recognition mechanism of the substrate and active sites. This paper systematically reviews these related aspects.

Advances in hydroxylation of hydrophobic amino acid / 生物工程学报

Hydroxy amino acids, constituents of chiral pharmaceutical intermediates or precursors, have a variety of unique functions in the research fields of biotechnology and molecular biology, i.e. antifungal, antibacterial, antiviral and anticancer properties. Biosynthesis of hydroxy amino acids is preferred because of its high specificity and selectivity. The hydroxylation of hydrophobic amino acids is catalyzed by hydroxylase, which belongs to the mononuclear non-heme Fe(Ⅱ)/α-ketoglutarate-dependent dioxygenases (Fe/αKGDs). Fe/αKGDs utilize an (Fe(Ⅳ)=O) intermediate to activate diverse oxidative transformations with key biological roles in the process of catalytic reaction. Here, we review the physiological properties and synthesis of hydroxy amino acids, especially for the 4-HIL and hydroxyproline. The catalytic mechanism of Fe/αKGDs is elucidated, and the applications of hydroxy amino acids in industrial engineering are also discussed.

Advances in isoprene synthase research / 生物工程学报

Isoprene emission can lead to significant consequence for atmospheric chemistry. In addition, isoprene is a chemical compound for various industrial applications. In the organisms, isoprene is produced by isoprene synthase that eliminates the pyrophosphate from the dimethylallyl diphosphate. As a key enzyme of isoprene formation, isoprene synthase plays an important role in the process of natural emission and artificial synthesis of isoprene. So far, isoprene synthase has been found in various plants. Isoprene synthases from different sources are of conservative structural and similar biochemical properties. In this review, the biochemical and structural characteristics of isoprene synthases from different sources were compared, the catalytic mechanism of isoprene synthase was discussed, and the perspective application of the enzyme in bioengineering was proposed.

Invertebrate lysozymes: Diversity and distribution, molecular mechanism and in vivo function.

Lysozymes are antibacterial enzymes widely distributed among organisms. Within the animal kingdom, mainly three major lysozyme types occur. Chicken (c)-type lysozyme and goose (g)-type lysozyme are predominantly, but not exclusively, found in vertebrate animals, while the invertebrate (i)-type lysozyme is typical for invertebrate organisms, and hence its name. Since their discovery in 1975, numerous research articles report on the identification of i-type lysozymes in a variety of invertebrate phyla. This review describes the current knowledge on i-type lysozymes, outlining their distribution, molecular mechanism and in vivo function taking the representative from Venerupis philippinarum (formerly Tapes japonica) (Vp-ilys) as a model. In addition, invertebrate g-type and ch-type (chalaropsis) lysozymes, which have been described in molluscs and nematodes, respectively, are also briefly discussed.

The Progress on Electron Transport Pathway and Catalytic Mechanism of Copper-containing Nitrite Reductase / 微生物学通报

Nitrite reductases (NiRs) are the key enzymes in the denitrification pathway of the nitrogen cycle. By the catalysis of NiRs, the nitrites are turned into nitric oxides and the nitrogen pollution is decreased in water body. NiRs are divided into two different types based on their prosthetic groups, namely heme-containing nitrite reductases (cd1-NiRs) and Copper-containing nitrite reductases (Cu-NiRs). As all know, Cu-NiRs have trimeric structures, in their each monomer, there exist two types of Cu centers that play pivotal roles as the components of electron transfer pathway in the process of catalysis. Furthermore, some residues alteration of Cu-NiRs would contribute to the catalytic reaction. In this review, the latest progresses about the construction features, the process of electron transfer and catalytic mechanism of Cu-NiRs were discussed.

ENZYMOLOGY OF MICROBIAL DEGRADATION OF ORGANOPHOSPHATE CHEMICALS / 微生物学通报

Organophosphate chemicals are widely used as agricultural pesticides and war reagents, their biodegradation is emphasized on the theoretical and practical aspects. Organophosphate hydrolases play important roles in the biodegradation of organophosphate chemicals. Great advancement was achieved recently in the determination of crystal structure and catalytic mechanisms of the hydrolase. This paper reviewed the research progresses in the enzymology, protein structure, catalytic mechanisms and application of the organophosphate hydrolase, and predicted the future research in this field.

Quantum-Chemical Study of Catalytic Mechanism of Serine Proteases (III) / 昆明医科大学学报

In this paper, the model system of proton transfer with the water molecule as an intermediate acceptor of Ser-195 was suggested and analysed by the CNDO/2 method. The acylation activation barrier of this system was shown to restrict the stage of synchronous transfer of the Ser-195 alcoholic proton and the water molecule proton hydrogen bound to His-57 N~(?_2)-atom to the water molecule oxygen atom and the N~(?_2)-atom, respectively. The substrate protonation in the case of the model system with the water molecule as the in ermediate acceptor was demonstrated to begin before the completion of the tetrahedral inermediate substance, only the protonated form of the tetrahedal intermediate being shown. A lypothesis of considering the role of this water molecule as a nuclephilic reagent in the leacylation stage is presented.

A Quantum Chemical Study on The Catalytic Mechanism of Serine Proteases(Ⅰ) / 昆明医科大学学报

Using the semi-empirical MNDO/H method several systems simulating the reaction of tetrahetral intermediate formation in the active site of serine proteases have been studied. The role played by elements of the《catalytic triad》in increasing the reactivity of serine hydroxyl has been discussed.The formation of a strong hydrogen bond between His and Asp was shown to be important in lowering the activation energy in the reaction of Ser with substrate.The change in position of the proten located between Ser and His and between His and Asp was analysed.The influence of substrate distortion on the energy of intermediate formation has been considered.

Ouantum Chemical Study on Catalytic Mechanism of Serine Proteases / 昆明医科大学学报

Using the semiempirical MNDO method,several systems simulating the active site of serine proteases have been studied.The stabilization energy was found depending strongly on the nucleophilicity of the attacking group.the decrease of the activation energy has been esti- mated at 9 kca/mole.It was shown that the substrate distortion did not vary with the form- ing of hydrogen bonds.