Structural basis for substrate recognition in the Phytolacca americana glycosyltransferase PaGT3

Functional characterization of a maize UDP-glucosyltransferase involved in the biosynthesis of flavonoid 7-O-glucosides and di-O-glucosides

Flavonoids are glycosylated in the final steps of their synthesis by UDP-dependent glycosyltransferase enzymes. We present the functional characterization of the first maize flavonoid O-glucosyltransferase enzyme from family 85, which exhibits properties not previously described. ZmUGT85W2 catalyzes the O-glucosylation of flavonols, flavones and flavanones, to form primarily 7-O-glucosides, but also flavonol O-glucoside positional isomers, flavones and flavonol di-O-glucosides. ZmUGT85W2 exhibited a differential kinetic behavior depending on the flavonoid acceptor, showing hyperbolic dependence for flavonols and sigmoidal response for flavanones and flavones. Structural and molecular docking analyses predicted conserved residues interacting with the sugar donor, with close contact with the 7-hydroxyl of the flavonoid acceptors, consistent with enzymatic activity results. In addition, ZmUGT85W2 is induced by UV-B radiation, and its expression is controlled by the B and PL1 transcription factors. Consistently, higher levels of flavone and flavonol O-glycosides are accumulated in leaves of plants exposed to solar UV-B compared to control plants, suggesting that ZmUGT85W2 is involved in the biosynthesis of these metabolites in maize leaves, contributing to UV-B tolerance. The activity of ZmUGT85W2, along with its elevated expression in silks and pericarps expressing the R2R3-MYB transcription factor P1, highlights its critical role in the accumulation of flavonoid O-glucosides in these tissues. Together, our findings reveal a key step in maize flavonoid O-glycosides biosynthesis, with the observed positive cooperative behaviors suggesting that ZmUGT85W2 plays a crucial role in finely regulating metabolic flux towards these compounds in planta.

Single-crystal structure of the spicy capsaicin

The crystal structure of capsaicin (C18H27NO3), or trans-8-methyl-N-vanillylnon-6-enamide, the natural product responsible for the spiciness of chilli peppers, was determined using low-temperature single-crystal X-ray diffraction. The reported crystal structure is in good agreement with previous determinations based on powder X-ray diffraction data. The localization and free refinement of all H atoms revealed that each capsaicin molecule is hydrogen bonded to four other molecules, with the O-H and N-H groups acting as hydrogen-bond donors, and the C=O group serving as a bifurcated hydrogen-bond acceptor.

Structural Insights into the Substrate Recognition of Ginsenoside Glycosyltransferase Pq3-O-UGT2

Ginsenosides are a group of tetracyclic triterpenoids with promising health benefits, consisting of ginseng aglycone attached to various glycans. Pq3-O-UGT2, an important UDP-dependent glycosyltransferase (UGT), catalyzes the production of Ginsenoside Rg3 and Rd by extending the glycan chain of Ginsenoside Rh2 and F2, respectively, with higher selectivity for F2. However, the mechanism underlying its substrate recognition remains unclear. In this study, the crystal structures of Pq3-O-UGT2 in complex with its acceptor substrates are solved. The structures revealed a Nα5-oriented acceptor binding pocket in Pq3-O-UGT2, shaped by the unique conformation of the Nα5-Nα6 linker. Hydrophobic interactions play a pivotal role in the recognition of both Rh2 and F2, while hydrogen bonds specifically aid in F2 recognition due to its additional glucose moiety. The hydrophobic nature of the acceptor binding pocket also enables Pq3-O-UGT2 to recognize flavonoids. Overall, this study provides novel insights into the substrate recognition mechanisms of ginsenoside UGTs, advancing the understanding of their function and specificity.

Insights into functional divergence, catalytic versatility and specificity of small molecule glycosyltransferases

Glycosylation is one of the most fundamental biochemical processes in cells. It plays crucial roles in diversifying plant natural products for structures, bioavailability and bioactivity, and thus, renders the glycosylated compounds valuable as food additives, nutraceuticals and pharmaceuticals. Moreover, glycosylated compounds impact plant growth, development and stress response. Therefore, understanding the biochemical function of the glycosyltransferases (GTs) is crucial to the elucidation of natural product biosynthetic pathways, improving plant traits and development of processes for industrially-important compounds. UDP-dependent glycosyltransferases (UGTs) that belong to the glycosyltransferase family-1 (GT1) and catalyze the transfer of glycosyl moieties from UDP-sugars to various small molecules, are the key players in natural product glycosylation. Recent studies also found the involvement of non-canonical cellulose synthase-like (CesAs) and glycosyl hydrolase (GH) family enzymes in the glycosylation of plant specialized metabolites. Decades of research on GTs provided critical insights into catalytic mechanism, substrate/product specificity and catalytic promiscuity, but biochemical function and physiological roles of GTs in majority of the natural product biosynthetic pathways remain to be understood. It is also important to redefine high-throughput strategies of GT mining to uncover novel biochemical function, considering that GTs are the large superfamily members in plants and other organisms. This review underscores the roles of GTs in small molecule glycosylation, plant development and stress responses, highlighting the catalytic versatility and substrate/product specificity of GTs in shaping plant metabolic diversity, and discusses the emerging strategies for mining of uncharacterized GTs to unravel biochemical and physiological functions and to elucidate natural product biosynthetic pathways.

Insights from Structure-Based Simulations into the Persulfidation of Uridine Diphosphate-Glycosyltransferase71c5 Facilitating the Reversible Inactivation of Abscisic Acid

The action of abscisic acid (ABA) is closely related to its level in plant tissues. Uridine diphosphate-glycosyltransferase71c5 (UGT71C5) was characterized as a major UGT enzyme to catalyze the formation of the ABA-glucose ester (ABA-GE), a reversible inactive form of free ABA in Arabidopsis thaliana (thale cress). UGTs function in a mode where the catalytic base deprotonates an acceptor to allow a nucleophilic attack at the anomeric center of the donor, achieving the transfer of a glucose moiety. The proteomic data revealed that UGT71C5 can be persulfidated. Herein, an experimental method was employed to detect the persulfidation site of UGT71C5, and the computational methods were further used to identify the yet unknown molecular basis of ABA glycosylation as well as the regulatory role of persulfidation in this process. Our results suggest that the linker and the U-shaped loop are regulatory structural elements: the linker is associated with the binding of uridine diphosphate glucose (UPG) and the U-shaped loop is involved in binding both UPG and ABA.It was also found that it is through tuning the dynamics of the U-shaped loop that is accompanied by the movement of tyrosine (Y388) that the persulfidation of cysteine (C311) leads to the catalytic residue histidine (H16) being in place, preparing for the deprotonation of ABA, and then reorientates UPG and deprotonated ABA closer to the 'Michaelis' complex, facilitating the transfer of a glucose moiety. Ultimately, the persulfidation of UGT71C5 is in favor of ABA glycosylation. Our results provide insights into the molecular details of UGT71C5 recognizing substrates and insights concerning persulfidation as a possible mechanism for hydrogen sulfide (H2S) to modulate the content of ABA, which helps us understand how modulating ABA level strengthens plant tolerance.

Supramolecular Synthons in Protein-Ligand Frameworks

Supramolecular synthons, defined as reproducible intermolecular structural units, have greatly aided small molecule crystal engineering. In this paper, we propose that supramolecular synthons guide ligand-mediated protein crystallization. The protein RSL and the macrocycle sulfonato-calix[8]arene cocrystallize in at least four ways. One of these cocrystals is a highly porous cube comprising protein nodes connected by calixarene dimers. We show that mutating an aspartic acid to an asparagine results in two new cubic assemblies that depend also on the crystallization method. One of the new cubic arrangements is mediated by calixarene trimers and has a ∼30% increased cell volume relative to the original crystal with calixarene dimers. Crystals of the sulfonato-calix[8]arene sodium salt were obtained from buffered conditions similar to those used to grow the protein-calix[8]arene cocrystals. X-ray analysis reveals a coordination polymer of the anionic calix[8]arene and sodium cation in which the macrocycle is arranged as staggered stacks of the pleated loop conformation. Remarkably, the calixarene packing arrangement is the same in the simple salt as in the protein cocrystal. With the pleated loop conformation, the calixarene presents an extended surface for binding other calixarenes (oligomerization) as well as binding to a protein patch (biomolecular complexation). Small-angle X-ray scattering data suggest pH-dependent calixarene assembly in solution. Therefore, the calix[8]arene-calix[8]arene structural unit may be regarded as a supramolecular synthon that directs at least two types of protein assembly, suggesting applications in protein crystal engineering.

Similarities in Structure and Function of UDP-Glycosyltransferase Homologs from Human and Plants

The uridine diphosphate glycosyltransferase (UGT) superfamily plays a key role in the metabolism of xenobiotics and metabolic wastes, which is essential for detoxifying those species. Over the last several decades, a huge effort has been put into studying human and mammalian UGT homologs, but family members in other organisms have been explored much less. Potentially, other UGT homologs can have desirable substrate specificity and biological activities that can be harnessed for detoxification in various medical settings. In this review article, we take a plant UGT homology, UGT71G1, and compare its structural and biochemical properties with the human homologs. These comparisons suggest that even though mammalian and plant UGTs are functional in different environments, they may support similar biochemical activities based on their protein structure and function. The known biological functions of these homologs are discussed so as to provide insights into the use of UGT homologs from other organisms for addressing human diseases related to UGTs.

Promiscuity and Quantitative Contribution of UGT2B17 in Drug and Steroid Metabolism Determined by Experimental and Computational Approaches

Uridine 5'-diphospho-glulcuronosyltransferase 2B17 (UGT2B17) is important in the metabolism of steroids and orally administered drugs due to its high interindividual variability. However, the structural basis governing the substrate selectivity or inhibition of UGT2B17 remains poorly understood. This study investigated 76 FDA-approved drugs and 20 steroids known to undergo glucuronidation for their metabolism by UGT2B17. Specifically, we assessed the substrate selectivity for UGT2B17 over other UGT enzymes using recombinant human UGT2B17 (rUGT2B17), human intestinal microsomes, and human liver microsomes. The quantitative contribution of intestinal UGT2B17 in the glucuronidation of these compounds was characterized using intestinal microsomes isolated from UGT2B17 expressors and nonexpressors. In addition, a structure-based pharmacophore model for UGT2B17 substrates was built and validated using the studied pool of substrates and nonsubstrates. The results show that UGT2B17 could metabolize 23 out of 96 compounds from various chemical classes, including alcohols and carboxylic acids, particularly in the intestine. Interestingly, amines were less susceptible to UGT2B17 metabolism, though they could inhibit the enzyme. Three main pharmacophoric features of UGT2B17 substrates include (1) the presence of an accessible -OH or -COOH group near His35 residue, (2) a hydrophobic functional group at ∼4.5-5 Å from feature 1, and (3) an aromatic ring ∼5-7 Å from feature 2. Most of the studied compounds inhibited UGT2B17 activity irrespective of their substrate potential, indicating the possibility of multiple mechanisms. These data suggest that UGT2B17 is promiscuous in substrate selectivity and inhibition and has a high potential to produce significant variability in the absorption and disposition of orally administered drugs.

Structure-function and engineering of plant UDP-glycosyltransferase

Natural products synthesized by plants have substantial industrial and medicinal values and are therefore attracting increasing interest in various related industries. Among the key enzyme families involved in the biosynthesis of natural products, uridine diphosphate-dependent glycosyltransferases (UGTs) play a crucial role in plants. In recent years, significant efforts have been made to elucidate the catalytic mechanisms and substrate recognition of plant UGTs and to improve them for desired functions. In this review, we presented a comprehensive overview of all currently published structures of plant UGTs, along with in-depth analyses of the corresponding catalytic and substrate recognition mechanisms. In addition, we summarized and evaluated the protein engineering strategies applied to improve the catalytic activities of plant UGTs, with a particular focus on high-throughput screening methods. The primary objective of this review is to provide readers with a comprehensive understanding of plant UGTs and to serve as a valuable reference for the latest techniques used to improve their activities.