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Current Opinion in Structural Biology Aug 2022The ubiquitous UbiX-UbiD system is associated with a wide range of microbial (de)carboxylation reactions. Recent X-ray crystallographic studies have contributed to... (Review)
Review
The ubiquitous UbiX-UbiD system is associated with a wide range of microbial (de)carboxylation reactions. Recent X-ray crystallographic studies have contributed to elucidating the enigmatic mechanism underpinning the conversion of α,β-unsaturated acids by this system. The UbiD component utilises a unique cofactor, prenylated flavin (prFMN), generated by the bespoke action of the associated UbiX flavin prenyltransferase. Structure determination of a range of UbiX/UbiD representatives has revealed a generic mode of action for both the flavin-to-prFMN metamorphosis and the (de)carboxylation. In contrast to the conserved UbiX, the UbiD superfamily is associated with a versatile substrate range. The latter is reflected in the considerable variety of UbiD quaternary structure, dynamic behaviour and active site architecture. Directed evolution of UbiD enzymes has taken advantage of this apparent malleability to generate new variants supporting in vivo hydrocarbon production. Other applications include coupling UbiD to carboxylic acid reductase to convert alkenes into α,β-unsaturated aldehydes via enzymatic CO fixation.
Topics: Aspergillus niger; Carboxy-Lyases; Decarboxylation; Flavins; Prenylation
PubMed: 35843126
DOI: 10.1016/j.sbi.2022.102432 -
Molecules (Basel, Switzerland) Aug 2020Prenylated natural products have interesting pharmacological properties and prenylation reactions play crucial roles in controlling the activities of biomolecules. They...
Prenylated natural products have interesting pharmacological properties and prenylation reactions play crucial roles in controlling the activities of biomolecules. They are difficult to synthesize chemically, but enzymatic synthesis production is a desirable pathway. Cyclic dipeptide prenyltransferase catalyzes the regioselective Friedel-Crafts alkylation of tryptophan-containing cyclic dipeptides. This class of enzymes, which belongs to the dimethylallyl tryptophan synthase superfamily, is known to be flexible to aromatic prenyl receptors, while mostly retaining its typical regioselectivity. In this study, seven tryptophan-containing cyclic dipeptides - were converted to their C7-regularly prenylated derivatives - in the presence of dimethylallyl diphosphate (DMAPP) by using the purified 7-dimethylallyl tryptophan synthase (7-DMATS) as catalyst. The HPLC analysis of the incubation mixture and the NMR analysis of the separated products showed that the stereochemical structure of the substrate had a great influence on their acceptance by 7-DMATS. Determination of the kinetic parameters proved that -l-Trp-Gly () consisting of a tryptophanyl and glycine was accepted as the best substrate with a value of 169.7 μM and a turnover number of 0.1307 s. Furthermore, docking studies simulated the prenyl transfer reaction of 7-DMATS and it could be concluded that the highest affinity between 7-DMATS and . Preliminary results have been clearly shown that prenylation at C7 led to a significant increase of the anticancer and antimicrobial activities of the prenylated derivatives - in all the activity test experiment, especially the prenylated product .
Topics: A549 Cells; Alkyl and Aryl Transferases; Anti-Infective Agents; Antineoplastic Agents; Bacteria; Dipeptides; HeLa Cells; Hep G2 Cells; Humans; MCF-7 Cells; Molecular Docking Simulation; Neoplasms; Peptides, Cyclic; Prenylation
PubMed: 32806659
DOI: 10.3390/molecules25163676 -
Biochemical and Biophysical Research... Jun 2016Increased activity of prenyl transferases is observed in pathological states of insulin resistance, diabetes, and obesity. Thus, functional inhibitors of farnesyl...
Increased activity of prenyl transferases is observed in pathological states of insulin resistance, diabetes, and obesity. Thus, functional inhibitors of farnesyl transferase (FTase) and geranylgeranyl transferase (GGTase) may be promising therapeutic treatments. We previously identified insulin responsive genes from a rat H4IIE hepatoma cell cDNA library, including β-actin, EGR1, Pip92, c-fos, and Hsp60. In the present study, we investigated whether acute treatment with FTase and GGTase inhibitors would alter insulin responsive gene initiation and/or elongation rates. We observed differential regulation of insulin responsive gene expression, suggesting a differential sensitivity of these genes to one or both of the specific protein prenylation inhibitors.
Topics: Actins; Animals; Cell Line; Chaperonin 60; Early Growth Response Protein 1; Gene Expression Regulation; Hepatocytes; Insulin; Mitochondrial Proteins; Prenylation; Proteins; Proto-Oncogene Proteins c-fos; RNA, Messenger; Rats; Transcription, Genetic
PubMed: 27086854
DOI: 10.1016/j.bbrc.2016.04.067 -
Journal of Natural Medicines Jun 2020Aromatic prenyltransferases (PTases), including ABBA-type and dimethylallyl tryptophan synthase (DMATS)-type enzymes from bacteria and fungi, play important role for... (Review)
Review
Aromatic prenyltransferases (PTases), including ABBA-type and dimethylallyl tryptophan synthase (DMATS)-type enzymes from bacteria and fungi, play important role for diversification of the natural products and improvement of the biological activities. For a decade, the characterization of enzymes and enzymatic synthesis of prenylated compounds by using ABBA-type and DMATS-type PTases have been demonstrated. Here, I introduce several examples of the studies on chemoenzymatic synthesis of unnatural prenylated compounds and the enzyme engineering of ABBA-type and DMATS-type PTases.
Topics: Alkyl and Aryl Transferases; Bacteria; Biological Products; Dimethylallyltranstransferase; Fungi; Prenylation; Protein Engineering
PubMed: 32180104
DOI: 10.1007/s11418-020-01393-x -
Organic & Biomolecular Chemistry Sep 2018Prenylated pterocarpans are valuable natural products that play significant roles in plant defence and possess diverse biological activities. However, structural...
Prenylated pterocarpans are valuable natural products that play significant roles in plant defence and possess diverse biological activities. However, structural diversity of prenylated pterocarpans is still limited. Prenyltransferases (PTs) could catalyze the transfer of prenyl moieties to acceptor molecules and increase the structural diversity and biological activity of natural products. Up to date, only two pterocarpan PTs have been identified from plants. In this study, a new pterocarpan prenyltransferase gene, designated as PcM4DT, was identified from Psoralea corylifolia. The deduced polypeptide is predicted to be a membrane-bound protein with eight transmembrane regions. Functional characterization of recombinant PcM4DT demonstrated this enzyme could catalyze C-4 prenylation of pterocarpans, and exhibited strict substrate specificity to maackiain and 3-hydroxy-9-methoxy-pterocarpan. It also showed a strict donor specificity to DMAPP. Furthermore, removal of the putative transit peptide of PcM4DT obviously increased the catalytic activity (up to 90%). PcM4DT represents the first PT identified from the Psoralea genus.
Topics: Antineoplastic Agents; Cell Membrane; Dimethylallyltranstransferase; HL-60 Cells; Humans; Kinetics; Prenylation; Psoralea; Pterocarpans; Stereoisomerism; Substrate Specificity
PubMed: 30187056
DOI: 10.1039/c8ob01724g -
Analytical Chemistry Oct 2021Protein prenylation is an important post-translational modification that regulates protein interactions, localizations, and signaling pathways in normal functioning of...
Protein prenylation is an important post-translational modification that regulates protein interactions, localizations, and signaling pathways in normal functioning of eukaryotic cells. It is also a critical step in the oncogenic developments of various cancers. Direct identification of native protein prenylation by mass spectrometry (MS) has been challenging due to high hydrophobicity and the lack of an efficient enrichment technique. Prior MS studies of prenylation revealed that prenyl peptides readily generate high-intensity fragments after neutral loss of the prenyl group (R group), and more recent investigation of oxidized prenyl peptides discovered more consistent neutral loss of the oxidized prenyl group (RSOH group). Here, a dual-stage neutral loss MS (DS-NLMS3)-based strategy is therefore developed by combining both gas-phase cleavable properties of the prenyl thioether bond and mono-oxidized thioether to improve the large-scale identification of prenylation. Both neutral losses can individually and distinctively confirm the prenylation type in MS and the sequence of the prenyl peptide upon targeted MS fragmentation. This dual-faceted NLMS3 strategy significantly improves the confidence in the identification of protein prenylation from large-scale samples, which enables the unambiguous identification of prenylated sites of the spiked low-abundance farnesyl peptide and native prenyl proteins from mouse macrophage cells, even without prior enrichment during sample preparation. The ease of incorporating this strategy into the prenylation study workflow and minimum disruption to the biological lipidome are advantageous for unraveling unknown native protein prenylation and further developments in profiling and quantifying prenylome.
Topics: Animals; Mice; Protein Prenylation
PubMed: 34558911
DOI: 10.1021/acs.analchem.1c01617 -
Analytica Chimica Acta Oct 2021Prenylated (iso)flavonoids are potent bioactive compounds found in the Fabaceae family. Analysis and quantification of this type of phytochemicals is challenging due to...
A targeted prenylation analysis by a combination of IT-MS and HR-MS: Identification of prenyl number, configuration, and position in different subclasses of (iso)flavonoids.
Prenylated (iso)flavonoids are potent bioactive compounds found in the Fabaceae family. Analysis and quantification of this type of phytochemicals is challenging due to their large structural diversity. In this study, the fragmentation of prenylated (iso)flavonoids was investigated using electrospray ionization ion trap mass spectrometry (ESI-IT-MS) with fragmentation by collision induced dissociation (CID) in combination and Orbitrap-MS (ESI-FT-MS) with fragmentation by higher energy C-trap dissociation (HCD). With this combination of IT-MS and high resolution MS (FT-MS), it was possible to determine the fragmentation pathways and characteristic spectral features of different subclasses of prenylated (iso)flavonoid standards, as well as characteristic fragmentations and neutral losses of different prenyl configurations. Based on our findings, a decision guideline was developed to (i) identify (iso)flavonoid backbones, (ii) annotate prenyl number, (iii) configuration, and (iv) position of unknown prenylated (iso)flavonoids, in complex plant extracts. In this guideline, structural characteristics were identified based on: (i) UV absorbance of the compound, (ii) mass-to-charge (m/z) ratio of the parent compound; (iii) ratio of relative abundances between neutral losses 42 and 56 u in MS; (iv) retro-Diels-Alder (RDA) fragments, neutral losses 54 and 68 u, and the ratio [M+H-CH]/[M+H]. Using this guideline, 196 prenylated (iso)flavonoids were annotated in a Glycyrrhiza glabra root extract. In total, 75 skeletons were single prenylated, 104 were double prenylated, and for merely 17 skeletons prenyl number could not unambiguously be annotated. Our prenylation guideline allows rapid screening for identification of prenylated (iso)flavonoids, including prenyl number, configuration, and position, in complex plant extracts. This guideline supports research on these bioactive compounds in the areas of plant metabolomics and natural products.
Topics: Flavonoids; Neoprene; Plant Extracts; Prenylation; Spectrometry, Mass, Electrospray Ionization
PubMed: 34538332
DOI: 10.1016/j.aca.2021.338874 -
Organic & Biomolecular Chemistry Nov 2022Bnd4 catalyzes the first committed step in the biosynthesis of the bacterial diterpenoid benditerpenoic acid and was the first eunicellane synthase identified from...
Bnd4 catalyzes the first committed step in the biosynthesis of the bacterial diterpenoid benditerpenoic acid and was the first eunicellane synthase identified from nature. We investigated the catalytic roles of the aromatic residues in the active site of Bnd4 through a series of mutation studies. These experiments revealed that large hydrophobic or aromatic side chains are required at F162 and Y197 for eunicellane formation and that selected mutations at W316 converted Bnd4 into a cembrane synthase. In addition, the Bnd4 variant expanded the native prenylation ability of Bnd4 from accepting C and C prenyl donors to C. This study supports the mechanism of eunicellane formation by Bnd4 and encourages further engineering of terpene synthases into practical and efficient prenyltransferases.
Topics: Prenylation; Dimethylallyltranstransferase; Mutation; Catalytic Domain
PubMed: 36321628
DOI: 10.1039/d2ob01931k -
Applied Microbiology and Biotechnology Jan 2023Ascomycetous fungi are often found in agricultural products and foods as contaminants. They produce hazardous mycotoxins for human and animals. On the other hand, the...
Ascomycetous fungi are often found in agricultural products and foods as contaminants. They produce hazardous mycotoxins for human and animals. On the other hand, the fungal metabolites including mycotoxins are important drug candidates and the enzymes involved in the biosynthesis of these compounds are valuable biocatalysts for production of designed compounds. One of the enzyme groups are members of the dimethylallyl tryptophan synthase superfamily, which mainly catalyze prenylations of tryptophan and tryptophan-containing cyclodipeptides (CDPs). Decoration of CDPs in the biosynthesis of multiple prenylated metabolites in nature is usually initiated by regiospecific C2-prenylation at the indole ring, followed by second and third ones as well as by other modifications. However, the strict substrate specificity can prohibit the further prenylation of unnatural C2-prenylated compounds. To overcome this, we firstly obtained C4-, C5-, C6-, and C7-prenylated cyclo-L-Trp-L-Pro. These products were then used as substrates for the promiscuous C2-prenyltransferase EchPT1, which normally uses the unprenylated CDPs as substrates. Four unnatural diprenylated cyclo-L-Trp-L-Pro including the unique unexpected N1,C6-diprenylated derivative with significant yields were obtained in this way. Our study provides an excellent example for increasing structural diversity by reprogramming the reaction orders of natural biosynthetic pathways. Furthermore, this is the first report that EchPT1 can also catalyze N1-prenylation at the indole ring. KEY POINTS: • Prenyltransferases as biocatalysts for unnatural substrates. • Chemoenzymatic synthesis of designed molecules. • A cyclodipeptide prenyltransferase as prenylating enzyme of already prenylated products.
Topics: Humans; Dimethylallyltranstransferase; Tryptophan; Prenylation; Indoles; Substrate Specificity; Mycotoxins
PubMed: 36441211
DOI: 10.1007/s00253-022-12303-4 -
Bioscience, Biotechnology, and... Mar 2009Prenylated flavonoids are natural products that exhibit diverse biological effects and often represent the active components of various medicinal plants. This study...
Prenylated flavonoids are natural products that exhibit diverse biological effects and often represent the active components of various medicinal plants. This study demonstrated the production of prenylated naringenin by biotransformation using transgenic yeast expressing naringenin 8-dimethylallyltransferase, a membrane-bound enzyme, without feeding of prenyl donors. This method provides the possibility of generating prenylated flavonoids that occur rarely in nature.
Topics: Cell Membrane; Dimethylallyltranstransferase; Flavonoids; Prenylation; Sophora; Yeasts
PubMed: 19270405
DOI: 10.1271/bbb.80729