- Identification of novel inhibitors of UDP-Glc 4′-epimerase, a validated drug target for african sleeping sickness
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Novel inhibitors of Trypanosoma brucei and mammalian UDP-Glc 4′-epimerase were identified by screening a small library of natural products and commercially available drug-like molecules. The inhibitors possess low micromolar potency against the T. brucei and human enzymes in vitro, display a degree of selectivity between the two enzymes, and are cytotoxic to cultured T. brucei and mammalian cells.
- Urbaniak, Michael D.,Tabudravu, Jioji N.,Msaki, Aichi,Matera, Kathy Mansfield,Brenk, Ruth,Jaspars, Marcel,Ferguson, Michael A.J.
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- Structural and kinetic evidence that catalytic reaction of human UPD-glucose 6-dehydrogenase involves covalent thiohemiacetal and thioester enzyme intermediates
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Biosynthesis of UDP-glucuronic acid by UDP-glucose 6-dehydrogenase (UGDH) occurs through the four-electron oxidation of the UDP-glucose C6 primary alcohol in two NAD+-dependent steps. The catalytic reaction of UGDH is thought to involve a Cys nucleophile that promotes formation of a thiohemiacetal enzyme intermediate in the course of the first oxidation step. The thiohemiacetal undergoes further oxidation into a thioester, and hydrolysis of the thioester completes the catalytic cycle. Herein we present crystallographic and kinetic evidence for the human form of UGDH that clarifies participation of covalent catalysis in the enzymatic mechanism. Substitution of the putative catalytic base for water attack on the thioester (Glu161) by an incompetent analog (Gln161) gave a UGDH variant (E161Q) in which the hydrolysis step had become completely rate-limiting so that a thioester enzyme intermediate accumulated at steady state. By crystallizing E161Q in the presence of 5 mM UDP-glucose and 2 mM NAD+, we succeeded in trapping a thiohemiacetal enzyme intermediate and determined its structure at 2.3 A resolution. Cys276 was covalently modified in the structure, establishing its role as catalytic nucleophile of the reaction. The thiohemiacetal reactive C6 was in a position suitable to become further oxidized by hydride transfer to NAD+. The proposed catalytic mechanism of human UGDH involves Lys220 as general base for UDP-glucose alcohol oxidation and for oxyanion stabilization during formation and breakdown of the thiohemiacetal and thioester enzyme intermediates. Water coordinated to Asp 280 deprotonates Cys276 to function as an aldehyde trap and also provides oxyanion stabilization. Glu161 is the Bronsted base catalytically promoting the thioester hydrolysis.
- Egger, Sigrid,Chaikuad, Apirat,Klimacek, Mario,Kavanagh, Kathryn L.,Oppermann, Udo,Nidetzky, Bernd
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- Enzymatic Synthesis of Uridine 5'-Diphosphoglucuronic Acid on a Gram Scale
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A pratical route to uridine 5'-diphosphoglucuronic acid (UDP-GlcUA) from uridine 5'-diphosphoglucose (UDP-Glc) on a 1-g scale has been developed using uridine 5'-diphosphoglucose dehydrogenase (UDP-Glc DH, EC 1.1.1.22) from bovine liver.Crude UDP-Glc dehydrogenase was isolated fron beef liver (450 units from 2.4 kg of frozen liver).Commercially available UDP-Glc dehydrogenase as well as a preparation fron calf liver acetone powder were also evaluated as catalysts for large-scale production of UDP-GlcUA: both preparations exhibited too little activity to be synthetically useful.A platinum-catalyzed oxygen oxidation of UDP-Glc was also examined as a possible route to UDP-GlcUA: enzymatic oxidation was superior.These results establish a route to another of the important activated monosaccharides required for cell-free enzymatic syntheses of mammalian oligo- and polysaccharides.
- Toone, Eric J.,Simon, Ethan S.,Whitesides, George M.
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- Catalytic mechanism of human UDP-glucose 6-dehydrogenase: In situ proton NMR studies reveal that the C-5 hydrogen of UDP-glucose is not exchanged with bulk water during the enzymatic reaction
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Human UDP-glucose 6-dehydrogenase (hUGDH) catalyzes the biosynthetic oxidation of UDP-glucose into UDP-glucuronic acid. The catalytic reaction proceeds in two NAD+-dependent steps via covalent thiohemiacetal and thioester enzyme intermediates. Formation of the thiohemiacetal adduct occurs through attack of Cys276 on C-6 of the UDP-gluco-hexodialdose produced in the first oxidation step. Because previous studies of the related enzyme from bovine liver had suggested loss of the C-5 hydrogen from UDP-gluco-hexodialdose due to keto-enol tautomerism, we examined incorporation of solvent deuterium into product(s) of UDP-glucose oxidation by hUGDH. We used wild-type enzyme and a slow-reacting Glu161→Gln mutant that accumulates the thioester adduct at steady state. In situ proton NMR measurements showed that UDP-glucuronic acid was the sole detectable product of both enzymatic transformations. The product contained no deuterium at C-5 within the detection limit (≤2%). The results are consistent with the proposed mechanistic idea for hUGDH that incipient UDP-gluco-hexodialdose is immediately trapped by thiohemiacetal adduct formation.
- Eixelsberger, Thomas,Brecker, Lothar,Nidetzky, Bernd
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- Uridine diphospho-α-D-gluco-hexodialdose: Synthesis and kinetic competence in the reaction catalyzed by UDP-glucose dehydrogenase
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The elusive aldehyde 1 has never been trapped nor detected during the enzymatic oxidation of UDP-glucose to UDP-glucuronic acid. Here the synthesis of 1 is reported; it proved to be kinetically competent to serve as an intermediate in the reaction catalyzed by UDP-glucose dehydrogenase.
- Campbell,Tanner
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- Gram-scale production of sugar nucleotides and their derivatives
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Here, we report a practical sugar nucleotide production strategy that combined a high-concentrated multi-enzyme catalyzed reaction and a robust chromatography-free selective precipitation purification process. Twelve sugar nucleotides were synthesized on a gram scale with a purity up to 98%.
- Li, Shuang,Wang, Shuaishuai,Wang, Yaqian,Qu, Jingyao,Liu, Xian-Wei,Wang, Peng George,Fang, Junqiang
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supporting information
p. 2628 - 2633
(2021/04/21)
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- Mechanistic characterization of UDP-glucuronic acid 4-epimerase
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UDP-glucuronic acid (UDP-GlcA) is a central precursor in sugar nucleotide biosynthesis and common substrate for C4-epimerases and decarboxylases releasing UDP-galacturonic acid (UDP-GalA) and UDP-pentose products, respectively. Despite the different reactions catalyzed, the enzymes are believed to share mechanistic analogy rooted in their joint membership to the short-chain dehydrogenase/reductase (SDR) protein superfamily: Oxidation at the substrate C4 by enzyme-bound NAD+ initiates the catalytic pathway. Here, we present mechanistic characterization of the C4-epimerization of UDP-GlcA, which in comparison with the corresponding decarboxylation has been largely unexplored. The UDP-GlcA 4-epimerase from Bacillus cereus functions as a homodimer and contains one NAD+/subunit (kcat?=?0.25?±?0.01?s?1). The epimerization of UDP-GlcA proceeds via hydride transfer from and to the substrate’s C4 while retaining the enzyme-bound cofactor in its oxidized form (≥?97%) at steady state and without trace of decarboxylation. The kcat for UDP-GlcA conversion shows a kinetic isotope effect of 2.0 (±0.1) derived from substrate deuteration at C4. The proposed enzymatic mechanism involves a transient UDP-4-keto-hexose-uronic acid intermediate whose formation is rate-limiting overall, and is governed by a conformational step before hydride abstraction from UDP-GlcA. Precise positioning of the substrate in a kinetically slow binding step may be important for the epimerase to establish stereo-electronic constraints in which decarboxylation of the labile β-keto acid species is prevented effectively. Mutagenesis and pH studies implicate the conserved Tyr149 as the catalytic base for substrate oxidation and show its involvement in the substrate positioning step. Collectively, this study suggests that based on overall mechanistic analogy, stereo-electronic control may be a distinguishing feature of catalysis by SDR-type epimerases and decarboxylases active on UDP-GlcA.
- Borg, Annika J. E.,Dennig, Alexander,Weber, Hansj?rg,Nidetzky, Bernd
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p. 1163 - 1178
(2020/08/07)
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- Toward Automated Enzymatic Glycan Synthesis in a Compartmented Flow Microreactor System
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Immobilized microfluidic enzyme reactors (IMER) are of particular interest for automation of enzyme cascade reactions. Within an IMER, substrates are converted by paralleled immobilized enzyme modules and intermediate products are transported for further conversion by subsequent enzyme modules. By optimizing substrate conversion in the spatially separated enzyme modules purification of intermediate products is not necessary, thus shortening process time and increasing space-time yields. The IMER enables the development of efficient enzyme cascades by combining compatible enzymatic reactions in different arrangements under optimal conditions and the possibility of a cost-benefit analysis prior to scale-up. These features are of special interest for automation of enzymatic glycan synthesis. We here demonstrate a compartmented flow microreactor system using six magnetic enzyme beads (MEBs) for the synthesis of the non-sulfated human natural killer cell-1 (HNK-1) glycan epitope. MEBs are assembled to build compartmented enzyme modules, consisting of enzyme cascades for the synthesis of uridine 5′- diphospho-α- d-galactose (UDP-Gal) and uridine 5′-diphospho-α-d-glucuronic acid (UDP-GlcA), the donor substrates for the Leloir glycosyltransferases β4-galactosyltransferase and β3-glucuronosyltransferase, respectively. Glycan synthesis was realized in an automated microreactor system by a cascade of individual enzyme module compartments each performing under optimal conditions. The products were analyzed inline by an MS-system connected to the microreactor. The high synthesis yield of 96% for the non-sulfated HNK-1 glycan epitope indicates the excellent performance of the automated enzyme module cascade. Furthermore, combinations of other MEBs for nucleotide sugars synthesis with MEBs of glycosyltransferases have the potential for a fully automated and programmed glycan synthesis in a compartmented flow microreactor system. (Figure presented.).
- Heinzler, Raphael,Fisch?der, Thomas,Elling, Lothar,Franzreb, Matthias
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supporting information
p. 4506 - 4516
(2019/08/20)
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- Isotope Probing of the UDP-Apiose/UDP-Xylose Synthase Reaction: Evidence of a Mechanism via a Coupled Oxidation and Aldol Cleavage
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The C-branched sugar d-apiose (Api) is essential for plant cell-wall development. An enzyme-catalyzed decarboxylation/pyranoside ring-contraction reaction leads from UDP-α-d-glucuronic acid (UDP-GlcA) to the Api precursor UDP-α-d-apiose (UDP-Api). We examined the mechanism of UDP-Api/UDP-α-d-xylose synthase (UAXS) with site-selectively2H-labeled and deoxygenated substrates. The analogue UDP-2-deoxy-GlcA, which prevents C-2/C-3 aldol cleavage as the plausible initiating step of pyranoside-to-furanoside conversion, did not give the corresponding Api product. Kinetic isotope effects (KIEs) support an UAXS mechanism in which substrate oxidation by enzyme-NAD+and retro-aldol sugar ring-opening occur coupled in a single rate-limiting step leading to decarboxylation. Rearrangement and ring-contracting aldol addition in an open-chain intermediate then give the UDP-Api aldehyde, which is intercepted via reduction by enzyme-NADH.
- Eixelsberger, Thomas,Horvat, Doroteja,Gutmann, Alexander,Weber, Hansj?rg,Nidetzky, Bernd
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supporting information
p. 2503 - 2507
(2017/02/23)
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- Enzyme Module Systems for the Synthesis of Uridine 5′-Diphospho-α- D -glucuronic Acid and Non-Sulfated Human Natural Killer Cell-1 (HNK-1) Epitope
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Tailor-made strategies for the stereo- and regioselective multi-step enzymatic synthesis of glycoconjugates require well characterized glycosyltransferases and carbohydrate modifying enzymes. We here report on a novel enzyme cascade for the synthesis of uridine 5′-diphospho-α-D-glucuronic acid (UDP-GlcA) and the non-sulfated human natural killer cell-1 (HNK-1) epitope including in situ regeneration of UDP-GlcA and the cofactor nicotinamide adenine dinucleotide NAD+ by the combination of four enzymes in one-pot. In the first enzyme module sucrose synthase 1 (SuSy1) is used to produce uridine 5′-diphospho-α-D-glucose (UDP-Glc) from sucrose and uridine 5′-diphosphate (UDP). The combination with UDP-Glc dehydrogenase in the second enzyme module leads to the synthesis of UDP-GlcA with concomitant in situ regeneration of the cofactor NAD+ by nicotinamide adenine dinucleotide hydride (NADH)-oxidase. In the third enzyme module the mammalian glucuronyltransferase GlcAT-P catalyzes the synthesis of the non-sulfated HNK-1 epitope by regioselective transfer of GlcA onto N-acetyllactosamine type 2 (LacNAc type 2). We present a comprehensive study on substrate kinetics, substrate specificities, variation and relation of enzyme activities as well as cross inhibition of intermediate products. With optimized reaction conditions we obtain superior product yields with streamlined synthesis costs for the expensive nucleotide sugar UDP-GlcA and cofactor NAD+.
- Engels, Leonie,Henze, Manja,Hummel, Werner,Elling, Lothar
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p. 1751 - 1762
(2015/06/02)
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- Comparing substrate specificity of two UDP-sugar pyrophosphorylases and efficient one-pot enzymatic synthesis of UDP-GlcA and UDP-GalA
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Uridine 5′-diphosphate-glucuronic acid (UDP-GlcA) and UDP-galacturonic acid (UDP-GalA), the unique carboxylic acid-formed sugar nucleotides, are key precursors involved in the biosynthesis of numerous cell components. Limited availability of those components has been hindering the development of efficient ways towards facile synthesis of bioactive glycans such as glycosaminoglycans. In current study, we biochemically characterized two UDP-sugar pyrophosphorylases from Arabidopsis thaliana (AtUSP) and Bifidobacterium infantis ATCC15697 (BiUSP), and compared their activities towards a panel of sugar-1-phosphates and derivatives. Both enzymes showed significant pyrophosphorylation activities towards GlcA-1-phosphate, and AtUSP also exhibited comparable activity towards GalA-1-phosphate. By combining with monosaccharide-1-phosphate kinases, we have developed an efficient and facile one-pot three-enzyme approach to quickly obtain hundreds milligrams of UDP-GlcA and UDP-GalA.
- Guo, Yuxi,Fang, Junqiang,Li, Tiehai,Li, Xu,Ma, Cheng,Wang, Xuan,Wang, Peng G.,Li, Lei
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- Improved one-pot multienzyme (OPME) systems for synthesizing UDP-uronic acids and glucuronides
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Arabidopsis thaliana glucuronokinase (AtGlcAK) was cloned and shown to be able to use various uronic acids as substrates to produce the corresponding uronic acid-1-phosphates. AtGlcAK or Bifidobacterium infantis galactokinase (BiGalK) was used with a UDP-sugar pyrophosphorylase, an inorganic pyrophosphatase, with or without a glycosyltransferase for highly efficient synthesis of UDP-uronic acids and glucuronides. These improved cost-effective one-pot multienzyme (OPME) systems avoid the use of nicotinamide adenine dinucleotide (NAD+)-cofactor in dehydrogenase-dependent UDP-glucuronic acid production processes and can be broadly applied for synthesizing various glucuronic acid-containing molecules. This journal is
- Muthana, Musleh M.,Qu, Jingyao,Xue, Mengyang,Klyuchnik, Timofey,Siu, Alex,Li, Yanhong,Zhang, Lei,Yu, Hai,Li, Lei,Wang, Peng G.,Chen, Xi
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supporting information
p. 4595 - 4598
(2015/05/27)
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- Biosynthesis of UDP-glucuronic acid and UDP-galacturonic acid in Bacillus cereus subsp. cytotoxis NVH 391-98
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The food borne pathogen Bacillus cereus produces uronic acid-containing glycans that are secreted in a shielding biofilm environment, and certain alkaliphilic Bacillus deposit uronate-glycan polymers in the cell wall when adapting to alkaline environments. The source of these acidic sugars is unknown and, in the present study, we describe the functional identification of an operon in Bacillus cerues subsp. cytotoxis NVH 391-98 that comprises genes involved in the synthesis of UDP-uronic acids in Bacillus spp. Within the operon, a UDP-glucose 6-dehydrogenase converts UDP-glucose in the presence of NAD+ to UDP-glucuronic acid and NADH, and a UDP-GlcA 4-epimerase (UGlcAE) converts UDP-glucuronic acid to UDP-galacturonic acid. Interestingly, in vitro, both enzymes can utilize the TDP-sugar forms as well, albeit at lower catalytic efficiency. Unlike most of the very few bacterial 4-epimerases that have been characterized, which are promiscuous, the B. cereus UGlcAE enzyme is very specific and cannot use UDP-glucose, UDP-N-acetylglucosamine, UDP-N-acetylglucosaminuronic acid or UDP-xylose as substrates. Size exclusion chromatography suggests that UGlcAE is active as a monomer, unlike the dimeric form of plant enzymes; the Bacillus UDP-glucose 6-dehydrogenase is also found as a monomer. Phylogenic analysis further suggests that the Bacillus UGlcAE may have evolved separately from other bacterial and plant epimerases. Our results provide insight into the formation and function of uronic acid-containing glycans in the lifecycle of B. cereus and related species containing homologous operons, as well as a basis for determining the importance of these acidic glycans. We also discuss the ability to target UGlcAE as a drug candidate.
- Broach, Bryan,Gu, Xiaogang,Bar-Peled, Maor
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experimental part
p. 100 - 112
(2012/04/11)
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- Synthesis of UDP-4-deoxy-4-fluoroglucose and UDP-4-deoxy-4-fluorogalactose and their interactions with enzymes of nucleotide sugar metabolism
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Fluorinated carbohydrates can be used as probes of enzymatic active sites. We report the synthesis of 4-deoxy-4-fluoro-α-D-galactose-1-phosphate and the substrate analogues of UDP-galactose, UDP4-deoxy-4-fluoro-α-D-galactose (UDP-FGal), and of UDP-glucose, UDP-4-deoxy-4-fluoro-α-D-glucose (UDP-FGlc), which may be useful in analyzing the binding properties of enzymes that utilize nucleotide sugars as substrates. As a first step in this study, we determine the kinetic and inhibition parameters for UDP-FGal and UDP-FGlc interacting with UDP-glucose dehydrogenase and UDP-galactose 4-epimerase. UDP-FGlc is a substrate for bovine liver UDP-glucose dehydrogenase: K(m) = 30.2 ± 4.5 μM slightly higher than the value 9.6 ± 0.7 μM for UDP-glucose, and V(m)(UDP-FGlc) = 0.46V(mUDP-Glc). UDP-FGal is not a substrate for UDP-glucose dehydrogenase but is a competitive inhibitor with respect to UDP-glucose (K(i) = 19.9 ± 6.6 μM). These analogs also bind to UDP-galactose 4-epimerase from E. coli with dissociation constants K(d) of 1.4 and 1.1 mM for UDP-FGlc and UDP-FGal, respectively.
- Chapeau,Frey
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p. 6994 - 6998
(2007/10/02)
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- Convenient syntheses of cytidine 5'-triphosphate, guanosine 5'-triphosphate, and uridine 5'-triphosphate and their use in the preparation of UDP-glucose, UDP-glucuronic acid, and GDP-mannose
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This paper compares enzymatic and chemical methods for the synthesis of cytidine 5'-triphosphate, guanosine 5'-triphosphate, and uridine 5'-triphosphate from the corresponding nucleoside monophosphates on scales of ~10 g. These nucleoside triphosphates are important as intermediates in Leloir pathway biosyntheses of complex carbohydrates; the nucleoside monophosphates are readily available commercially. The best route to CTP is based on phosphorylation of CMP using adenylate kinase (EC 2.7.4.3); the route to GTP involves phosphorylation of GMP using guanylate kinase (EC 2.7.4.8); chemical deamination of CTP (prepared enzymatically from CMP) is the best synthesis of UTP. For the 10-200-mmol-scale reactions described in this paper, it is more convenient to prepare phosphoenolpyruvate (PEP), used in the enzymatic preparations, from D-(-)-3-phosphoglyceric acid (3-PGA) in the reaction mixture rather than to synthesize PEP in a separate chemical step. The in situ conversion of 3-PGA to PEP requires the coupled action of phosphoglycerate mutase (EC 2.7.5.3) and enolase (EC 4.2.1.11). The enzyme-catalyzed syntheses of uridine 5'-diphosphoglucose (UDP-Glc), uridine 5'-diphosphoglucuronic acid (UDP-GlcUA), and guanosine 5'-diphosphomannose (GDP-Man) illustrate the use of the nucleoside triphosphates.
- Simon,Grabowski,Whitesides
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p. 1834 - 1841
(2007/10/02)
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