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1.
J Chem Inf Model ; 62(3): 632-646, 2022 02 14.
Article in English | MEDLINE | ID: mdl-35043627

ABSTRACT

Uridine diphosphate (UDP)-apiose/UDP-xylose synthase (UAXS) is a member of the short-chain dehydrogenase/reductase superfamily (SDR), which catalyzes the ring contraction and closure of UDP-d-glucuronic acid (UDP-GlcA), affording UDP-apiose and UDP-xylose. UAXS is a special enzyme that integrates ring-opening, decarboxylation, rearrangement, and ring closure/contraction in a single active site. Recently, the ternary complex structure of UAXS was crystallized from Arabidopsis thaliana. In this work, to gain insights into the detailed formation mechanism of UDP-apiose and UDP-xylose, an enzyme-substrate reactant model has been constructed and quantum mechanical/molecular mechanical (QM/MM) calculations have been performed. Our calculation results reveal that the reaction starts from the C4-OH oxidation, which is accompanied by the conformational transformation of the sugar ring from chair type to boat type. The sugar ring-opening is prior to decarboxylation, and the deprotonation of the C2-OH group is the prerequisite for sugar ring-opening. Moreover, the keto-enol tautomerization of the decarboxylated intermediate is a necessary step for ring closure/contraction. Based on our calculation results, more UDP-apiose product was expected, which is in line with the experimental observation. Three titratable residues, Tyr185, Cys100, and Cys140, steer the reaction by proton transfer from or to UDP-GlcA, and Arg182, Glu141, and D337 constitute a proton conduit for sugar C2-OH deprotonation. Although Thr139 and Tyr105 are not directly involved in the enzymatic reaction, they are responsible for promoting the catalysis by forming hydrogen-bonding interactions with GlcA. Our calculations may provide useful information for understanding the catalysis of the SDR family.


Subject(s)
Carboxy-Lyases , Xylose , Carboxy-Lyases/chemistry , Catalysis , Pentoses , Sugars , Uridine Diphosphate Sugars/chemistry
2.
FEBS J ; 288(4): 1163-1178, 2021 02.
Article in English | MEDLINE | ID: mdl-32645249

ABSTRACT

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 ß-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.


Subject(s)
Bacillus cereus/enzymology , Bacterial Proteins/metabolism , Racemases and Epimerases/metabolism , Recombinant Proteins/metabolism , Uridine Diphosphate Sugars/metabolism , Bacterial Proteins/genetics , Biocatalysis , Carbohydrate Sequence , Catalytic Domain , Chromatography, High Pressure Liquid , Escherichia coli/genetics , Hydrogen-Ion Concentration , Kinetics , Magnetic Resonance Spectroscopy , Molecular Sequence Data , Mutant Proteins/metabolism , Mutation , Racemases and Epimerases/genetics , Recombinant Proteins/genetics , Uridine Diphosphate Sugars/chemistry
3.
Acta Crystallogr F Struct Biol Commun ; 76(Pt 11): 557-567, 2020 Nov 01.
Article in English | MEDLINE | ID: mdl-33135674

ABSTRACT

Bacterial nonhydrolyzing UDP-N-acetylglucosamine 2-epimerases catalyze the reversible interconversion of UDP-N-acetylglucosamine (UDP-GlcNAc) and UDP-N-acetylmannosamine (UDP-ManNAc). UDP-ManNAc is an important intermediate in the biosynthesis of certain cell-surface polysaccharides, including those in some pathogenic bacteria, such as Neisseria meningitidis and Streptococcus pneumoniae. Many of these epimerases are allosterically regulated by UDP-GlcNAc, which binds adjacent to the active site and is required to initiate UDP-ManNAc epimerization. Here, two crystal structures of UDP-N-acetylglucosamine 2-epimerase from Neisseria meningitidis serogroup A (NmSacA) are presented. One crystal structure is of the substrate-free enzyme, while the other structure contains UDP-GlcNAc substrate bound to the active site. Both structures form dimers as seen in similar epimerases, and substrate binding to the active site induces a large conformational change in which two Rossmann-like domains clamp down on the substrate. Unlike other epimerases, NmSacA does not require UDP-GlcNAc to instigate the epimerization of UDP-ManNAc, although UDP-GlcNAc was found to enhance the rate of epimerization. In spite of the conservation of residues involved in binding the allosteric UDP-GlcNAc observed in similar UDP-GlcNAc 2-epimerases, the structures presented here do not contain UDP-GlcNAc bound in the allosteric site. These structural results provide additional insight into the mechanism and regulation of this critical enzyme and improve the structural understanding of the ability of NmSacA to epimerize modified substrates.


Subject(s)
Neisseria meningitidis, Serogroup A/enzymology , Allosteric Site , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Carbohydrate Epimerases/chemistry , Carbohydrate Epimerases/genetics , Carbohydrate Epimerases/metabolism , Catalytic Domain , Crystallography, X-Ray , Hydrolysis , Models, Molecular , Protein Conformation , Sodium/chemistry , Sodium/metabolism , Uridine Diphosphate N-Acetylglucosamine/chemistry , Uridine Diphosphate N-Acetylglucosamine/metabolism , Uridine Diphosphate Sugars/chemistry , Uridine Diphosphate Sugars/metabolism
4.
Protein Sci ; 29(11): 2164-2174, 2020 11.
Article in English | MEDLINE | ID: mdl-32797646

ABSTRACT

For the field of virology, perhaps one of the most paradigm-shifting events so far in the 21st century was the identification of the giant double-stranded DNA virus that infects amoebae. Remarkably, this virus, known as Mimivirus, has a genome that encodes for nearly 1,000 proteins, some of which are involved in the biosynthesis of unusual sugars. Indeed, the virus is coated by a layer of glycosylated fibers that contain d-glucose, N-acetyl-d-glucosamine, l-rhamnose, and 4-amino-4,6-dideoxy-d-glucose. Here we describe a combined structural and enzymological investigation of the protein encoded by the open-reading frame L780, which corresponds to an l-rhamnose synthase. The structure of the L780/NADP+ /UDP-l-rhamnose ternary complex was determined to 1.45 Å resolution and refined to an overall R-factor of 19.9%. Each subunit of the dimeric protein adopts a bilobal-shaped appearance with the N-terminal domain harboring the dinucleotide-binding site and the C-terminal domain positioning the UDP-sugar into the active site. The overall molecular architecture of L780 places it into the short-chain dehydrogenase/reductase superfamily. Kinetic analyses indicate that the enzyme can function on either UDP- and dTDP-sugars but displays a higher catalytic efficiency with the UDP-linked substrate. Site-directed mutagenesis experiments suggest that both Cys 108 and Lys 175 play key roles in catalysis. This structure represents the first model of a viral UDP-l-rhamnose synthase and provides new details into these fascinating enzymes.


Subject(s)
Acanthamoeba/virology , Carbohydrate Epimerases/chemistry , Mimiviridae/enzymology , Uridine Diphosphate Sugars/chemistry , Viral Proteins/chemistry , Crystallography, X-Ray , Mimiviridae/genetics , Protein Domains
5.
J Biol Chem ; 295(35): 12461-12473, 2020 08 28.
Article in English | MEDLINE | ID: mdl-32661196

ABSTRACT

UDP-glucuronic acid is converted to UDP-galacturonic acid en route to a variety of sugar-containing metabolites. This reaction is performed by a NAD+-dependent epimerase belonging to the short-chain dehydrogenase/reductase family. We present several high-resolution crystal structures of the UDP-glucuronic acid epimerase from Bacillus cereus The geometry of the substrate-NAD+ interactions is finely arranged to promote hydride transfer. The exquisite complementarity between glucuronic acid and its binding site is highlighted by the observation that the unligated cavity is occupied by a cluster of ordered waters whose positions overlap the polar groups of the sugar substrate. Co-crystallization experiments led to a structure where substrate- and product-bound enzymes coexist within the same crystal. This equilibrium structure reveals the basis for a "swing and flip" rotation of the pro-chiral 4-keto-hexose-uronic acid intermediate that results from glucuronic acid oxidation, placing the C4' atom in position for receiving a hydride ion on the opposite side of the sugar ring. The product-bound active site is almost identical to that of the substrate-bound structure and satisfies all hydrogen-bonding requirements of the ligand. The structure of the apoenzyme together with the kinetic isotope effect and mutagenesis experiments further outlines a few flexible loops that exist in discrete conformations, imparting structural malleability required for ligand rotation while avoiding leakage of the catalytic intermediate and/or side reactions. These data highlight the double nature of the enzymatic mechanism: the active site features a high degree of precision in substrate recognition combined with the flexibility required for intermediate rotation.


Subject(s)
Bacillus cereus/enzymology , Bacterial Proteins/chemistry , Carbohydrate Epimerases/chemistry , Crystallography, X-Ray , Ligands , NAD/chemistry , Oxidation-Reduction , Rotation , Uridine Diphosphate Sugars/chemistry
6.
Glycobiology ; 29(12): 839-846, 2019 11 20.
Article in English | MEDLINE | ID: mdl-31679023

ABSTRACT

l-arabinofuranose is a ubiquitous component of the cell wall and various natural products in plants, where it is synthesized from cytosolic UDP-arabinopyranose (UDP-Arap). The biosynthetic machinery long remained enigmatic in terms of responsible enzymes and subcellular localization. With the discovery of UDP-Arap mutase in plant cytosol, the demonstration of its role in cell-wall arabinose incorporation and the identification of UDP-arabinofuranose transporters in the Golgi membrane, it is clear that the cytosolic UDP-Arap mutases are the key enzymes converting UDP-Arap to UDP-arabinofuranose for cell wall and natural product biosynthesis. This has recently been confirmed by several genotype/phenotype studies. In contrast to the solid evidence pertaining to UDP-Arap mutase function in vivo, the molecular features, including enzymatic mechanism and oligomeric state, remain unknown. However, these enzymes belong to the small family of proteins originally identified as reversibly glycosylated polypeptides (RGPs), which has been studied for >20 years. Here, we review the UDP-Arap mutase and RGP literature together, to summarize and systemize reported molecular characteristics and relations to other proteins.


Subject(s)
Intramolecular Transferases/chemistry , Intramolecular Transferases/metabolism , Oryza/enzymology , Uridine Diphosphate Sugars/chemistry , Uridine Diphosphate Sugars/metabolism , Biological Products/chemistry , Biological Products/metabolism , Cell Wall/chemistry , Cell Wall/metabolism , Oryza/cytology
7.
Molecules ; 24(17)2019 Aug 22.
Article in English | MEDLINE | ID: mdl-31443364

ABSTRACT

Isorhamnetin-3-O-rhamnoside was synthesized by a highly efficient three-enzyme (rhamnosyltransferase, glycine max sucrose synthase and uridine diphosphate (UDP)-rhamnose synthase) cascade using a UDP-rhamnose regeneration system. The rhamnosyltransferase gene (78D1) from Arabidopsis thaliana was cloned, expressed, and characterized in Escherichia coli. The optimal activity was at pH 7.0 and 45 °C. The enzyme was stable over the pH range of 6.5 to 8.5 and had a 1.5-h half-life at 45 °C. The Vmax and Km for isorhamnetin were 0.646 U/mg and 181 µM, respectively. The optimal pH and temperature for synergistic catalysis were 7.5 and 25 °C, and the optimal concentration of substrates were assayed, respectively. The highest titer of isorhamnetin-3-O-rhamnoside production reached 231 mg/L with a corresponding molar conversion of 100%. Isorhamnetin-3-O-rhamnoside was purified and the cytotoxicity against HepG2, MCF-7, and A549 cells were evaluated. Therefore, an efficient method for isorhamnetin-3-O-rhamnoside production described herein could be widely used for the rhamnosylation of flavonoids.


Subject(s)
Carbohydrate Epimerases/chemistry , Chemistry Techniques, Synthetic , Flavonols/chemical synthesis , Glucosyltransferases/chemistry , Hexosyltransferases/chemistry , Uridine Diphosphate Sugars/chemistry , Antineoplastic Agents/chemical synthesis , Antineoplastic Agents/pharmacology , Catalysis , Cell Line, Tumor , Flavonols/pharmacology , Humans
8.
Carbohydr Res ; 477: 20-25, 2019 May 15.
Article in English | MEDLINE | ID: mdl-30933787

ABSTRACT

UDP-apiose, a donor substrate of apiosyltransferases, is labile because of its intramolecular self-cyclization ability, resulting in the formation of apiofuranosyl-1,2-cyclic phosphate. Therefore, stabilization of UDP-apiose is indispensable for its availability and identifying and characterizing the apiosyltransferases involved in the biosynthesis of apiosylated sugar chains and glycosides. Here, we established a method for stabilizing UDP-apiose using bulky cations as counter ions. Bulky cations such as triethylamine effectively suppressed the degradation of UDP-apiose in solution. The half-life of UDP-apiose was increased to 48.1 ±â€¯2.4 h at pH 6.0 and 25 °C using triethylamine as a counter cation. UDP-apiose coordinated with a counter cation enabled long-term storage under freezing conditions. UDP-apiose was utilized as a donor substrate for apigenin 7-O-ß-D-glucoside apiosyltransferase to produce the apiosylated glycoside apiin. This apiosyltransferase assay will be useful for identifying genes encoding apiosyltransferases.


Subject(s)
Enzyme Assays/methods , Pentosyltransferases/metabolism , Uridine Diphosphate Sugars/chemical synthesis , Uridine Diphosphate Sugars/metabolism , Carbohydrate Conformation , Pentosyltransferases/genetics , Uridine Diphosphate Sugars/chemistry
9.
Biotechnol J ; 14(4)2019 Apr.
Article in English | MEDLINE | ID: mdl-30367549

ABSTRACT

The availability of nucleotide sugars is considered as bottleneck for Leloir-glycosyltransferases mediated glycan synthesis. A breakthrough for the synthesis of nucleotide sugars is the development of salvage pathway like enzyme cascades with high product yields from affordable monosaccharide substrates. In this regard, the authors aim at high enzyme productivities of these cascades by a repetitive batch approach. The authors report here for the first time that the exceptional high enzyme cascade stability facilitates the synthesis of Uridine-5'-diphospho-α-d-galactose (UDP-Gal), Uridine-5'-diphospho-N-acetylglucosamine (UDP-GlcNAc), and Uridine-5'-diphospho-N-acetylgalactosamine (UDP-GalNAc) in a multi-gram scale by repetitive batch mode. The authors obtained 12.8 g UDP-Gal through a high mass based total turnover number (TTNmass ) of 494 [gproduct /genzyme ] and space-time-yield (STY) of 10.7 [g/L*h]. Synthesis of UDP-GlcNAc in repetitive batch mode gave 11.9 g product with a TTNmass of 522 [gproduct /genzyme ] and a STY of 9.9 [g/L*h]. Furthermore, the scale-up to a 200 mL scale using a pressure operated concentrator was demonstrated for a UDP-GalNAc producing enzyme cascade resulting in an exceptional high STY of 19.4 [g/L*h] and 23.3 g product. In conclusion, the authors demonstrate that repetitive batch mode is a versatile strategy for the multi-gram scale synthesis of nucleotide sugars by stable enzyme cascades.


Subject(s)
Polysaccharides/chemistry , Uridine Diphosphate Galactose/biosynthesis , Uridine Diphosphate N-Acetylglucosamine/biosynthesis , Uridine Diphosphate Sugars/biosynthesis , Glycosyltransferases/chemistry , Nucleotides/biosynthesis , Nucleotides/chemistry , Transferases (Other Substituted Phosphate Groups)/chemistry , Uridine Diphosphate Galactose/chemistry , Uridine Diphosphate N-Acetylglucosamine/chemistry , Uridine Diphosphate Sugars/chemistry
10.
PLoS One ; 13(11): e0207521, 2018.
Article in English | MEDLINE | ID: mdl-30458018

ABSTRACT

SLC35B4 belongs to the solute carrier 35 (SLC35) family whose best-characterized members display a nucleotide sugar transporting activity. Using an experimental model of HepG2 cells and indirect immunofluorescent staining, we verified that SLC35B4 was localized to the endoplasmic reticulum (ER). We demonstrated that dilysine motif, especially lysine at position 329, is crucial for the ER localization of this protein in human cells and therefore one should use protein C-tagging with caution. To verify the importance of the protein in glycoconjugates synthesis, we generated SLC35B4-deficient HepG2 cell line using CRISPR-Cas9 approach. Our data showed that knock-out of the SLC35B4 gene does not affect major UDP-Xyl- and UDP-GlcNAc-dependent glycosylation pathways.


Subject(s)
Amino Acid Motifs/genetics , Endoplasmic Reticulum/chemistry , Golgi Apparatus/chemistry , Nucleotide Transport Proteins/chemistry , Amino Acid Sequence/genetics , CRISPR-Cas Systems/genetics , Dipeptides/chemistry , Dipeptides/genetics , Endoplasmic Reticulum/genetics , Glucosamine/analogs & derivatives , Glucosamine/chemistry , Glycosylation , Golgi Apparatus/genetics , Hep G2 Cells , Humans , Lysine/chemistry , Lysine/genetics , Nucleotide Transport Proteins/antagonists & inhibitors , Nucleotide Transport Proteins/genetics , Signal Transduction , Uridine Diphosphate Sugars/chemistry
11.
Methods Enzymol ; 597: 145-186, 2017.
Article in English | MEDLINE | ID: mdl-28935101

ABSTRACT

This method describes the chemoenzymatic synthesis of several nucleotide sugars, which are essential substrates in the biosynthesis of prokaryotic N- and O-linked glycoproteins. Protein glycosylation is now known to be widespread in prokaryotes and proceeds via sequential action of several enzymes, utilizing both common and modified prokaryote-specific sugar nucleotides. The latter, which include UDP-hexoses such as UDP-diNAc-bacillosamine (UDP-diNAcBac), UDP-diNAcAlt, and UDP-2,3-diNAcManA, are also important components of other bacterial and archaeal glycoconjugates. The ready availability of these "high-value" intermediates will enable courses of study into inhibitor screening, glycoconjugate biosynthesis pathway discovery, and unnatural carbohydrate incorporation toward metabolic engineering.


Subject(s)
Carbohydrates/biosynthesis , Glycoconjugates/genetics , Metabolic Engineering/methods , Uridine Diphosphate Sugars/biosynthesis , Archaea/chemistry , Archaea/genetics , Bacteria/chemistry , Bacteria/genetics , Carbohydrates/chemistry , Carbohydrates/genetics , Glycoconjugates/biosynthesis , Glycoconjugates/chemistry , Glycoproteins/chemistry , Glycoproteins/genetics , Glycosylation , Nucleotides/biosynthesis , Nucleotides/chemistry , Nucleotides/genetics , Uridine Diphosphate Sugars/chemistry , Uridine Diphosphate Sugars/genetics
12.
Sci Rep ; 7(1): 4139, 2017 06 23.
Article in English | MEDLINE | ID: mdl-28646159

ABSTRACT

In Bacillus subtilis, Listeria monocytogenes and in two Mycobacteria, it was previously shown that yvcK is a gene required for normal cell shape, for optimal carbon source utilization and for virulence of pathogenic bacteria. Here we report that the B. subtilis protein YvcK binds to Uridine diphosphate-sugars like Uridine diphosphate-Glucose (UDP-Glc) and Uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc) in vitro. Using the crystal structure of Bacillus halodurans YvcK, we identified residues involved in this interaction. We tested the effect of point mutations affecting the ability of YvcK to bind UDP-sugars on B. subtilis physiology and on cell size. Indeed, it was shown that UDP-Glc serves as a metabolic signal to regulate B. subtilis cell size. Interestingly, we observed that, whereas a yvcK deletion results in the formation of unusually large cells, inactivation of YvcK UDP-sugar binding site does not affect cell length. However, these point mutations result in an increased sensitivity to bacitracin, an antibiotic which targets peptidoglycan synthesis. We thus propose that UDP-GlcNAc, a precursor of peptidoglycan, could be a good physiological ligand candidate of YvcK.


Subject(s)
Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Cell Wall/genetics , Cell Wall/metabolism , Uridine Diphosphate Sugars/metabolism , Amino Acid Sequence , Bacitracin/chemistry , Bacitracin/pharmacology , Bacterial Physiological Phenomena , Bacterial Proteins/chemistry , Binding Sites , Carbon/metabolism , Gene Deletion , Gluconates , Models, Molecular , Molecular Conformation , Point Mutation , Protein Binding , Uridine Diphosphate Sugars/chemistry
13.
J Biol Chem ; 292(27): 11499-11507, 2017 07 07.
Article in English | MEDLINE | ID: mdl-28490633

ABSTRACT

The enzyme UDP-glucose:glycoprotein glucosyltransferase (UGGT) mediates quality control of glycoproteins in the endoplasmic reticulum by attaching glucose to N-linked glycan of misfolded proteins. As a sensor, UGGT ensures that misfolded proteins are recognized by the lectin chaperones and do not leave the secretory pathway. The structure of UGGT and the mechanism of its selectivity for misfolded proteins have been unknown for 25 years. Here, we used negative-stain electron microscopy and small-angle X-ray scattering to determine the structure of UGGT from Drosophila melanogaster at 18-Å resolution. Three-dimensional reconstructions revealed a cage-like structure with a large central cavity. Particle classification revealed flexibility that precluded determination of a high-resolution structure. Introduction of biotinylation sites into a fungal UGGT expressed in Escherichia coli allowed identification of the catalytic and first thioredoxin-like domains. We also used hydrogen-deuterium exchange mass spectrometry to map the binding site of an accessory protein, Sep15, to the first thioredoxin-like domain. The UGGT structural features identified suggest that the central cavity contains the catalytic site and is lined with hydrophobic surfaces. This enhances the binding of misfolded substrates with exposed hydrophobic residues and excludes folded proteins with hydrophilic surfaces. In conclusion, we have determined the UGGT structure, which enabled us to develop a plausible functional model of the mechanism for UGGT's selectivity for misfolded glycoproteins.


Subject(s)
Glucosyltransferases/chemistry , Protein Folding , Uridine Diphosphate Sugars/chemistry , Animals , Deuterium Exchange Measurement , Drosophila Proteins/chemistry , Drosophila Proteins/genetics , Drosophila Proteins/metabolism , Drosophila melanogaster , Glucosyltransferases/genetics , Glucosyltransferases/metabolism , Hydrophobic and Hydrophilic Interactions , Protein Domains , Selenoproteins/chemistry , Selenoproteins/genetics , Selenoproteins/metabolism , Uridine Diphosphate Sugars/genetics , Uridine Diphosphate Sugars/metabolism
14.
Acta Crystallogr F Struct Biol Commun ; 73(Pt 4): 241-245, 2017 04 01.
Article in English | MEDLINE | ID: mdl-28368284

ABSTRACT

The role of seemingly non-enzymatic proteins in complexes interconverting UDP-arabinopyranose and UDP-arabinofuranose (UDP-arabinosemutases; UAMs) in the plant cytosol remains unknown. To shed light on their function, crystallographic and functional studies of the seemingly non-enzymatic UAM2 protein from Oryza sativa (OsUAM2) were undertaken. Here, X-ray diffraction data are reported, as well as analysis of the oligomeric state in the crystal and in solution. OsUAM2 crystallizes readily but forms highly radiation-sensitive crystals with limited diffraction power, requiring careful low-dose vector data acquisition. Using size-exclusion chromatography, it is shown that the protein is monomeric in solution. Finally, limited proteolysis was employed to demonstrate DTT-enhanced proteolytic digestion, indicating the existence of at least one intramolecular disulfide bridge or, alternatively, a requirement for a structural metal ion.


Subject(s)
Intramolecular Transferases/chemistry , Oryza/chemistry , Plant Proteins/chemistry , Uridine Diphosphate Sugars/chemistry , Amino Acid Sequence , Cloning, Molecular , Crystallization , Crystallography, X-Ray , Dithiothreitol/chemistry , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Genetic Vectors/chemistry , Genetic Vectors/metabolism , Intramolecular Transferases/genetics , Intramolecular Transferases/metabolism , Oryza/enzymology , Plant Proteins/genetics , Plant Proteins/metabolism , Proteolysis , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Subtilisin/chemistry , Uridine Diphosphate Sugars/metabolism , X-Ray Diffraction
15.
Biochim Biophys Acta Proteins Proteom ; 1865(5): 510-519, 2017 May.
Article in English | MEDLINE | ID: mdl-28192204

ABSTRACT

UDP-arabinopyranose mutase (UAM) is a plant enzyme which interconverts UDP-arabinopyranose (UDP-Arap; a six-membered sugar) to UDP-arabinofuranose (UDP-Araf; a five-membered sugar). Plant mutases belong to a small gene family called Reversibly Glycosylated Proteins (RGPs). So far, UAM has been identified in Oryza sativa (Rice), Arabidopsis thaliana and Hordeum vulgare (Barley). The enzyme requires divalent metal ions for catalytic activity. Here, the divalent metal ion dependency of UAMs from O. sativa (rice) and A. thaliana have been studied using HPLC-based kinetic assays. It was determined that UAM from these species had the highest relative activity in a range of 40-80µM Mn2+. Excess Mn2+ ion concentration decreased the enzyme activity. This trend was observed when other divalent metal ions were used to test activity. To gain a perspective of the role played by the metal ion in activity, an ab initio structural model was generated based on the UAM amino acid sequence and a potential metal binding region was identified. Based on our results, we propose that the probable role of the metal in UAM is stabilizing the diphosphate of the substrate, UDP-Arap.


Subject(s)
Arabidopsis/enzymology , Intramolecular Transferases/chemistry , Oryza/enzymology , Uridine Diphosphate Sugars/chemistry , Binding Sites , Catalysis , Cell Wall/enzymology , Gene Expression Regulation, Plant , Intramolecular Transferases/genetics , Intramolecular Transferases/metabolism , Ions/chemistry , Kinetics , Metals/chemistry , Protein Binding , Uridine Diphosphate Sugars/metabolism
16.
J Org Chem ; 82(4): 2243-2248, 2017 02 17.
Article in English | MEDLINE | ID: mdl-28128958

ABSTRACT

Unnatural uridine diphosphate (UDP)-sugar donors, UDP-4-deoxy-4-fluoro-N-acetylglucosamine (4FGlcNAc) and UDP-4-deoxy-4-fluoro-N-acetylgalactosamine (4FGalNAc), were prepared using both chemical and chemoenzymatic syntheses relying on N-acetylglucosamine-1-phosphate uridylyltransferase (GlmU). The resulting unnatural UDP-sugar donors were then tested as substrates in glycosaminoglycan synthesis catalyzed by various synthases. UDP-4FGlcNAc was transferred onto an acceptor by Pastuerella multocida heparosan synthase 1 and subsequently served as a chain terminator.


Subject(s)
Glycosaminoglycans/biosynthesis , Nucleotidyltransferases/metabolism , Biocatalysis , Carbohydrate Conformation , Glycosaminoglycans/chemistry , Nucleotidyltransferases/chemistry , Uridine Diphosphate Sugars/biosynthesis , Uridine Diphosphate Sugars/chemistry
17.
Plant Cell Rep ; 35(11): 2403-2421, 2016 Nov.
Article in English | MEDLINE | ID: mdl-27591771

ABSTRACT

KEY MESSAGE: The present study first identified the involvement of OcUAXS2 and OcUXS1-3 in anticancer polysaccharides biosynthesis in O. caudatum. UDP-xylose synthase (UXS) and UDP-D-apiose/UDP-D-xylose synthase (UAXS), both capable of converting UDP-D-glucuronic acid to UDP-D-xylose, are believed to transfer xylosyl residue to anticancer polysaccharides biosynthesis in Ornithogalum caudatum Ait. However, the cDNA isolation and functional characterization of genes encoding the two enzymes from O. caudatum has never been documented. Previously, the transcriptome sequencing of O. caudatum was performed in our laboratory. In this study, a total of six and two unigenes encoding UXS and UAXS were first retrieved based on RNA-Seq data. The eight putative genes were then successfully isolated from transcriptome of O. caudatum by reverse transcription polymerase chain reaction (RT-PCR). Phylogenetic analysis revealed the six putative UXS isoforms can be classified into three types, one soluble and two distinct putative membrane-bound. Moreover, the two UAXS isoenzymes were predicted to be soluble forms. Subsequently, these candidate cDNAs were characterized to be bona fide genes by functional expression in Escherichia coli individually. Although UXS and UAXS catalyzed the same reaction, their biochemical properties varied significantly. It is worth noting that a ratio switch of UDP-D-xylose/UDP-D-apiose for UAXS was established, which is assumed to be helpful for its biotechnological application. Furthermore, a series of mutants were generated to test the function of NAD+ binding motif GxxGxxG. Most importantly, the present study determined the involvement of OcUAXS2 and OcUXS1-3 in xylose-containing polysaccharides biosynthesis in O. caudatum. These data provide a comprehensive knowledge for UXS and UAXS families in plants.


Subject(s)
Carboxy-Lyases/genetics , Genes, Plant , Multigene Family , Ornithogalum/enzymology , Ornithogalum/genetics , Transcriptome/genetics , Uridine Diphosphate Sugars/metabolism , Uridine Diphosphate Xylose/metabolism , Amino Acid Motifs , Amino Acid Sequence , Ammonium Compounds/pharmacology , Biocatalysis/drug effects , Buffers , Calcium/pharmacology , Carboxy-Lyases/chemistry , Carboxy-Lyases/metabolism , Chromatography, High Pressure Liquid , DNA, Complementary/genetics , DNA, Complementary/isolation & purification , Hydrogen-Ion Concentration , Kinetics , Organ Specificity/drug effects , Organ Specificity/genetics , Ornithogalum/drug effects , Proton Magnetic Resonance Spectroscopy , RNA, Messenger/genetics , RNA, Messenger/metabolism , Recombinant Proteins/metabolism , Sequence Alignment , Sequence Analysis, DNA , Temperature , Transcriptome/drug effects , Uridine Diphosphate Sugars/chemistry , Uridine Diphosphate Xylose/chemistry
18.
Protein Sci ; 25(8): 1555-62, 2016 08.
Article in English | MEDLINE | ID: mdl-27171345

ABSTRACT

ArnA from Escherichia coli is a key enzyme involved in the formation of 4-amino-4-deoxy-l-arabinose. The addition of this sugar to the lipid A moiety of the lipopolysaccharide of pathogenic Gram-negative bacteria allows these organisms to evade the cationic antimicrobial peptides of the host immune system. Indeed, it is thought that such modifications may be responsible for the repeated infections of cystic fibrosis patients with Pseudomonas aeruginosa. ArnA is a bifunctional enzyme with the N- and C-terminal domains catalyzing formylation and oxidative decarboxylation reactions, respectively. The catalytically competent cofactor for the formylation reaction is N(10) -formyltetrahydrofolate. Here we describe the structure of the isolated N-terminal domain of ArnA in complex with its UDP-sugar substrate and N(5) -formyltetrahydrofolate. The model presented herein may prove valuable in the development of new antimicrobial therapeutics.


Subject(s)
Amino Sugars/chemistry , Carboxy-Lyases/chemistry , Coenzymes/chemistry , Escherichia coli/chemistry , Formyltetrahydrofolates/chemistry , Uridine Diphosphate Sugars/chemistry , Amino Sugars/metabolism , Carboxy-Lyases/genetics , Carboxy-Lyases/metabolism , Cloning, Molecular , Coenzymes/metabolism , Escherichia coli/enzymology , Escherichia coli/genetics , Formyltetrahydrofolates/metabolism , Gene Expression , Models, Molecular , Protein Domains , Protein Structure, Secondary , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Uridine Diphosphate Sugars/metabolism
19.
Glycobiology ; 26(10): 1059-1071, 2016 10.
Article in English | MEDLINE | ID: mdl-27233805

ABSTRACT

P-selectin glycoprotein ligand-1 (PSGL-1, CD162) is a cell-surface glycoprotein that is expressed, either constitutively or inducibly, on all myeloid and lymphoid cell lineages. PSGL-1 is implicated in cell-cell interactions between platelets, leukocytes and endothelial cells, and a key mediator of inflammatory cell recruitment and transmigration into tissues. Here, we have investigated the effects of the ß-1,4-galactosyltransferase inhibitor 5-(5-formylthien-2-yl) UDP-Gal (5-FT UDP-Gal, compound 1: ) and two close derivatives on the cell surface levels of PSGL-1 on human peripheral blood mononuclear cells (hPBMCs). PSGL-1 levels were studied both under basal conditions, and upon stimulation of hPBMCs with interleukin-1ß (IL-1ß). Between 1 and 24 hours after IL-1ß stimulation, we observed initial PSGL-1 shedding, followed by an increase in PSGL-1 levels on the cell surface, with a maximal window between IL-1ß-induced and basal levels after 72 h. All three inhibitors reduce PSGL-1 levels on IL-1ß-stimulated cells in a concentration-dependent manner, but show no such effect in resting cells. Compound 1: also affects the cell surface levels of adhesion molecule CD11b in IL-1ß-stimulated hPBMCs, but not of glycoproteins CD14 and CCR2. This activity profile may be linked to the inhibition of global Sialyl Lewis presentation on hPBMCs by compound 1: , which we have also observed. Although this mechanistic explanation remains hypothetical at present, our results show, for the first time, that small molecules can discriminate between IL-1ß-induced and basal levels of cell surface PSGL-1. These findings open new avenues for intervention with PSGL-1 presentation on the cell surface of primed hPBMCs and may have implications for anti-inflammatory drug development.


Subject(s)
Interleukin-1beta/metabolism , Leukocytes, Mononuclear/drug effects , Membrane Glycoproteins/antagonists & inhibitors , Uridine Diphosphate Sugars/pharmacology , Carbohydrate Conformation , Dose-Response Relationship, Drug , Humans , Leukocytes, Mononuclear/metabolism , Membrane Glycoproteins/metabolism , Structure-Activity Relationship , Uridine Diphosphate Sugars/chemistry
20.
Arch Biochem Biophys ; 597: 21-9, 2016 05 01.
Article in English | MEDLINE | ID: mdl-27036853

ABSTRACT

The storage polymer glycogen normally contains small amounts of covalently attached phosphate as phosphomonoesters at C2, C3 and C6 atoms of glucose residues. In the absence of the laforin phosphatase, as in the rare childhood epilepsy Lafora disease, the phosphorylation level is elevated and is associated with abnormal glycogen structure that contributes to the pathology. Laforin therefore likely functions in vivo as a glycogen phosphatase. The mechanism of glycogen phosphorylation is less well-understood. We have reported that glycogen synthase incorporates phosphate into glycogen via a rare side reaction in which glucose-phosphate rather than glucose is transferred to a growing polyglucose chain (Tagliabracci et al. (2011) Cell Metab13, 274-282). We proposed a mechanism to account for phosphorylation at C2 and possibly at C3. Our results have since been challenged (Nitschke et al. (2013) Cell Metab17, 756-767). Here we extend the evidence supporting our conclusion, validating the assay used for the detection of glycogen phosphorylation, measurement of the transfer of (32)P from [ß-(32)P]UDP-glucose to glycogen by glycogen synthase. The (32)P associated with the glycogen fraction was stable to ethanol precipitation, SDS-PAGE and gel filtration on Sephadex G50. The (32)P-signal was not affected by inclusion of excess unlabeled UDP before analysis or by treatment with a UDPase, arguing against the signal being due to contaminating [ß-(32)P]UDP generated in the reaction. Furthermore, [(32)P]UDP did not bind non-covalently to glycogen. The (32)P associated with glycogen was released by laforin treatment, suggesting that it was present as a phosphomonoester. The conclusion is that glycogen synthase can mediate the introduction of phosphate into glycogen, thereby providing a possible mechanism for C2, and perhaps C3, phosphorylation.


Subject(s)
Glycogen Synthase/chemistry , Glycogen/chemistry , Phosphates/chemistry , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae/enzymology , Glycogen/biosynthesis , Glycogen Synthase/metabolism , Humans , Phosphates/metabolism , Protein Tyrosine Phosphatases, Non-Receptor/chemistry , Protein Tyrosine Phosphatases, Non-Receptor/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Uridine Diphosphate Sugars/chemistry , Uridine Diphosphate Sugars/metabolism
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