7132-58-3

Upstream product

• 2196-62-5 thymidine 5'-(α-D-glucopyranosyl diphosphate) 
• 365-08-2 dTTP 
• 59-56-3 α-D-glucopyranosyl-1-phosphate 
• 365-07-1 thymidine 5'-phosphate 
• 260430-88-4 C₂₀H₁₉O₁₀P 

Relevant academic research and scientific papers

Cloning and in vitro characterization of dTDP-6-deoxy-l-talose biosynthetic genes from Kitasatospora kifunensis featuring the dTDP-6-deoxy-l-lyxo-4- hexulose reductase that synthesizes dTDP-6-deoxy-l-talose

Kitasatospora kifunensis, the talosin producer, was used as a source for the dTDP-6-deoxy-l-talose (dTDP-6dTal) biosynthetic gene cluster, serving as a template for four recombinant proteins of RmlAKkf, RmlB Kkf, RmlCKkf, and Tal, which complete the biosynthesis of dTDP-6dTal from dTTP, α-d-glucose-1-phosphate, and NAD(P)H. The identity of dTDP-6dTal was validated using 1H and 13C NMR spectroscopy. K. kifunensis tal and tll, the known dTDP-6dTal synthase gene of Actinobacillus actinomycetemcomitans origin, have low sequence similarity and are distantly related within the NDP-6-deoxy-4-ketohexose reductase family, providing an example of the genetic diversity within the dTDP-6dTal biosynthetic pathway.

Mechanistic studies of the radical S-adenosyl-l-methionine enzyme DesII: EPR characterization of a radical intermediate generated during its catalyzed dehydrogenation of TDP-d-quinovose

DesII, a radical S-adenosyl-l-methionine (SAM) enzyme from Streptomyces venezuelae, catalyzes the deamination of TDP-4-amino-4,6-dideoxy-d-glucose to TDP-3-keto-4,6-dideoxy-d-glucose in the desosamine biosynthetic pathway. DesII can also catalyze the dehydrogenation of TDP-d-quinovose to the corresponding 3-keto sugar. Similar to other radical SAM enzymes, DesII catalysis has been proposed to proceed via a radical mechanism. This hypothesis is now confirmed by EPR spectroscopy with the detection of a TDP-d-quinovose radical intermediate having a g-value of 2.0025 with hyperfine coupling to two spin 1/2 nuclei, each with a splitting constant of 33.6 G. A significant decrease in the EPR line width is observed when the radical is generated in reactions conducted in D 2O versus H2O. These results are consistent with a C3 β-hydroxyalkyl radical in which the p-orbital harboring the unpaired electron spin at C3 is periplanar with the C-H bonds at both C2 and C4.

Investigation of the enzymes required for the biosynthesis of an unusual formylated sugar in the emerging human pathogen Helicobacter canadensis

It is now well established that the Gram-negative bacterium, Helicobacter pylori, causes gastritis in humans. In recent years, it has become apparent that the so-called non-pylori Helicobacters, normally infecting pigs, cats, and dogs, may also be involved in human pathology via zoonotic transmission. Indeed, more than 30 species of non-pylori Helicobacters have been identified thus far. One such organism is Helicobacter canadensis, an emerging pathogen whose genome sequence was published in 2009. Given our long-standing interest in the biosynthesis of N-formylated sugars found in the O-antigens of some Gram-negative bacteria, we were curious as to whether H. canadensis produces such unusual carbohydrates. Here, we demonstrate using both biochemical and structural techniques that the proteins encoded by the HCAN_0198, HCAN_0204, and HCAN_0200 genes in H. canadensis, correspond to a 3,4-ketoisomerase, a pyridoxal 5′-phosphate aminotransferase, and an N-formyltransferase, respectively. For this investigation, five high-resolution X-ray structures were determined and the kinetic parameters for the isomerase and the N-formyltransferase were measured. Based on these data, we suggest that the unusual sugar, 3-formamido-3,6-dideoxy-d-glucose, will most likely be found in the O-antigen of H. canadensis. Whether N-formylated sugars found in the O-antigen contribute to virulence is presently unclear, but it is intriguing that they have been observed in such pathogens as Francisella tularensis, Mycobacterium tuberculosis, and Brucella melitensis.

Stoichiometry of the redox neutral deamination and oxidative dehydrogenation reactions catalyzed by the radical SAM enzyme desll

Desll from Streptomyces venezuelae is a radical SAM (S-adenosyl-L- methionine) enzyme that catalyzes the deamination of TDP-4-amino-4,6-dideoxy-D- glucose to form TDP-3-keto-4,6-dideoxy-D-glucose in the biosynthesis of TDP-D-desosamine. Desll also catalyzes the dehydrogenation of the nonphysiological substrate TDP-D-quinovose to TDP-3-keto-6-deoxy-D-glucose. These properties prompted an investigation of how Desll handles SAM in the redox neutral deamination versus the oxidative dehydrogenation reactions. This work was facilitated by the development of an enzymatic synthesis of TDP-4-amino-4,6-dideoxy-Dglucose that couples a transamination equilibrium to the thermodynamically favorable oxidation of formate. In this study, Desll is found to consume SAM versus TDP-sugar with stoichiometries of 0.96 ± 0.05 and 1.01 ± 0.05 in the deamination and dehydrogenation reactions, respectively, using Na2S2O4 as the reductant. Importantly, no significant change in stoichiometry is observed when the flavodoxin/flavodoxin NADP+ oxidoreductase/NADPH reducing system is used in place of Na2S2O4. Moreover, there is no evidence of an uncoupled or abortive process in the deamination reaction, as indicated by the observation that dehydrogenation can take place in the absence of an external source of reductant whereas deamination cannot. Mechanistic and biochemical implications of these results are discussed.

Structure and mechanism of ORF36, an amino sugar oxidizing enzyme in everninomicin biosynthesis

Everninomicin is a highly modified octasaccharide that belongs to the orthosomycin family of antibiotics and possesses potent Gram-positive antibiotic activity, including broad-spectrum efficacy against multidrug resistant enterococci and Staphylococcus aureus. Among its distinctive structural features is a nitro sugar, l-evernitrose, analogues of which decorate a variety of natural products. Recently, we identified a nitrososynthase enzyme encoded by orf36 from Micromonospora carbonacea var. africana that mediates the flavin-dependent double oxidation of synthetically generated thymidine diphosphate (TDP)-l-epi-vancosamine to the corresponding nitroso sugar. Herein, we utilize a five-enzyme in vitro pathway both to verify that ORF36 catalyzes oxidation of biogenic TDP-l-epi-vancosamine and to determine whether ORF36 exhibits catalytic competence for any of its biosynthetic progenitors, which are candidate substrates for nitrososynthases in vivo. Progenitors solely undergo single-oxidation reactions and terminate in the hydroxylamine oxidation state. Performing the in vitro reactions in the presence of 18O2 establishes that molecular oxygen, rather than oxygen from water, is incorporated into ORF36-generated intermediates and products and identifies an off-pathway product that correlates with the oxidation product of a progenitor substrate. The 3.15 A resolution X-ray crystal structure of ORF36 reveals a tetrameric enzyme that shares a fold with acyl-CoA dehydrogenases and class D flavin-containing monooxygenases, including the nitrososynthase KijD3. However, ORF36 and KijD3 have unusually open active sites in comparison to these related enzymes. Taken together, these studies map substrate determinants and allow the proposal of a minimal monooxygenase mechanism for amino sugar oxidation by ORF36.

One-pot four-enzyme synthesis of thymidinediphosphate-l-rhamnose

A new, robust one-pot four-enzyme synthetic method was developed for thymidinediphosphate-l-rhamnose starting from d-glucose-1-phosphate. The enzymes, Glc-1-P thymidylyltransferase, dTDP-Glc-4,6-dehydratase, dTDP-4-keto-6-deoxy-Glc-3,5-epimerase and dTDP-4-keto-Rha reductase were derived from Streptococcus pneumonia serotype 23F, expressed in Escherichia coli, and studied in detail to provide the first direct evidence for their functions.

Characterization of the TDP-d-ravidosamine biosynthetic pathway: One-pot enzymatic synthesis of TDP-d-ravidosamine from thymidine-5-phosphate and glucose-1-phosphate

Ravidomycin V and related compounds, e.g., FE35A-B, exhibit potent anticancer activities against various cancer cell lines in the presence of visible light. The amino sugar moieties (d-ravidosamine and its analogues, respectively) in these molecules contribute to the higher potencies of ravidomycin and analogues when compared to closely related compounds with neutral or branched sugars. Within the ravidomycin V biosynthetic gene cluster, five putative genes encoding NDP-d-ravidosamine biosynthetic enzymes were identified. Through the activities of the isolated enzymes in vitro, it is demonstrated that ravD, ravE, ravIM, ravAMT and ravNMT encode TDP-d-glucose synthase, TDP-4-keto-6-deoxy-d-glucose-4,6-dehydratase, TDP-4-keto-6-deoxy-d- glucose-3,4-ketoisomerase, TDP-3-keto-6-deoxy-d-galactose-3-aminotransferase, and TDP-3-amino-3,6-dideoxy-d-galactose-N,N-dimethyl-transferase, respectively. A protocol for a one-pot enzymatic synthesis of TDP-d-ravidosamine has been developed. The results presented here now set the stage to produce TDP-d-ravidosamine routinely for glycosylation studies.

A convenient route to keto-glycosyl phosphates

The reagent combination, ruthenium dioxide/sodium periodate/benzyltriethyl ammonium chloride in dichloromethane/aqueous bicarbonate buffer simultaneously oxidises alcohol functions in the sugar ring and glycosyl H-phosphonates to yield keto-glycosyl phosphates. These can be coupled to the respective nucleoside diphosphates to render biosynthetically relevant sugar metabolites and derivatives thereof, useful for further investigation of the polysaccharide biosynthesis in bacteria and plants.

Synthesen von dTDP-6-Desoxy-4-ketoglucose und deren Analoga mit nativer und rekombinanter dTDP-Glucose-4,6-dehydratase

Keywords: Biotechnologie; Chromatographie; Dehydratasen; Desoxyzucker; Enzyme