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Carretero-Molina D, Ortiz-López FJ, Gren T, Oves-Costales D, Martín J, Román-Hurtado F, Sparholt Jørgensen T, de la Cruz M, Díaz C, Vicente F, Blin K, Reyes F, Weber T, Genilloud O. Discovery of gargantulides B and C, new 52-membered macrolactones from Amycolatopsis sp. Complete absolute stereochemistry of the gargantulide family. Org Chem Front 2022. [DOI: 10.1039/d1qo01480c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Gargantulides B and C are among the most complex bacterial polyketides discovered so far. A combination of NMR and genome-based bioinformatics analyses allowed us to complete and revise the absolute stereochemistry of the entire gargantulide family.
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Affiliation(s)
- Daniel Carretero-Molina
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Francisco Javier Ortiz-López
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Tetiana Gren
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark
| | - Daniel Oves-Costales
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Fernando Román-Hurtado
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Tue Sparholt Jørgensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark
| | - Mercedes de la Cruz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Caridad Díaz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Francisca Vicente
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
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2
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Thoden JB, Vinogradov E, Gilbert M, Salinger AJ, Holden HM. Bacterial Sugar 3,4-Ketoisomerases: Structural Insight into Product Stereochemistry. Biochemistry 2015; 54:4495-506. [PMID: 26125548 DOI: 10.1021/acs.biochem.5b00541] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
3-Acetamido-3,6-dideoxy-d-galactose (Fuc3NAc) and 3-acetamido-3,6-dideoxy-d-glucose (Qui3NAc) are unusual sugars found on the lipopolysaccharides of Gram-negative bacteria and on the S-layers of Gram-positive bacteria. The 3,4-ketoisomerases, referred to as FdtA and QdtA, catalyze the third steps in the respective biosynthetic pathways for these sugars. Whereas both enzymes utilize the same substrate, the stereochemistries of their products are different. Specifically, the hydroxyl groups at the hexose C-4' positions assume the "galactose" and "glucose" configurations in the FdtA and QdtA products, respectively. In 2007 we reported the structure of the apoform of FdtA from Aneurinibacillus thermoaerophilus, which was followed in 2014 by the X-ray analysis of QdtA from Thermoanaerobacterium thermosaccharolyticum as a binary complex. Both of these enzymes belong to the cupin superfamily. Here we report a combined structural and enzymological study to explore the manner in which these enzymes control the stereochemistry of their products. Various site-directed mutant proteins of each enzyme were constructed, and their dTDP-sugar products were analyzed by NMR spectroscopy. In addition, the kinetic parameters for these protein variants were measured, and the structure of one, namely, the QdtA Y17R/R97H double mutant form, was determined to 2.3-Å resolution. Finally, in an attempt to obtain a model of FdtA with a bound dTDP-linked sugar, the 3,4-ketoisomerase domain of a bifunctional enzyme from Shewanella denitrificans was cloned, purified, and crystallized in the presence of a dTDP-linked sugar analogue. Taken together, the results from this investigation demonstrate that it is possible to convert a "galacto" enzyme into a "gluco" enzyme and vice versa.
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Affiliation(s)
- James B Thoden
- †Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Evgeny Vinogradov
- ‡Human Health Therapeutics, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario Canada, K1A OR6
| | - Michel Gilbert
- ‡Human Health Therapeutics, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario Canada, K1A OR6
| | - Ari J Salinger
- †Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Hazel M Holden
- †Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
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3
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Thoden JB, Holden HM. The molecular architecture of QdtA, a sugar 3,4-ketoisomerase from Thermoanaerobacterium thermosaccharolyticum. Protein Sci 2014; 23:683-92. [PMID: 24616215 DOI: 10.1002/pro.2451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 03/01/2014] [Accepted: 03/03/2014] [Indexed: 11/05/2022]
Abstract
Unusual di- and trideoxysugars are often found on the O-antigens of Gram-negative bacteria, on the S-layers of Gram-positive bacteria, and on various natural products. One such sugar is 3-acetamido-3,6-dideoxy-D-glucose. A key step in its biosynthesis, catalyzed by a 3,4-ketoisomerase, is the conversion of thymidine diphosphate (dTDP)-4-keto-6-deoxyglucose to dTDP-3-keto-6-deoxyglucose. Here we report an X-ray analysis of a 3,4-ketoisomerase from Thermoanaerobacterium thermosaccharolyticum. For this investigation, the wild-type enzyme, referred to as QdtA, was crystallized in the presence of dTDP and its structure solved to 2.0-Å resolution. The dimeric enzyme adopts a three-dimensional architecture that is characteristic for proteins belonging to the cupin superfamily. In order to trap the dTDP-4-keto-6-deoxyglucose substrate into the active site, a mutant protein, H51N, was subsequently constructed, and the structure of this protein in complex with the dTDP-sugar ligand was solved to 1.9-Å resolution. Taken together, the structures suggest that His 51 serves as a catalytic base, that Tyr 37 likely functions as a catalytic acid, and that His 53 provides a proton shuttle between the C-3' hydroxyl and the C-4' keto group of the hexose. This study reports the first three-dimensional structure of a 3,4-ketoisomerase in complex with its dTDP-sugar substrate and thus sheds new molecular insight into this fascinating class of enzymes.
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Affiliation(s)
- James B Thoden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706
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4
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Chantigian DP, Thoden JB, Holden HM. Structural and biochemical characterization of a bifunctional ketoisomerase/N-acetyltransferase from Shewanella denitrificans. Biochemistry 2013; 52:8374-85. [PMID: 24128043 DOI: 10.1021/bi401170t] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Unusual N-acetylated sugars have been observed on the O-antigens of some Gram-negative bacteria and on the S-layers of both Gram-positive and Gram-negative bacteria. One such sugar is 3-acetamido-3,6-dideoxy-α-d-galactose or Fuc3NAc. The pathway for its production requires five enzymes with the first step involving the attachment of dTMP to glucose-1-phosphate. Here, we report a structural and biochemical characterization of a bifunctional enzyme from Shewanella denitificans thought to be involved in the biosynthesis of dTDP-Fuc3NAc. On the basis of a bioinformatics analysis, the enzyme, hereafter referred to as FdtD, has been postulated to catalyze the third and fifth steps in the pathway, namely, a 3,4-keto isomerization and an N-acetyltransferase reaction. For the X-ray analysis reported here, the enzyme was crystallized in the presence of dTDP and CoA. The crystal structure shows that FdtD adopts a hexameric quaternary structure with 322 symmetry. Each subunit of the hexamer folds into two distinct domains connected by a flexible loop. The N-terminal domain adopts a left-handed β-helix motif and is responsible for the N-acetylation reaction. The C-terminal domain folds into an antiparallel flattened β-barrel that harbors the active site responsible for the isomerization reaction. Biochemical assays verify the two proposed catalytic activities of the enzyme and reveal that the 3,4-keto isomerization event leads to the inversion of configuration about the hexose C-4' carbon.
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Affiliation(s)
- Daniel P Chantigian
- Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
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5
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Borisova SA, Liu HW. Characterization of glycosyltransferase DesVII and its auxiliary partner protein DesVIII in the methymycin/picromycin biosynthetic pathway. Biochemistry 2010; 49:8071-84. [PMID: 20695498 DOI: 10.1021/bi1007657] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The in vitro characterization of the catalytic activity of DesVII, the glycosyltransferase involved in the biosynthesis of the macrolide antibiotics methymycin, neomethymycin, narbomycin, and pikromycin in Streptomyces venezuelae, is described. DesVII is unique among glycosyltransferases in that it requires an additional protein component, DesVIII, for activity. Characterization of the metabolites produced by a S. venezuelae mutant lacking the desVIII gene confirmed that desVIII is important for the biosynthesis of glycosylated macrolides but can be replaced by at least one of the homologous genes from other pathways. The addition of recombinant DesVIII protein significantly improves the glycosylation efficiency of DesVII in the in vitro assay. When affinity-tagged DesVII and DesVIII proteins were coproduced in Escherichia coli, they formed a tight (αβ)(3) complex that is at least 10(3)-fold more active than DesVII alone. The formation of the DesVII/DesVIII complex requires coexpression of both genes in vivo and cannot be fully achieved by mixing the individual protein components in vitro. The ability of the DesVII/DesVIII system to catalyze the reverse reaction with the formation of TDP-desosamine was also demonstrated in a transglycosylation experiment. Taken together, our data suggest that DesVIII assists the folding of DesVII during protein production and remains tightly bound during catalysis. This requirement must be taken into consideration in the design of combinatorial biosynthetic experiments with new glycosylated macrolides.
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Affiliation(s)
- Svetlana A Borisova
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712, USA
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6
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Hutchinson E, Murphy B, Dunne T, Breen C, Rawlings B, Caffrey P. Redesign of polyene macrolide glycosylation: engineered biosynthesis of 19-(O)-perosaminyl-amphoteronolide B. ACTA ACUST UNITED AC 2010; 17:174-82. [PMID: 20189107 DOI: 10.1016/j.chembiol.2010.01.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Revised: 12/03/2009] [Accepted: 01/11/2010] [Indexed: 11/17/2022]
Abstract
Most polyene macrolide antibiotics are glycosylated with mycosamine (3,6-dideoxy-3-aminomannose). In the amphotericin B producer, Streptomyces nodosus, mycosamine biosynthesis begins with AmphDIII-catalyzed conversion of GDP-mannose to GDP-4-keto-6-deoxymannose. This is converted to GDP-3-keto-6-deoxymannose, which is transaminated to GDP-mycosamine by the AmphDII protein. The glycosyltransferase AmphDI transfers mycosamine to amphotericin aglycones (amphoteronolides). The aromatic heptaene perimycin is unusual among polyenes in that the sugar is perosamine (4,6-dideoxy-4-aminomannose), which is synthesized by direct transamination of GDP-4-keto-6-deoxymannose. Here, we use the Streptomyces aminophilus perDII perosamine synthase and perDI perosaminyltransferase genes to engineer biosynthesis of perosaminyl-amphoteronolide B in S. nodosus. Efficient production required a hybrid glycosyltransferase containing an N-terminal region of AmphDI and a C-terminal region of PerDI. This work will assist efforts to generate glycorandomized amphoteronolides for drug discovery.
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Affiliation(s)
- Eve Hutchinson
- School of Biomolecular and Biomedical Science and Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
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Gu X, Glushka J, Yin Y, Xu Y, Denny T, Smith J, Jiang Y, Bar-Peled M. Identification of a bifunctional UDP-4-keto-pentose/UDP-xylose synthase in the plant pathogenic bacterium Ralstonia solanacearum strain GMI1000, a distinct member of the 4,6-dehydratase and decarboxylase family. J Biol Chem 2010; 285:9030-40. [PMID: 20118241 DOI: 10.1074/jbc.m109.066803] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The UDP-sugar interconverting enzymes involved in UDP-GlcA metabolism are well described in eukaryotes but less is known in prokaryotes. Here we identify and characterize a gene (RsU4kpxs) from Ralstonia solanacearum str. GMI1000, which encodes a dual function enzyme not previously described. One activity is to decarboxylate UDP-glucuronic acid to UDP-beta-l-threo-pentopyranosyl-4''-ulose in the presence of NAD(+). The second activity converts UDP-beta-l-threo-pentopyranosyl-4''-ulose and NADH to UDP-xylose and NAD(+), albeit at a lower rate. Our data also suggest that following decarboxylation, there is stereospecific protonation at the C5 pro-R position. The identification of the R. solanacearum enzyme enables us to propose that the ancestral enzyme of UDP-xylose synthase and UDP-apiose/UDP-xylose synthase was diverged to two distinct enzymatic activities in early bacteria. This separation gave rise to the current UDP-xylose synthase in animal, fungus, and plant as well as to the plant Uaxs and bacterial ArnA and U4kpxs homologs.
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Affiliation(s)
- Xiaogang Gu
- Department of Biochemistry and Molecular Biology, and the Institute of Bioinformatics, Universityof Georgia, Complex Carbohydrate Research Center, Athens, Georgia 30602, USA
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Cipolla L, Gabrielli L, Bini D, Russo L, Shaikh N. Kdo: a critical monosaccharide for bacteria viability. Nat Prod Rep 2010; 27:1618-29. [DOI: 10.1039/c004750n] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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9
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Sommaruga S, Gioia LD, Tortora P, Polissi A. Structure prediction and functional analysis of KdsD, an enzyme involved in lipopolysaccharide biosynthesis. Biochem Biophys Res Commun 2009; 388:222-7. [DOI: 10.1016/j.bbrc.2009.07.154] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Accepted: 07/28/2009] [Indexed: 10/20/2022]
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10
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Errey JC, Mann MC, Fairhurst SA, Hill L, McNeil MR, Naismith JH, Percy JM, Whitfield C, Field RA. Sugar nucleotide recognition by Klebsiella pneumoniae UDP-D-galactopyranose mutase: fluorinated substrates, kinetics and equilibria. Org Biomol Chem 2009; 7:1009-16. [PMID: 19225684 PMCID: PMC3326532 DOI: 10.1039/b815549f] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of selectively fluorinated and other substituted UDP-D-galactose derivatives have been evaluated as substrates for Klebsiella pneumoniae UDP-D-galactopyranose mutase. This enzyme, which catalyses the interconversion of the pyranose and furanose forms of galactose as its UDP adduct, is a prospective drug target for a variety of microbial infections. We show that none of the 2''-, 3''- or 6''-hydroxyl groups of UDP-D-galactopyranose are essential for substrate binding and turnover. However, steric factors appear to play an important role in limiting the range of substitutions that can be accommodated at C-2'' and C-6'' of the sugar nucleotide substrate. Attempts to invert the C-2'' stereochemistry from equatorial to axial, changing D-galacto- to D-talo-configuration, in an attempt to exploit the higher percentage of furanose at equilibrium in the talo-series, met with no turnover of substrate.
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Affiliation(s)
- James C. Errey
- School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, UK
| | - Maretta C. Mann
- School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, UK
| | | | - Lionel Hill
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Michael R. McNeil
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1619, USA
| | - James H. Naismith
- School of Chemistry and Centre for Biomolecular Sciences, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
| | - Jonathan M. Percy
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XLC, UK
| | - Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Robert A. Field
- School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, UK
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, UK,
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Caravano A, Field RA, Percy JM, Rinaudo G, Roig R, Singh K. Developing an asymmetric, stereodivergent route to selected 6-deoxy-6-fluoro-hexoses. Org Biomol Chem 2009; 7:996-1008. [PMID: 19225683 DOI: 10.1039/b815342f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Free radical bromination and nucleophilic fluorination allows the conversion of methyl sorbate into the 6-fluoro analogue which undergoes sequential asymmetric dihydroxylation reactions. A range of 6-deoxy-6-fluorosugars were prepared by using different combinations of ligands. While the enantiomeric excesses obtained were comparable to those from other 6-substituted sorbates, the regioselectivity of dihydroxylation was moderate, with both 2,3- and 4,5-diols being obtained. A successful temporary persilylation strategy was evolved to convert the products of dihydroxylation rapidly to the fluorosugars 6-deoxy-6-fluoro-L-idose, 6-fluoro-L-fucose and 6-deoxy-6-fluoro-D-galactose, which were obtained in overall yields of 4%, 6% and 8% from methyl 6-fluoro-hexa-2E,4E-dienoate .
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Affiliation(s)
- Audrey Caravano
- Department of Chemistry, University of Leicester, University Road, Leicester LE17RH, UK
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