1
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Zheng M, Zheng M, Lupoli TJ. Expanding the Substrate Scope of a Bacterial Nucleotidyltransferase via Allosteric Mutations. ACS Infect Dis 2022; 8:2035-2044. [PMID: 36106727 DOI: 10.1021/acsinfecdis.2c00402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Bacterial glycoconjugates, such as cell surface polysaccharides and glycoproteins, play important roles in cellular interactions and survival. Enzymes called nucleotidyltransferases use sugar-1-phosphates and nucleoside triphosphates (NTPs) to produce nucleoside diphosphate sugars (NDP-sugars), which serve as building blocks for most glycoconjugates. Research spanning several decades has shown that some bacterial nucleotidyltransferases have broad substrate tolerance and can be exploited to produce a variety of NDP-sugars in vitro. While these enzymes are known to be allosterically regulated by NDP-sugars and their fragments, much work has focused on the effect of active site mutations alone. Here, we show that rational mutations in the allosteric site of the nucleotidyltransferase RmlA lead to expanded substrate tolerance and improvements in catalytic activity that can be explained by subtle changes in quaternary structure and interactions with ligands. These observations will help inform future studies on the directed biosynthesis of diverse bacterial NDP-sugars and downstream glycoconjugates.
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Affiliation(s)
- Maggie Zheng
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Meng Zheng
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Tania J Lupoli
- Department of Chemistry, New York University, New York, New York 10003, United States
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2
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Li S, Chen F, Li Y, Wang L, Li H, Gu G, Li E. Rhamnose-Containing Compounds: Biosynthesis and Applications. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27165315. [PMID: 36014553 PMCID: PMC9415975 DOI: 10.3390/molecules27165315] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022]
Abstract
Rhamnose-associated molecules are attracting attention because they are present in bacteria but not mammals, making them potentially useful as antibacterial agents. Additionally, they are also valuable for tumor immunotherapy. Thus, studies on the functions and biosynthetic pathways of rhamnose-containing compounds are in progress. In this paper, studies on the biosynthetic pathways of three rhamnose donors, i.e., deoxythymidinediphosphate-L-rhamnose (dTDP-Rha), uridine diphosphate-rhamnose (UDP-Rha), and guanosine diphosphate rhamnose (GDP-Rha), are firstly reviewed, together with the functions and crystal structures of those associated enzymes. Among them, dTDP-Rha is the most common rhamnose donor, and four enzymes, including glucose-1-phosphate thymidylyltransferase RmlA, dTDP-Glc-4,6-dehydratase RmlB, dTDP-4-keto-6-deoxy-Glc-3,5-epimerase RmlC, and dTDP-4-keto-Rha reductase RmlD, are involved in its biosynthesis. Secondly, several known rhamnosyltransferases from Geobacillus stearothermophilus, Saccharopolyspora spinosa, Mycobacterium tuberculosis, Pseudomonas aeruginosa, and Streptococcus pneumoniae are discussed. In these studies, however, the functions of rhamnosyltransferases were verified by employing gene knockout and radiolabeled substrates, which were almost impossible to obtain and characterize the products of enzymatic reactions. Finally, the application of rhamnose-containing compounds in disease treatments is briefly described.
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Affiliation(s)
- Siqiang Li
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
- Institute of Agricultural Products Fermentation Engineering and Application, Huanghuai University, Zhumadian 463000, China
| | - Fujia Chen
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
- Institute of Agricultural Products Fermentation Engineering and Application, Huanghuai University, Zhumadian 463000, China
| | - Yun Li
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
- Institute of Agricultural Products Fermentation Engineering and Application, Huanghuai University, Zhumadian 463000, China
| | - Lizhen Wang
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250100, China
| | - Hongyan Li
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
| | - Guofeng Gu
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 72 Binhai Road, Qingdao 266237, China
- Correspondence: (G.G.); (E.L.)
| | - Enzhong Li
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
- Institute of Agricultural Products Fermentation Engineering and Application, Huanghuai University, Zhumadian 463000, China
- Correspondence: (G.G.); (E.L.)
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3
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Zheng M, Zheng M, Epstein S, Harnagel AP, Kim H, Lupoli TJ. Chemical Biology Tools for Modulating and Visualizing Gram-Negative Bacterial Surface Polysaccharides. ACS Chem Biol 2021; 16:1841-1865. [PMID: 34569792 DOI: 10.1021/acschembio.1c00341] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacterial cells present a wide diversity of saccharides that decorate the cell surface and help mediate interactions with the environment. Many Gram-negative cells express O-antigens, which are long sugar polymers that makeup the distal portion of lipopolysaccharide (LPS) that constitutes the surface of the outer membrane. This review highlights chemical biology tools that have been developed in recent years to facilitate the modulation of O-antigen synthesis and composition, as well as related bacterial polysaccharide pathways, and the detection of unique glycan sequences. Advances in the biochemistry and structural biology of O-antigen biosynthetic machinery are also described, which provide guidance for the design of novel chemical and biomolecular probes. Many of the tools noted here have not yet been utilized in biological systems and offer researchers the opportunity to investigate the complex sugar architecture of Gram-negative cells.
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Affiliation(s)
- Meng Zheng
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Maggie Zheng
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Samuel Epstein
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Alexa P. Harnagel
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Hanee Kim
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Tania J. Lupoli
- Department of Chemistry, New York University, New York, 10003 New York, United States
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4
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Liu H, Tegl G, Nidetzky B. Glycosyltransferase Co‐Immobilization for Natural Product Glycosylation: Cascade Biosynthesis of the
C
‐Glucoside Nothofagin with Efficient Reuse of Enzymes. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202001549] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hui Liu
- Institute of Biotechnology and Biochemical Engineering Graz University of Technology, NAWI Graz Petersgasse 12 8010 Graz Austria
| | - Gregor Tegl
- Institute of Biotechnology and Biochemical Engineering Graz University of Technology, NAWI Graz Petersgasse 12 8010 Graz Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering Graz University of Technology, NAWI Graz Petersgasse 12 8010 Graz Austria
- Austrian Centre of Industrial Biotechnology (acib) Petersgasse 14 8010 Graz Austria
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5
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Goel B, Tripathi N, Mukherjee D, Jain SK. Glycorandomization: A promising diversification strategy for the drug development. Eur J Med Chem 2021; 213:113156. [PMID: 33460832 DOI: 10.1016/j.ejmech.2021.113156] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/04/2021] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
Glycorandomization is a natural product derivatization strategy in which different sugar moieties are linked to the aglycone part of the naturally existing glycosides to create glycorandomized libraries. Sugars attached to the natural products are responsible for affecting their solubility, mechanism of action, target recognition, and toxicity and thus, by changing the sugar part, these properties could be modified. Glycorandomization can be done via two approaches (i) a synthetic approach known as neoglycorandomization, and (ii) chemoenzymatic approach including in-vitro and in-vivo glycorandomization. Glycorandomization can be a promising technology for the drug discovery that has proved its potential to improve pharmacokinetic (solubility) and pharmacodynamic profile (mechanism of action, toxicity, and target recognition) of the parent compounds. The substrate flexibility of glycosyltransferases and other enzymes towards sugars and/or aglycone substrates has made this technique versatile. Further, the enzymes can be altered by genetic engineering to generate glycorandomized libraries of diverse natural product scaffolds. This technique has the potential to produce new compounds that can be helpful to the mankind by treating the threatening disease states. This review covers the different strategies for glycorandomization as a tool in drug discovery and development. The fundamentals of glycorandomization, different types, and further development of differentially glycorandomized libraries of natural products and small molecule based drugs have been discussed.
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Affiliation(s)
- Bharat Goel
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, Uttar Pradesh, India
| | - Nancy Tripathi
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, Uttar Pradesh, India
| | - Debaraj Mukherjee
- Natural Product Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, 180001, India
| | - Shreyans K Jain
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, Uttar Pradesh, India.
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6
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Li S, Wang H, Jin G, Chen Z, Gu G. Exploring the broad nucleotide triphosphate and sugar-1-phosphate specificity of thymidylyltransferase Cps23FL from Streptococcus pneumonia serotype 23F. RSC Adv 2020; 10:30110-30114. [PMID: 35518267 PMCID: PMC9056299 DOI: 10.1039/d0ra05799a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/07/2020] [Indexed: 11/21/2022] Open
Abstract
Glucose-1-phosphate thymidylyltransferase (Cps23FL) from Streptococcus pneumonia serotype 23F is the initial enzyme that catalyses the thymidylyl transfer reaction in prokaryotic deoxythymidine diphosphate-l-rhamnose (dTDP-Rha) biosynthetic pathway. In this study, the broad substrate specificity of Cps23FL towards six glucose-1-phosphates and nine nucleoside triphosphates as substrates was systematically explored, eventually providing access to nineteen sugar nucleotide analogs. The broad substrate specificities of thymidylyltransferase Cps23FL towards nucleotide triphosphates and sugar-1-phosphates were systemically investigated.![]()
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Affiliation(s)
- Siqiang Li
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University 72 Binhai Road Qingdao 266237 China .,School of Biological and Food Processing Engineering, Huanghuai University 76 Kaiyuan Road Zhumadian 463000 China
| | - Hong Wang
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University 72 Binhai Road Qingdao 266237 China
| | - Guoxia Jin
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University 88 Wenhua Dong Lu Jinan 250014 China
| | - Zonggang Chen
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University 72 Binhai Road Qingdao 266237 China
| | - Guofeng Gu
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University 72 Binhai Road Qingdao 266237 China
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7
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Zhu JS, Stiers KM, Soleimani E, Groves BR, Beamer LJ, Jakeman DL. Inhibitory Evaluation of αPMM/PGM from Pseudomonas aeruginosa: Chemical Synthesis, Enzyme Kinetics, and Protein Crystallographic Study. J Org Chem 2019; 84:9627-9636. [DOI: 10.1021/acs.joc.9b01305] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jian-She Zhu
- College of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
| | - Kyle M. Stiers
- Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
| | - Ebrahim Soleimani
- College of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
- Department of Chemistry, Razi University, Kermanshah 67149-67346, Iran
| | - Brandon R. Groves
- College of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
| | - Lesa J. Beamer
- Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
| | - David L. Jakeman
- College of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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8
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Zhu JS, Stiers KM, Winter SM, Garcia AD, Versini AF, Beamer LJ, Jakeman DL. Synthesis, Derivatization, and Structural Analysis of Phosphorylated Mono-, Di-, and Trifluorinated d-Gluco-heptuloses by Glucokinase: Tunable Phosphoglucomutase Inhibition. ACS OMEGA 2019; 4:7029-7037. [PMID: 31179410 PMCID: PMC6547622 DOI: 10.1021/acsomega.9b00008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/08/2019] [Indexed: 05/16/2023]
Abstract
Glucokinase phosphorylated a series of C-1 fluorinated α-d-gluco-heptuloses. These phosphorylated products were discovered to be inhibitors of α-phosphomannomutase/phosphoglucomutase (αPMM/PGM) and β-phosphoglucomutase (βPGM). Inhibition potency with both mutases inversely correlated to the degree of fluorination. Structural analysis with αPMM demonstrated the inhibitor binding to the active site, with the phosphate in the phosphate binding site and the anomeric hydroxyl directed to the catalytic site.
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Affiliation(s)
- Jian-She Zhu
- College
of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
| | - Kyle M. Stiers
- Biochemistry
Department, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
| | - Sherany M. Winter
- College
of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
- Department
of Chemistry, Hogeschool Leiden (UAS Leiden), Zernikedreef 11, CK Leiden 2333, The Netherlands
| | - Anthony D. Garcia
- College
of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
- École
Nationale Supérieure de Chimie de Rennes, 11 Allée de Beaulieu, CS 50837, Rennes Cedex 7 35708, France
| | - Antoine F. Versini
- College
of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
- École
Supérieure de Physique et de Chimie Industrielles de la Ville
de Paris, 10 rue Vauquelin, Paris 75005, France
| | - Lesa J. Beamer
- College
of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
- E-mail: (L.J.B.)
| | - David L. Jakeman
- College
of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada
- Department
of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- E-mail: (D.L.J.)
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9
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Honda Y, Nakano S, Ito S, Dadashipour M, Zhang Z, Kawarabayasi Y. Improvement of ST0452 N-Acetylglucosamine-1-Phosphate Uridyltransferase Activity by the Cooperative Effect of Two Single Mutations Identified through Structure-Based Protein Engineering. Appl Environ Microbiol 2018; 84:e02213-18. [PMID: 30291121 PMCID: PMC6275352 DOI: 10.1128/aem.02213-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 09/25/2018] [Indexed: 11/20/2022] Open
Abstract
We showed previously that the Y97N mutant of the ST0452 protein, isolated from Sulfolobus tokodaii, exhibited over 4 times higher N-acetylglucosamine-1-phosphate (GlcNAc-1-P) uridyltransferase (UTase) activity, compared with that of the wild-type ST0452 protein. We determined the three-dimensional structure of the Y97N protein to explore the detailed mechanism underlying this increased activity. The overall structure was almost identical to that of the wild-type ST0452 protein (PDB ID 2GGO), with residue 97 (Asn) interacting with the O-5 atom of N-acetylglucosamine (GlcNAc) in the complex without metal ions. The same interaction was observed for Escherichia coli GlmU in the absence of metal ions. These observations indicated that the three-dimensional structure of the Y97N protein was not changed by this substitution but the interactions with the substrate were slightly modified, which might cause the activity to increase. The crystal structure of the Y97N protein also showed that positions 146 (Glu) and 80 (Thr) formed interactions with GlcNAc, and an engineering strategy was applied to these residues to increase activity. All proteins substituted at position 146 had drastically decreased activities, whereas several proteins substituted at position 80 showed higher GlcNAc-1-P UTase activity, compared to that of the wild-type protein. The substituted amino acids at positions 80 and 97 might result in optimized interactions with the substrate; therefore, we predicted that the combination of these two substitutions might cooperatively increase GlcNAc-1-P UTase activity. Of the four double mutant ST0452 proteins generated, T80S/Y97N showed 6.5-times-higher activity, compared to that of the wild-type ST0452 protein, revealing that these two substituted residues functioned cooperatively to increase GlcNAc-1-P UTase activity.IMPORTANCE We demonstrated that the enzymatic activity of a thermostable protein was over 4 times higher than that of the wild-type protein following substitution of a single amino acid, without affecting its thermostability. The three-dimensional structure of the improved mutant protein complexed with substrate was determined. The same overall structure and interaction between the substituted residue and the GlcNAc substrate as observed in the well-characterized bacterial enzyme suggested that the substitution of Tyr at position 97 by Asn might slightly change the interaction. This subtle change in the interaction might potentially increase the GlcNAc-1-P UTase activity of the mutant protein. These observations indicated that a drastic change in the structure of a natural thermostable enzyme is not necessary to increase its activity; a subtle change in the interaction with the substrate might be sufficient. Cooperative effects were observed in the appropriate double mutant protein. This work provides useful information for the future engineering of natural enzymes.
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Affiliation(s)
- Yuki Honda
- Laboratory for Functional Genomics of Extremophiles, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Faculty of Science, Nara Women's University, Nara, Japan
| | - Shogo Nakano
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka, Japan
| | - Sohei Ito
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka, Japan
| | - Mohammad Dadashipour
- Laboratory for Functional Genomics of Extremophiles, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Zilian Zhang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China
| | - Yutaka Kawarabayasi
- Laboratory for Functional Genomics of Extremophiles, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- National Institute of Advanced Industrial Science and Technology (AIST), Bioproduction Research Institute, Ibaraki, Japan
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10
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General assay for enzymes in the heptose biosynthesis pathways using electrospray ionization mass spectrometry. Appl Microbiol Biotechnol 2017; 101:4521-4532. [DOI: 10.1007/s00253-017-8148-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/12/2017] [Accepted: 01/25/2017] [Indexed: 10/20/2022]
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11
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Kulmer ST, Gutmann A, Lemmerer M, Nidetzky B. Biocatalytic Cascade of Polyphosphate Kinase and Sucrose Synthase for Synthesis of Nucleotide-Activated Derivatives of Glucose. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201601078] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sandra T. Kulmer
- Institute of Biotechnology and Biochemical Engineering; Graz University of Technology, NAWI Graz; Petersgasse 12 8010 Graz Austria
| | - Alexander Gutmann
- Institute of Biotechnology and Biochemical Engineering; Graz University of Technology, NAWI Graz; Petersgasse 12 8010 Graz Austria
| | - Martin Lemmerer
- Austrian Centre of Industrial Biotechnology; Petersgasse 14 8010 Graz Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering; Graz University of Technology, NAWI Graz; Petersgasse 12 8010 Graz Austria
- Austrian Centre of Industrial Biotechnology; Petersgasse 14 8010 Graz Austria
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12
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Zhu JS, McCormick NE, Timmons SC, Jakeman DL. Synthesis of α-Deoxymono and Difluorohexopyranosyl 1-Phosphates and Kinetic Evaluation with Thymidylyl- and Guanidylyltransferases. J Org Chem 2016; 81:8816-8825. [DOI: 10.1021/acs.joc.6b01485] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jian-She Zhu
- College
of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 3J5, Canada
| | - Nicole E. McCormick
- College
of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 3J5, Canada
| | - Shannon C. Timmons
- Department
of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - David L. Jakeman
- College
of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 3J5, Canada
- Department
of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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13
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Willbur JF, Vail JD, Mitchell LN, Jakeman DL, Timmons SC. Expression, purification, and characterization of a carbohydrate-active enzyme: A research-inspired methods optimization experiment for the biochemistry laboratory. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 44:75-85. [PMID: 26710673 DOI: 10.1002/bmb.20928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/08/2015] [Accepted: 09/29/2015] [Indexed: 06/05/2023]
Abstract
The development and implementation of research-inspired, discovery-based experiences into science laboratory curricula is a proven strategy for increasing student engagement and ownership of experiments. In the novel laboratory module described herein, students learn to express, purify, and characterize a carbohydrate-active enzyme using modern techniques and instrumentation commonly found in a research laboratory. Unlike in a traditional cookbook-style experiment, students generate their own hypotheses regarding expression conditions and quantify the amount of protein isolated using their selected variables. Over the course of three 3-hour laboratory periods, students learn to use sterile technique to express a protein using recombinant DNA in E. coli, purify the resulting enzyme via affinity chromatography and dialysis, analyze the success of their purification scheme via SDS-PAGE, assess the activity of the enzyme via an HPLC-based assay, and quantify the amount of protein isolated via a Bradford assay. Following the completion of this experiment, students were asked to evaluate their experience via an optional survey. All students strongly agreed that this laboratory module was more interesting to them than traditional experiments because of its lack of a pre-determined outcome and desired additional opportunities to participate in the experimental design process. This experiment serves as an example of how research-inspired, discovery-based experiences can benefit both the students and instructor; students learned important skills necessary for real-world biochemistry research and a more concrete understanding of the research process, while generating new knowledge to enhance the scholarly endeavors of the instructor.
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Affiliation(s)
- Jaime F Willbur
- From the Department of Natural Sciences, Lawrence Technological University, Southfield, Michigan, 48075, USA
| | - Justin D Vail
- From the Department of Natural Sciences, Lawrence Technological University, Southfield, Michigan, 48075, USA
| | - Lindsey N Mitchell
- From the Department of Natural Sciences, Lawrence Technological University, Southfield, Michigan, 48075, USA
| | - David L Jakeman
- College of Pharmacy, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Shannon C Timmons
- From the Department of Natural Sciences, Lawrence Technological University, Southfield, Michigan, 48075, USA
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14
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Forget SM, Jee A, Smithen DA, Jagdhane R, Anjum S, Beaton SA, Palmer DRJ, Syvitski RT, Jakeman DL. Kinetic evaluation of glucose 1-phosphate analogues with a thymidylyltransferase using a continuous coupled enzyme assay. Org Biomol Chem 2015; 13:866-75. [PMID: 25408103 DOI: 10.1039/c4ob02057j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cps2L, a thymidylytransferase, is the first enzyme in Streptococcus pneumoniae L-rhamnose biosynthesis and an antibacterial target. We herein report the evaluation of six sugar phosphate analogues selected to further probe Cps2L substrate tolerance. A modified continuous spectrophotometric assay was employed for facile detection of pyrophosphate (PPi) released from nucleotidylyltransfase-catalysed condensation of sugar 1-phosphates and nucleoside triphosphates to produce sugar nucleotides. Additionally, experiments using waterLOGSY NMR spectroscopy were investigated as a complimentary method to evaluate binding affinity to Cps2L.
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Affiliation(s)
- S M Forget
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd, PO Box 15, 000, Halifax, Nova Scotia B3H 4R2, Canada.
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15
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McCormick NE, Jakeman DL. On the mechanism of phosphoenolpyruvate synthetase (PEPs) and its inhibition by sodium fluoride: potential magnesium and aluminum fluoride complexes of phosphoryl transfer. Biochem Cell Biol 2015; 93:236-40. [DOI: 10.1139/bcb-2014-0153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Phosphoenolpyruvate synthase (PEPs) catalyzes the conversion of pyruvate to phosphoenolpyruvate (PEP) using a two-step mechanism invoking a phosphorylated-His intermediate. Formation of PEP is an initial step in gluconeogenesis, and PEPs is essential for growth of Escherichia coli on 3-carbon sources such as pyruvate. The production of PEPs has also been linked to bacterial virulence and antibiotic resistance. As such, PEPs is of interest as a target for antibiotic development, and initial investigations of PEPs have indicated inhibition by sodium fluoride. Similar inhibition has been observed in a variety of phospho-transfer enzymes through the formation of metal fluoride complexes within the active site. Herein we quantify the inhibitory capacity of sodium fluoride through a coupled spectrophotometric assay. The observed inhibition provides indirect evidence for the formation of a MgF3−complex within the enzyme active site and insight into the phospho-transfer mechanism of PEPs. The effect of AlCl3on PEPs enzyme activity was also assessed and found to decrease substrate binding and turnover.
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Affiliation(s)
- Nicole E. McCormick
- College of Pharmacy, Dalhousie University, 5968 College St., Halifax, NS B3H 4R2, Canada
| | - David L. Jakeman
- College of Pharmacy, Dalhousie University, 5968 College St., Halifax, NS B3H 4R2, Canada
- Department of Chemistry, Dalhousie University, 6274 Coberg Rd., Halifax, NS B3H 4R2, Canada
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16
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17
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Forget SM, Smithen DA, Jee A, Jakeman DL. Mechanistic evaluation of a nucleoside tetraphosphate with a thymidylyltransferase. Biochemistry 2015; 54:1703-7. [PMID: 25647009 DOI: 10.1021/bi501438p] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pyrimidine polyphosphates were first detected in cells 5 decades ago; however, their biological significance remains only partially resolved. Such nucleoside polyphosphates are believed to be produced nonspecifically by promiscuous enzymes. Herein, synthetically prepared deoxythymidine 5'-tetraphosphate (p4dT) was evaluated with a thymidylyltransferase, Cps2L. We have identified p4dT as a substrate for Cps2L and evaluated the reaction pathway by analysis of products using high-performance liquid chromatography, liquid chromatography and tandem mass spectrometry, and 31P nuclear magnetic resonance spectroscopy. Product analysis confirmed production of dTDP-Glc and triphosphate (P3) and showed no trace of dTTP-Glc and PPi, which could arise from alternative pathways for the reaction mechanism.
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Affiliation(s)
- Stephanie M Forget
- Department of Chemistry, Dalhousie University , P.O. Box 15000, Halifax, Canada B3H 4R2
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18
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Smithen DA, Forget SM, McCormick NE, Syvitski RT, Jakeman DL. Polyphosphate-containing bisubstrate analogues as inhibitors of a bacterial cell wall thymidylyltransferase. Org Biomol Chem 2015; 13:3347-50. [DOI: 10.1039/c4ob02583k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first synthesis and evaluation of bisubstrate analogues with a thymidylyltransferase is reported. WaterLOGSY NMR and kinetic analyses provide insight into bisubstrate analogue binding.
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Affiliation(s)
| | | | | | | | - David L. Jakeman
- Department of Chemistry
- Dalhousie University
- Halifax
- Canada
- College of Pharmacy
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19
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Beaton SA, Jiang PM, Melong JC, Loranger MW, Mohamady S, Veinot TI, Jakeman DL. The effect of bisphosphonate acidity on the activity of a thymidylyltransferase. Org Biomol Chem 2014; 11:5473-80. [PMID: 23857455 DOI: 10.1039/c3ob41017j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Thymidylyltransferases (thymidine diphospho pyrophosphorylases) are nucleotidylyltransferases that play key roles in the biosynthesis of carbohydrate components within bacterial cell walls and in the biosynthesis of glycosylated natural products. They catalyze the formation of sugar nucleotides concomitant with the release of pyrophosphate. Protein engineering of thymidylyltransferases has been an approach for the production of a variety of non-physiological sugar nucleotides. In this work, we have explored chemical approaches towards modifying the activity of the thymidylyltransferase (Cps2L) cloned from S. pneumoniae, through the use of chemically synthesized 'activated' nucleoside triphosphates with enhanced leaving groups, or by switching the metal ion co-factor specificity. Within a series of phosphonate-containing nucleoside triphosphate analogues, thymidylyltransferase activity is enhanced based on the acidity of the leaving group and a Brønsted-type analysis indicated that leaving group departure is rate limiting. We have also determined IC50 values for a series of bisphosphonates as inhibitors of thymidylyltransferases. No correlation between the acidity of the inhibitors (pKa) and the magnitude of enzyme inhibition was found.
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Affiliation(s)
- Stephen A Beaton
- Department of Chemistry, Dalhousie University, 1459 Oxford St., Halifax, Nova Scotia B3H 4R2, Canada
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20
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Chien WT, Liang CF, Yu CC, Lin CH, Li SP, Primadona I, Chen YJ, Mong KKT, Lin CC. Sequential one-pot enzymatic synthesis of oligo-N-acetyllactosamine and its multi-sialylated extensions. Chem Commun (Camb) 2014; 50:5786-9. [DOI: 10.1039/c4cc01227e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A simple and efficient protocol for the preparative-scale synthesis of various lengths of oligo-N-acetyllactosamine (oligo-LacNAc) and its multi-sialylated extensions.
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Affiliation(s)
- Wei-Ting Chien
- Department of Chemistry
- National Tsing Hua University
- Hsinchu, Taiwan
| | - Chien-Fu Liang
- Department of Chemistry
- National Tsing Hua University
- Hsinchu, Taiwan
| | - Ching-Ching Yu
- Department of Chemistry
- National Tsing Hua University
- Hsinchu, Taiwan
| | - Chien-Hung Lin
- Department of Chemistry
- National Tsing Hua University
- Hsinchu, Taiwan
| | - Si-Peng Li
- Department of Chemistry
- National Tsing Hua University
- Hsinchu, Taiwan
| | - Indah Primadona
- Department of Chemistry
- National Tsing Hua University
- Hsinchu, Taiwan
- Institute of Chemistry
- Academia Sinica
| | - Yu-Ju Chen
- Institute of Chemistry
- Academia Sinica
- Taipei 11529, Taiwan
- Genomic Research Center
- Academia Sinica
| | - Kwok Kong T. Mong
- Applied Chemistry Department
- National Chiao Tung University
- Hsinchu 30010, Taiwan
| | - Chun-Cheng Lin
- Department of Chemistry
- National Tsing Hua University
- Hsinchu, Taiwan
- Genomic Research Center
- Academia Sinica
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21
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Snitynsky RB, Lowary TL. Synthesis of nitrogen-containing furanose sugar nucleotides for use as enzymatic probes. Org Lett 2013; 16:212-5. [PMID: 24328953 DOI: 10.1021/ol4032073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The sugar nucleotides UDP-2-acetamido-2-deoxy-α-D-galactofuranose (UDP-GalfNAc) and UDP-2-azido-2-deoxy-α-D-galactofuranose (UDP-GalfN3) have been synthesized in preparative scale for the first time. These compounds are useful probes for studying the biosynthesis of glycans containing galactofuranose and/or 2-acetamido-2-deoxy-α-D-galactofuranose residues.
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Affiliation(s)
- Ryan B Snitynsky
- Alberta Glycomics Centre and Department of Chemistry, Gunning-Lemieux Chemistry Centre, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
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22
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Loranger MW, Forget SM, McCormick NE, Syvitski RT, Jakeman DL. Synthesis and evaluation of l-rhamnose 1C-phosphonates as nucleotidylyltransferase inhibitors. J Org Chem 2013; 78:9822-33. [PMID: 24020932 DOI: 10.1021/jo401542s] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We report the synthesis of a series of phosphonates and ketosephosphonates possessing an L-rhamnose scaffold with varying degrees of fluorination. These compounds were evaluated as potential inhibitors of α-D-glucose 1-phosphate thymidylyltransferase (Cps2L), the first enzyme in Streptococcus pneumoniae L-rhamnose biosynthesis, and a novel antibiotic target. Enzyme-substrate and enzyme-inhibitor binding experiments were performed using water-ligand observed binding via gradient spectroscopy (WaterLOGSY) NMR for known sugar nucleotide substrates and selected phosphonate analogues. IC50 values were measured and Ki values were calculated for inhibitors. New insights were gained into the binding promiscuity of enzymes within the prokaryotic L-rhamnose biosynthetic pathway (Cps2L, RmlB-D) and into the mechanism of inhibition for the most potent inhibitor in the series, L-rhamnose 1C-phosphonate.
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Affiliation(s)
- Matthew W Loranger
- Department of Chemistry, Dalhousie University , 6274 Coberg Road, P.O. Box 15,000, Halifax, Nova Scotia B3H 4R2, Canada
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23
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Loranger MW, Beaton SA, Lines KL, Jakeman DL. Thiophosphate and thiophosphonate analogues of glucose-1-phosphate: synthesis and enzymatic activity with a thymidylyltransferase. Carbohydr Res 2013; 379:43-50. [PMID: 23872276 DOI: 10.1016/j.carres.2013.06.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 06/10/2013] [Accepted: 06/11/2013] [Indexed: 11/17/2022]
Abstract
Synthetic methods were investigated for the preparation of O and S-glucosyl thiophosphates and glucosyl 1C-thiophosphonate. Four protected glucosyl thiophosphate compounds were synthesized and characterized as precursors to glucose 1-thiophosphate. The effect of various reaction conditions and the nature of the carbohydrate and thiophosphate protecting groups and how they impact both the yields and α/β diastereoselectivity of the glucosyl thiophosphate products were explored. A novel isomerization from an O-linked to S-linked glucosyl thiophosphate was observed. α-D-Glucose-1C-thiophosphonate was synthesized and evaluated as a substrate for the thymidylyltransferase, Cps2L. Tandem mass spectrometric analysis determined the position of sulfur in the sugar nucleotide product.
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Affiliation(s)
- Matthew W Loranger
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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24
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Global probabilistic annotation of metabolic networks enables enzyme discovery. Nat Chem Biol 2013; 8:848-54. [PMID: 22960854 PMCID: PMC3696893 DOI: 10.1038/nchembio.1063] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 08/07/2012] [Indexed: 11/08/2022]
Abstract
Annotation of organism-specific metabolic networks is one of the main challenges of systems biology. Importantly, due to inherent uncertainty of computational annotations, predictions of biochemical function need to be treated probabilistically. We present a global probabilistic approach to annotate genome-scale metabolic networks that integrates sequence homology and context-based correlations under a single principled framework. The developed method for Global Biochemical reconstruction Using Sampling (GLOBUS) not only provides annotation probabilities for each functional assignment, but also suggests likely alternative functions. GLOBUS is based on statistical Gibbs sampling of probable metabolic annotations and is able to make accurate functional assignments even in cases of remote sequence identity to known enzymes. We apply GLOBUS to genomes of Bacillus subtilis and Staphylococcus aureus, and validate the method predictions by experimentally demonstrating the 6-phosphogluconolactonase activity of ykgB and the role of the sps pathway for rhamnose biosynthesis in B. subtilis.
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25
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Chi X, Baba S, Tibrewal N, Funabashi M, Nonaka K, Van Lanen SG. The muraminomicin biosynthetic gene cluster and enzymatic formation of the 2-deoxyaminoribosyl appendage. MEDCHEMCOMM 2012; 4:239-243. [PMID: 23476724 DOI: 10.1039/c2md20245j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Muraminomicin is a lipopeptidyl nucleoside antibiotic produced by Streptosporangium amethystogenes SANK 60709. Similar to several members of this antibiotic family such as A-90289 and muraymycin, the structure of muraminomicin consists of a disaccharide comprised of two modified ribofuranose units linked by an O-β(1 → 5) glycosidic bond; however, muraminomicin holds the distinction in that both ribose units are 2-deoxy sugars. The biosynthetic gene cluster of muraminomicin has been identified, cloned and sequenced, and bioinformatic analysis revealed a minimum of 24 open reading frames putatively involved in the biosynthesis, resistance, and regulation of muraminomicin. Fives enzymes are likely involved in the assembly and attachment of the 2,5-dideoxy-5-aminoribose saccharide unit, and two are now functionally assigned and characterized: Mra20, a 5'-amino-2',5'-dideoxyuridine phosphorylase and Mra23, a UTP:5-amino-2,5-dideoxy-α-D-ribose-1-phosphate uridylyltransferase. The cumulative results are consistent with the incorporation of the ribosyl appendage of muraminomicin via the archetypical sugar biosynthetic pathway that parallels A-90289 biosynthesis, and the specificity for this appendage is dictated primarily by the two characterized enzymes.
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Affiliation(s)
- Xiuling Chi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, United States
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26
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Poulin MB, Zhou R, Lowary TL. Synthetic UDP-galactofuranose analogs reveal critical enzyme-substrate interactions in GlfT2-catalyzed mycobacterial galactan assembly. Org Biomol Chem 2012; 10:4074-87. [PMID: 22499274 DOI: 10.1039/c2ob25159k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mycobacterial cell wall galactan, composed of alternating β-(1→5) and β-(1→6) galactofuranosyl residues, is assembled by the action of two bifunctional galactofuranosyltransferases, GlfT1 and GlfT2, which use UDP-galactofuranose (UDP-Galf) as the donor substrate. Kinetic analysis of synthetic UDP-Galf analogs identified critical interactions involved in donor substrate recognition by GlfT2, a processive polymerizing glycosyltransferase. Testing of methylated UDP-Galf analogs showed the donor substrate-binding pocket is sterically crowded. Evaluation of deoxy UDP-Galf analogs revealed that the C-6 hydroxyl group is not essential for substrate activity, and that interactions with the UDP-Galf C-3 hydroxyl group orient the substrate for turnover but appears to play no role in substrate recognition, making the 3-deoxy-analog a moderate competitive inhibitor of the enzyme. Moreover, the addition of a Galf residue deoxygenated at C-5 or C-6, or an l-arabinofuranose residue, to the growing galactan chain resulted in "dead end" reaction products, which no longer act as an acceptor for the enzyme. This finding shows dual recognition of both the terminal C-5 and C-6 hydroxyl groups of the acceptor substrate are required for GlfT2 activity, which is consistent with a recent model developed based upon a crystal structure of the enzyme. These observations provide insight into specific protein-carbohydrate interactions in the GlfT2 active site and may facilitate the design of future inhibitors.
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Affiliation(s)
- Myles B Poulin
- Alberta Glycomics Centre and Department of Chemistry, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada
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27
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Singh B, Lee CB, Park JW, Sohng JK. The amino acid sequences in the C-terminal region of glucose-1-phosphate thymidylyltransferases determine their soluble expression in Escherichia coli. Protein Eng Des Sel 2012; 25:179-87. [DOI: 10.1093/protein/gzs002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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28
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Chien W, Liang C, Yu C, Lin JH, Wu H, Lin C. Glucose 1‐Phosphate Thymidylyltransferase in the Synthesis of Uridine 5′‐Diphosphate Galactose and its Application in the Synthesis ofN‐Acetyllactosamine. Adv Synth Catal 2012. [DOI: 10.1002/adsc.201100402] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Wei‐Ting Chien
- Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd., Hsinchu 30013, Taiwan, Republic of China, Fax: +(886)‐3‐571‐1082; phone: (+886)‐3‐575‐3147
| | - Chien‐Fu Liang
- Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd., Hsinchu 30013, Taiwan, Republic of China, Fax: +(886)‐3‐571‐1082; phone: (+886)‐3‐575‐3147
| | - Ching‐Ching Yu
- Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd., Hsinchu 30013, Taiwan, Republic of China, Fax: +(886)‐3‐571‐1082; phone: (+886)‐3‐575‐3147
| | - Jian‐ Hong Lin
- Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd., Hsinchu 30013, Taiwan, Republic of China, Fax: +(886)‐3‐571‐1082; phone: (+886)‐3‐575‐3147
| | - Haung‐Ting Wu
- Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd., Hsinchu 30013, Taiwan, Republic of China, Fax: +(886)‐3‐571‐1082; phone: (+886)‐3‐575‐3147
| | - Chun‐Cheng Lin
- Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd., Hsinchu 30013, Taiwan, Republic of China, Fax: +(886)‐3‐571‐1082; phone: (+886)‐3‐575‐3147
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29
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Forget SM, Bhattasali D, Hart VC, Cameron TS, Syvitski RT, Jakeman DL. Synthesis and enzymatic evaluation of ketose phosphonates: the interplay between mutarotation, monofluorination and acidity. Chem Sci 2012. [DOI: 10.1039/c2sc01077a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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30
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Chi X, Pahari P, Nonaka K, Van Lanen SG. Biosynthetic origin and mechanism of formation of the aminoribosyl moiety of peptidyl nucleoside antibiotics. J Am Chem Soc 2011; 133:14452-9. [PMID: 21819104 PMCID: PMC3174061 DOI: 10.1021/ja206304k] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Several peptidyl nucleoside antibiotics that inhibit bacterial translocase I involved in peptidoglycan cell wall biosynthesis contain an aminoribosyl moiety, an unusual sugar appendage in natural products. We present here the delineation of the biosynthetic pathway for this moiety upon in vitro characterization of four enzymes (LipM-P) that are functionally assigned as (i) LipO, an L-methionine:uridine-5'-aldehyde aminotransferase; (ii) LipP, a 5'-amino-5'-deoxyuridine phosphorylase; (iii) LipM, a UTP:5-amino-5-deoxy-α-D-ribose-1-phosphate uridylyltransferase; and (iv) LipN, a 5-amino-5-deoxyribosyltransferase. The cumulative results reveal a unique ribosylation pathway that is highlighted by, among other features, uridine-5'-monophosphate as the source of the sugar, a phosphorylase strategy to generate a sugar-1-phosphate, and a primary amine-requiring nucleotidylyltransferase that generates the NDP-sugar donor.
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Affiliation(s)
- Xiuling Chi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S. Limestone, Lexington, KY 40536, USA
| | - Pallab Pahari
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S. Limestone, Lexington, KY 40536, USA
| | - Koichi Nonaka
- Biopharmaceutical Research Group I, Biopharmaceutical Technology Research Laboratories, Pharmaceutical Technology Division, Daiichi Sankyo Co., Ltd., 389-4 Aza-ohtsurugi, Shimokawa, Izumi-machi, Iwaki-shi, Fukushima 971-8183, Japan
| | - Steven G. Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S. Limestone, Lexington, KY 40536, USA
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32
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Gantt RW, Peltier-Pain P, Cournoyer WJ, Thorson JS. Using simple donors to drive the equilibria of glycosyltransferase-catalyzed reactions. Nat Chem Biol 2011; 7:685-91. [PMID: 21857660 PMCID: PMC3177962 DOI: 10.1038/nchembio.638] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Accepted: 06/24/2011] [Indexed: 12/17/2022]
Abstract
We report that simple glycoside donors can drastically shift the equilibria of glycosyltransferase-catalyzed reactions, transforming NDP-sugar formation from an endothermic to an exothermic process. To demonstrate the utility of this thermodynamic adaptability, we highlight the glycosyltransferase-catalyzed synthesis of 22 sugar nucleotides from simple aromatic sugar donors, as well as the corresponding in situ formation of sugar nucleotides as a driving force in the context of glycosyltransferase-catalyzed reactions for small-molecule glycodiversification. These simple aromatic donors also enabled a general colorimetric assay for glycosyltransfer, applicable to drug discovery, protein engineering and other fundamental sugar nucleotide-dependent investigations. This study directly challenges the general notion that NDP-sugars are 'high-energy' sugar donors when taken out of their traditional biological context.
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Affiliation(s)
- Richard W. Gantt
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for Natural Products Research, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, USA
| | - Pauline Peltier-Pain
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for Natural Products Research, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, USA
| | - William J. Cournoyer
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for Natural Products Research, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, USA
| | - Jon S. Thorson
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for Natural Products Research, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, USA
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33
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Moretti R, Chang A, Peltier-Pain P, Bingman CA, Phillips GN, Thorson JS. Expanding the nucleotide and sugar 1-phosphate promiscuity of nucleotidyltransferase RmlA via directed evolution. J Biol Chem 2011; 286:13235-43. [PMID: 21317292 DOI: 10.1074/jbc.m110.206433] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Directed evolution is a valuable technique to improve enzyme activity in the absence of a priori structural knowledge, which can be typically enhanced via structure-guided strategies. In this study, a combination of both whole-gene error-prone polymerase chain reaction and site-saturation mutagenesis enabled the rapid identification of mutations that improved RmlA activity toward non-native substrates. These mutations have been shown to improve activities over 10-fold for several targeted substrates, including non-native pyrimidine- and purine-based NTPs as well as non-native D- and L-sugars (both α- and β-isomers). This study highlights the first broadly applicable high throughput sugar-1-phosphate nucleotidyltransferase screen and the first proof of concept for the directed evolution of this enzyme class toward the identification of uniquely permissive RmlA variants.
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Affiliation(s)
- Rocco Moretti
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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34
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Gantt RW, Peltier-Pain P, Thorson JS. Enzymatic methods for glyco(diversification/randomization) of drugs and small molecules. Nat Prod Rep 2011; 28:1811-53. [DOI: 10.1039/c1np00045d] [Citation(s) in RCA: 194] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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35
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Mizanur RM, Pohl NLB. Phosphomannose isomerase/GDP-mannose pyrophosphorylase from Pyrococcus furiosus: a thermostable biocatalyst for the synthesis of guanidinediphosphate-activated and mannose-containing sugar nucleotides. Org Biomol Chem 2009; 7:2135-9. [PMID: 19421452 DOI: 10.1039/b822794b] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein we present an analysis of the chemical function of a recombinant bifunctional phosphomannose isomerase/GDP-mannose pyrophosphorylase (manC) from Pyrococcus furiosus DSM 3638 and its use in the synthesis of guanidinediphospho-hexoses and a range of nucleotidediphospho-mannoses. This enzyme is unusually promiscuous in both its nucleotide triphosphate (NTP) and sugar-1-phosphate acceptance. It accepts all five naturally occurring NTPs (ATP, CTP, GTP, dTTP and UTP) and a range of sugar-1-phosphates (glucose-, mannose-, galactose-, glucosamine-, N-acetylglucosamine- and fucose-1-phosphate). A truncated GDP-mannose pyrophosphorylase domain of the whole length enzyme showed almost 100-fold less sugar nucleotidyltransferase activity with only GTP and mannose 1-phosphate as substrates. The temperature stability and inherently broad substrate tolerance of this archaeal enzyme make it an effective reagent for the rapid chemoenzymatic synthesis of a range of natural and unnatural sugar nucleotides that are challenging to make by chemical means alone.
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Affiliation(s)
- Rahman M Mizanur
- Department of Chemistry and Plant Sciences Institute, Gilman Hall, Iowa State University, Ames, Iowa 50011-3111, USA
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36
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Williams GJ, Gantt RW, Thorson JS. The impact of enzyme engineering upon natural product glycodiversification. Curr Opin Chem Biol 2009; 12:556-64. [PMID: 18678278 DOI: 10.1016/j.cbpa.2008.07.013] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Accepted: 07/07/2008] [Indexed: 12/20/2022]
Abstract
Glycodiversification of natural products is an effective strategy for small molecule drug development. Recently, improved methods for chemo-enzymatic synthesis of glycosyl donors has spurred the characterization of natural product glycosyltransferases (GTs), revealing that the substrate specificity of many naturally occurring GTs as too stringent for use in glycodiversification. Protein engineering of natural product GTs has emerged as an attractive approach to overcome this limitation. This review highlights recent progress in the engineering/evolution of enzymes relevant to natural product glycodiversification with a particular focus upon GTs.
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Affiliation(s)
- Gavin J Williams
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, National Cooperative Drug Discovery Program, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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Beaton SA, Huestis MP, Sadeghi-Khomami A, Thomas NR, Jakeman DL. Enzyme-catalyzed synthesis of isosteric phosphono-analogues of sugar nucleotides. Chem Commun (Camb) 2008:238-40. [PMID: 19099081 DOI: 10.1039/b808078j] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Efficient enzymatic syntheses of isosteric phosphono analogues of sugar nucleotides have been accomplished using a thymidylyltransferase.
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Affiliation(s)
- Stephen A Beaton
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4J3
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Timmons SC, Jakeman DL. Stereoselective synthesis of sugar nucleotides using neighboring group participation. ACTA ACUST UNITED AC 2008; Chapter 13:Unit 13.7. [PMID: 18428969 DOI: 10.1002/0471142700.nc1307s31] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A straightforward, efficient method for the chemical synthesis of sugar nucleotides derived from D-mannose and L-fucose precursors is described. This synthetic strategy involves the coupling of acylated glycosyl bromides with nucleoside 5'-diphosphates, which enables the exploitation of neighboring group participation to exclusively prepare diastereomerically pure sugar nucleotides of desired 1,2-trans anomeric configuration. This is the first stereoselective direct coupling approach to sugar nucleotide synthesis. Following deprotection using triethylamine and purification via C18 reversed-phase ion-pair chromatography, UDP- and GDP-alpha-D-mannose as well as UDP- and GDP-beta-L-fucose were obtained in good yield in only four synthetic steps from D-mannose and L-fucose.
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Jakeman DL, Young JL, Huestis MP, Peltier P, Daniellou R, Nugier-Chauvin C, Ferrières V. Engineering ribonucleoside triphosphate specificity in a thymidylyltransferase. Biochemistry 2008; 47:8719-25. [PMID: 18656961 DOI: 10.1021/bi800978u] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nature's glycosylation catalysts, glycosyltransferases, indirectly manipulate and control many important biological processes by transferring sugar nucleotide donors onto acceptors. Challenging chemical synthesis impedes synthetic access to sugar nucleotides and limits the study of many glycosyltransferases. Enzymatic access to sugar nucleotides is a rapidly expanding avenue of research, limited only by the substrate specificity of the enzyme. We have explored the promiscuous thymidylyltransferase from Streptococcus pneumoniae, Cps2L, and enhanced its uridylyltransferase and guanidyltransferase activities by active site engineering. Mutagenesis at position Q24 resulted in a variant with 10-, 3-, and 2-fold enhancement of UDP-glucosamine, UDP-mannose, and UDP- N-acetylglucosamine production, respectively. New catalytic activities were observed for the Cps2L variant over the wild-type enzyme, including the formation of GDP-mannose. The variant was evaluated as a catalyst for the formation of a series of dTDP- and UDP-furanoses and notably produced dTDP-Gal f in 90% yield and UDP-Ara f in 30% yield after 12 h. A series of 3- O-alkylglucose 1-phosphates were also evaluated as substrates, and notable conversions to UDP-3- O-methylglucose and UDP-3- O-dodecylglucose were achieved with the variant but not the wild-type enzyme. The Q24S variant also enhanced essentially all thymidylyltransferase activities relative to the wild-type enzyme. Comparison of active sites of uridylyltransferases and thymidylyltransferases with products bound indicate the Q24S variant to be a new approach in broadening nucleotidylyltransferase activity.
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Affiliation(s)
- David L Jakeman
- College of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia, Canada.
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40
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Timmons SC, Jakeman DL. Stereospecific synthesis of sugar-1-phosphates and their conversion to sugar nucleotides. Carbohydr Res 2008; 343:865-74. [PMID: 18299123 DOI: 10.1016/j.carres.2008.01.046] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2007] [Revised: 01/23/2008] [Accepted: 01/31/2008] [Indexed: 11/16/2022]
Abstract
As Leloir glycosyltransferases are increasingly being used to prepare oligosaccharides, glycoconjugates, and glycosylated natural products, efficient access to stereopure sugar nucleotide donor substrates is required. Herein, the rapid synthesis and purification of eight sugar nucleotides is described by a facile 30 min activation of nucleoside 5'-monophosphates bearing purine and pyrimidine bases with trifluoroacetic anhydride and N-methylimidazole, followed by a 2 h coupling with stereospecifically prepared sugar-1-phosphates. Tributylammonium bicarbonate and tributylammonium acetate were the ion-pair reagents of choice for the C18 reversed-phase purification of 6-deoxysugar nucleotides, and hexose or pentose-derived sugar nucleotides, respectively.
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Affiliation(s)
- Shannon C Timmons
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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Mizanur RM, Pohl NL. A thermostable promiscuous glucose-1-phosphate uridyltransferase from Helicobacter pylori for the synthesis of nucleotide sugars. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.molcatb.2007.09.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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43
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Timmons SC, Hui JPM, Pearson JL, Peltier P, Daniellou R, Nugier-Chauvin C, Soo EC, Syvitski RT, Ferrières V, Jakeman DL. Enzyme-catalyzed synthesis of furanosyl nucleotides. Org Lett 2007; 10:161-3. [PMID: 18092787 DOI: 10.1021/ol7023949] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A bacterial alpha-d-glucopyranosyl-1-phosphate thymidylyltransferase was found to couple four hexofuranosyl-1-phosphates, as well as a pentofuranosyl-1-phosphate, with deoxythymidine 5'-triphosphate, providing access to furanosyl nucleotides. The enzymatic reaction mixtures were analyzed by electrospray ionization mass spectrometry and NMR spectroscopy to determine the anomeric stereochemistry of furanosyl nucleotide products. This is the first demonstration of a nucleotidylyltransferase discriminating between diastereomeric mixtures of sugar-1-phosphates to produce stereopure, biologically relevant furanosyl nucleotides.
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Affiliation(s)
- Shannon C Timmons
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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Huestis MP, Aish GA, Hui JPM, Soo EC, Jakeman DL. Lipophilic sugar nucleotide synthesis by structure-based design of nucleotidylyltransferase substrates. Org Biomol Chem 2007; 6:477-84. [PMID: 18219417 DOI: 10.1039/b716955h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structure-based design of alkyl sugar-1-phosphates provides an efficient nucleotidylyltransferase-catalyzed synthesis of a series of new lipophilic sugar nucleotides possessing long or branched alkyl chains, thereby demonstrating the utility of nucleotidylyltransferases to catalyze the synthesis of sugar nucleotides with potential applications in lipopolysaccharide and lipoglycopeptide biosynthesis.
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Affiliation(s)
- Malcolm P Huestis
- College of Pharmacy, Dalhousie University, Halifax, Nova Scotia, CanadaB3H 3J5
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