1
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Cross AR, Roy S, Vivoli Vega M, Rejzek M, Nepogodiev SA, Cliff M, Salmon D, Isupov MN, Field RA, Prior JL, Harmer NJ. Spinning sugars in antigen biosynthesis: characterization of the Coxiella burnetii and Streptomyces griseus TDP-sugar epimerases. J Biol Chem 2022; 298:101903. [PMID: 35398092 PMCID: PMC9095892 DOI: 10.1016/j.jbc.2022.101903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 04/02/2022] [Accepted: 04/04/2022] [Indexed: 11/25/2022] Open
Abstract
The sugars streptose and dihydrohydroxystreptose (DHHS) are unique to the bacteria Streptomyces griseus and Coxiella burnetii, respectively. Streptose forms the central moiety of the antibiotic streptomycin, while DHHS is found in the O-antigen of the zoonotic pathogen C. burnetii. Biosynthesis of these sugars has been proposed to follow a similar path to that of TDP-rhamnose, catalyzed by the enzymes RmlA, RmlB, RmlC, and RmlD, but the exact mechanism is unclear. Streptose and DHHS biosynthesis unusually requires a ring contraction step that could be performed by orthologs of RmlC or RmlD. Genome sequencing of S. griseus and C. burnetii has identified StrM and CBU1838 proteins as RmlC orthologs in these respective species. Here, we demonstrate that both enzymes can perform the RmlC 3'',5'' double epimerization activity necessary to support TDP-rhamnose biosynthesis in vivo. This is consistent with the ring contraction step being performed on a double epimerized substrate. We further demonstrate that proton exchange is faster at the 3''-position than the 5''-position, in contrast to a previously studied ortholog. We additionally solved the crystal structures of CBU1838 and StrM in complex with TDP and show that they form an active site highly similar to those of the previously characterized enzymes RmlC, EvaD, and ChmJ. These results support the hypothesis that streptose and DHHS are biosynthesized using the TDP pathway and that an RmlD paralog most likely performs ring contraction following double epimerization. This work will support the elucidation of the full pathways for biosynthesis of these unique sugars.
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Affiliation(s)
- Alice R Cross
- Living Systems Institute, University of Exeter, Exeter, United Kingdom; Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Sumita Roy
- Living Systems Institute, University of Exeter, Exeter, United Kingdom; Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Mirella Vivoli Vega
- Living Systems Institute, University of Exeter, Exeter, United Kingdom; Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Martin Rejzek
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Sergey A Nepogodiev
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Matthew Cliff
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Debbie Salmon
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Michail N Isupov
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom; Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Joann L Prior
- Dstl, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Nicholas J Harmer
- Living Systems Institute, University of Exeter, Exeter, United Kingdom; Department of Biosciences, University of Exeter, Exeter, United Kingdom.
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2
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Hulst MB, Grocholski T, Neefjes JJC, van Wezel GP, Metsä-Ketelä M. Anthracyclines: biosynthesis, engineering and clinical applications. Nat Prod Rep 2021; 39:814-841. [PMID: 34951423 DOI: 10.1039/d1np00059d] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Covering: January 1995 to June 2021Anthracyclines are glycosylated microbial natural products that harbour potent antiproliferative activities. Doxorubicin has been widely used as an anticancer agent in the clinic for several decades, but its use is restricted due to severe side-effects such as cardiotoxicity. Recent studies into the mode-of-action of anthracyclines have revealed that effective cardiotoxicity-free anthracyclines can be generated by focusing on histone eviction activity, instead of canonical topoisomerase II poisoning leading to double strand breaks in DNA. These developments have coincided with an increased understanding of the biosynthesis of anthracyclines, which has allowed generation of novel compound libraries by metabolic engineering and combinatorial biosynthesis. Coupled to the continued discovery of new congeners from rare Actinobacteria, a better understanding of the biology of Streptomyces and improved production methodologies, the stage is set for the development of novel anthracyclines that can finally surpass doxorubicin at the forefront of cancer chemotherapy.
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Affiliation(s)
- Mandy B Hulst
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.
| | - Thadee Grocholski
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Jacques J C Neefjes
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Centre, Leiden, The Netherlands
| | - Gilles P van Wezel
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.
| | - Mikko Metsä-Ketelä
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
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3
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Huddleston JP, Anderson TK, Girardi NM, Thoden JB, Taylor Z, Holden HM, Raushel FM. Biosynthesis of d- glycero-l- gluco-Heptose in the Capsular Polysaccharides of Campylobacter jejuni. Biochemistry 2021; 60:1552-1563. [PMID: 33900734 DOI: 10.1021/acs.biochem.1c00183] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Campylobacter jejuni is the leading cause of food poisoning in the United States and Europe. The exterior cell surface of C. jejuni is coated with a capsular polysaccharide (CPS) that is essential for the maintenance and integrity of the bacterial cell wall and evasion of the host immune response. The identity and sequences of the monosaccharide components of the CPS are quite variable and dependent on the specific strain of C. jejuni. It is currently thought that the immediate precursor for the multiple variations found in the heptose moieties of the C. jejuni CPS is GDP-d-glycero-α-d-manno-heptose. In C. jejuni NCTC 11168, the heptose moiety is d-glycero-l-gluco-heptose. It has previously been shown that Cj1427 catalyzes the oxidation of GDP-d-glycero-α-d-manno-heptose to GDP-d-glycero-4-keto-α-d-lyxo-heptose using α-ketoglutarate as a cosubstrate. Cj1430 was now demonstrated to catalyze the double epimerization of this product at C3 and C5 to form GDP-d-glycero-4-keto-β-l-xylo-heptose. Cj1428 subsequently catalyzes the stereospecific reduction of this GDP-linked heptose by NADPH to form GDP-d-glycero-β-l-gluco-heptose. The three-dimensional crystal structure of Cj1430 was determined to a resolution of 1.85 Å in the presence of bound GDP-d-glycero-β-l-gluco-heptose, a product analogue. The structure shows that it belongs to the cupin superfamily. The three-dimensional crystal structure of Cj1428 was solved in the presence of NADPH to a resolution of 1.50 Å. Its fold places it into the short-chain dehydrogenase/reductase superfamily. Typically, members in this family display a characteristic signature sequence of YXXXK, with the conserved tyrosine serving a key role in catalysis. In Cj1428, this residue is a phenylalanine.
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Affiliation(s)
- Jamison P Huddleston
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Thomas K Anderson
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 553706, United States
| | - Nicholas M Girardi
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 553706, United States
| | - James B Thoden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 553706, United States
| | - Zane Taylor
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Hazel M Holden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 553706, United States
| | - Frank M Raushel
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States.,Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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4
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Barnawi H, Woodward L, Fava N, Roubakha M, Shaw SD, Kubinec C, Naismith JH, Creuzenet C. Structure-function studies of the C3/C5 epimerases and C4 reductases of the Campylobacter jejuni capsular heptose modification pathways. J Biol Chem 2021; 296:100352. [PMID: 33524389 PMCID: PMC7949155 DOI: 10.1016/j.jbc.2021.100352] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 01/14/2023] Open
Abstract
Many bacteria produce polysaccharide-based capsules that protect them from environmental insults and play a role in virulence, host invasion, and other functions. Understanding how the polysaccharide components are synthesized could provide new means to combat bacterial infections. We have previously characterized two pairs of homologous enzymes involved in the biosynthesis of capsular sugar precursors GDP-6-deoxy-D-altro-heptose and GDP-6-OMe-L-gluco-heptose in Campylobacter jejuni. However, the substrate specificity and mechanism of action of these enzymes-C3 and/or C5 epimerases DdahB and MlghB and C4 reductases DdahC and MlghC-are unknown. Here, we demonstrate that these enzymes are highly specific for heptose substrates, using mannose substrates inefficiently with the exception of MlghB. We show that DdahB and MlghB feature a jellyroll fold typical of cupins, which possess a range of activities including epimerizations, GDP occupying a similar position as in cupins. DdahC and MlghC contain a Rossman fold, a catalytic triad, and a small C-terminal domain typical of short-chain dehydratase reductase enzymes. Integrating structural information with site-directed mutagenesis allowed us to identify features unique to each enzyme and provide mechanistic insight. In the epimerases, mutagenesis of H67, D173, N121, Y134, and Y132 suggested the presence of alternative catalytic residues. We showed that the reductases could reduce GDP-4-keto-6-deoxy-mannulose without prior epimerization although DdahC preferred the pre-epimerized substrate and identified T110 and H180 as important for substrate specificity and catalytic efficacy. This information can be exploited to identify inhibitors for therapeutic applications or to tailor these enzymes to synthesize novel sugars useful as glycobiology tools.
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Affiliation(s)
- Heba Barnawi
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Laura Woodward
- Biomedical Sciences Research Complex, St Andrews University, St Andrews, UK
| | - Natalie Fava
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Mikhail Roubakha
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Steve D Shaw
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Chelsea Kubinec
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - James H Naismith
- Biomedical Sciences Research Complex, St Andrews University, St Andrews, UK; Rosalind Franklin Institute, Research Complex at Harwell, Harwell Campus, Didcot, UK; Division of Structural Biology, Oxford University, Oxford, UK.
| | - Carole Creuzenet
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada.
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5
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Dhaked DK, Bala Divya M, Guruprasad L. A structural and functional perspective on the enzymes of Mycobacterium tuberculosis involved in the L-rhamnose biosynthesis pathway. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 145:52-64. [PMID: 30550737 DOI: 10.1016/j.pbiomolbio.2018.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 11/12/2018] [Accepted: 12/06/2018] [Indexed: 11/19/2022]
Abstract
Tuberculosis is one of the leading causes of death from bacterial infections. The multi-drug resistant strain has warranted the development of new drug molecules which can inhibit the growth of Mycobacterium tuberculosis (M.tb). Most of the known drugs inhibit the enzymes in the cell wall biosynthesis pathway. One such pathway is L-rhamnose, which involves four druggable enzymes RmlA, B, C and D. The 3D structure analyses of these protein models (RmlA, B and D) and crystal structure (RmlC) has been carried out. Multiple sequence alignments of homologs from distant species of 32 taxa and analyses of available structures were performed in order to study the conservation of sequence and structural motifs, and catalytically important residues. Based on these results and reported mechanism in other organisms, we have predicted putative catalytic mechanism of M.tb enzymes involved in the L-rhamnose biosynthesis pathway.
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Affiliation(s)
- Devendra K Dhaked
- School of Chemistry, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - M Bala Divya
- School of Chemistry, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Lalitha Guruprasad
- School of Chemistry, University of Hyderabad, Hyderabad, Telangana, 500046, India.
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6
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Shornikov A, Tran H, Macias J, Halavaty AS, Minasov G, Anderson WF, Kuhn ML. Structure of the Bacillus anthracis dTDP-L-rhamnose-biosynthetic enzyme dTDP-4-dehydrorhamnose 3,5-epimerase (RfbC). Acta Crystallogr F Struct Biol Commun 2017; 73:664-671. [PMID: 29199987 PMCID: PMC5713671 DOI: 10.1107/s2053230x17015849] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/31/2017] [Indexed: 11/10/2022] Open
Abstract
The exosporium layer of Bacillus anthracis spores is rich in L-rhamnose, a common bacterial cell-wall component, which often contributes to the virulence of pathogens by increasing their adherence and immune evasion. The biosynthetic pathway used to form the activated L-rhamnose donor dTDP-L-rhamnose consists of four enzymes (RfbA, RfbB, RfbC and RfbD) and is an attractive drug target because there are no homologs in mammals. It was found that co-purifying and screening RfbC (dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase) from B. anthracis in the presence of the other three B. anthracis enzymes of the biosynthetic pathway yielded crystals that were suitable for data collection. RfbC crystallized as a dimer and its structure was determined at 1.63 Å resolution. Two different ligands were bound in the protein structure: pyrophosphate in the active site of one monomer and dTDP in the other monomer. A structural comparison with RfbC homologs showed that the key active-site residues are conserved across kingdoms.
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Affiliation(s)
| | - Ha Tran
- Department of Chemistry and Biochemistry, San Francisco State University, USA
| | - Jennifer Macias
- Department of Chemistry and Biochemistry, San Francisco State University, USA
| | - Andrei S. Halavaty
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - George Minasov
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - Wayne F. Anderson
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - Misty L. Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, USA
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7
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Van Overtveldt S, Verhaeghe T, Joosten HJ, van den Bergh T, Beerens K, Desmet T. A structural classification of carbohydrate epimerases: From mechanistic insights to practical applications. Biotechnol Adv 2015; 33:1814-28. [DOI: 10.1016/j.biotechadv.2015.10.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/15/2015] [Accepted: 10/22/2015] [Indexed: 12/26/2022]
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8
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Salinger AJ, Brown HA, Thoden JB, Holden HM. Biochemical studies on WbcA, a sugar epimerase from Yersinia enterocolitica. Protein Sci 2015; 24:1633-9. [PMID: 26174084 DOI: 10.1002/pro.2747] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 07/09/2015] [Accepted: 07/10/2015] [Indexed: 11/08/2022]
Abstract
Yersinia enterocolitica is a Gram-negative bacterium that causes yersiniosis, a zoonotic disease affecting the gastrointestinal tract of humans, cattle, and pigs, among others. The lipopolysaccharide of Y. enterocolitica O:8 contains an unusual sugar, 6-deoxy-d-gulose, which requires four enzymes for its biosynthesis. Here, we describe a combined structural and functional investigation of WbcA, which catalyzes the third step in the pathway, namely an epimerization about the C-3' carbon of a CDP-linked sugar. The structure of WbcA was determined to 1.75-Å resolution, and the model was refined to an overall R-factor of 19.5%. The fold of WbcA places it into the well-defined cupin superfamily of sugar epimerases. Typically, these enzymes contain both a conserved histidine and a tyrosine residue that play key roles in catalysis. On the basis of amino acid sequence alignments, it was anticipated that the "conserved" tyrosine had been replaced with a cysteine residue in WbcA (Cys 133), and indeed this was the case. However, what was not anticipated was the fact that another tyrosine residue (Tyr 50) situated on a neighboring β-strand moved into the active site. Site-directed mutant proteins were subsequently constructed and their kinetic properties analyzed to address the roles of Cys 133 and Tyr 50 in WbcA catalysis. This study emphasizes the continuing need to experimentally verify assumptions that are based solely on bioinformatics approaches.
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Affiliation(s)
- Ari J Salinger
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706
| | - Haley A Brown
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706
| | - James B Thoden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706
| | - Hazel M Holden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706
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9
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Zou Y, Fang Q, Yin H, Liang Z, Kong D, Bai L, Deng Z, Lin S. Stereospecific biosynthesis of β-methyltryptophan from (L)-tryptophan features a stereochemical switch. Angew Chem Int Ed Engl 2013; 52:12951-5. [PMID: 24166888 DOI: 10.1002/anie.201306255] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 09/04/2013] [Indexed: 11/10/2022]
Abstract
Make the switch: The three-enzyme cassette MarG/H/I is responsible for stereospecific biosynthesis of β-methyltryptophan from L-tryptophan (1). MarG/I convert 1 into (2S,3R)-β-methyltryptophan, while MarG/I combined with MarH convert 1 into (2S,3S)-β-methyltryptophan. MarH serves as a stereochemical switch by catalyzing the stereoinversion of the β-stereocenter.
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Affiliation(s)
- Yi Zou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240 (P.R. China)
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10
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Zou Y, Fang Q, Yin H, Liang Z, Kong D, Bai L, Deng Z, Lin S. Stereospecific Biosynthesis of β-Methyltryptophan fromL-Tryptophan Features a Stereochemical Switch. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306255] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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Kubiak RL, Phillips RK, Zmudka MW, Ahn MR, Maka EM, Pyeatt GL, Roggensack SJ, Holden HM. Structural and functional studies on a 3'-epimerase involved in the biosynthesis of dTDP-6-deoxy-D-allose. Biochemistry 2012; 51:9375-83. [PMID: 23116432 DOI: 10.1021/bi3012737] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Unusual deoxy sugars are often attached to natural products such as antibiotics, antifungals, and chemotherapeutic agents. One such sugar is mycinose, which has been found on the antibiotics chalcomycin and tylosin. An intermediate in the biosynthesis of mycinose is dTDP-6-deoxy-D-allose. Four enzymes are required for the production of dTDP-6-deoxy-D-allose in Streptomyces bikiniensis, a soil-dwelling microbe first isolated from the Bikini and Rongelap atolls. Here we describe a combined structural and functional study of the enzyme ChmJ, which reportedly catalyzes the third step in the pathway leading to dTDP-6-deoxy-D-allose formation. Specifically, it has been proposed that ChmJ is a 3'-epimerase that converts dTDP-4-keto-6-deoxyglucose to dTDP-4-keto-6-deoxyallose. This activity, however, has never been verified in vitro. As reported here, we demonstrate using (1)H nuclear magnetic resonance that ChmJ, indeed, functions as a 3'-epimerase. In addition, we determined the structure of ChmJ complexed with dTDP-quinovose to 2.0 Å resolution. The structure of ChmJ shows that it belongs to the well-characterized "cupin" superfamily. Two active site residues, His 60 and Tyr 130, were subsequently targeted for study via site-directed mutagenesis and kinetic analyses, and the three-dimensional architecture of the H60N/Y130F mutant protein was determined to 1.6 Å resolution. Finally, the structure of the apoenzyme was determined to 2.2 Å resolution. It has been previously suggested that the position of a conserved tyrosine, Tyr 130 in the case of ChmJ, determines whether an enzyme in this superfamily functions as a mono- or diepimerase. Our results indicate that the orientation of the tyrosine residue in ChmJ is a function of the ligand occupying the active site cleft.
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Affiliation(s)
- Rachel L Kubiak
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
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12
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Singh S, Phillips GN, Thorson JS. The structural biology of enzymes involved in natural product glycosylation. Nat Prod Rep 2012; 29:1201-37. [PMID: 22688446 DOI: 10.1039/c2np20039b] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The glycosylation of microbial natural products often dramatically influences the biological and/or pharmacological activities of the parental metabolite. Over the past decade, crystal structures of several enzymes involved in the biosynthesis and attachment of novel sugars found appended to natural products have emerged. In many cases, these studies have paved the way to a better understanding of the corresponding enzyme mechanism of action and have served as a starting point for engineering variant enzymes to facilitate to production of differentially-glycosylated natural products. This review specifically summarizes the structural studies of bacterial enzymes involved in biosynthesis of novel sugar nucleotides.
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Affiliation(s)
- Shanteri Singh
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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13
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Crystal structure of the enzyme CapF of Staphylococcus aureus reveals a unique architecture composed of two functional domains. Biochem J 2012; 443:671-80. [PMID: 22320426 DOI: 10.1042/bj20112049] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
CP (capsular polysaccharide) is an important virulence factor during infections by the bacterium Staphylococcus aureus. The enzyme CapF is an attractive therapeutic candidate belonging to the biosynthetic route of CP of pathogenic strains of S. aureus. In the present study, we report two independent crystal structures of CapF in an open form of the apoenzyme. CapF is a homodimer displaying a characteristic dumb-bell-shaped architecture composed of two domains. The N-terminal domain (residues 1-252) adopts a Rossmann fold belonging to the short-chain dehydrogenase/reductase family of proteins. The C-terminal domain (residues 252-369) displays a standard cupin fold with a Zn2+ ion bound deep in the binding pocket of the β-barrel. Functional and thermodynamic analyses indicated that each domain catalyses separate enzymatic reactions. The cupin domain is necessary for the C3-epimerization of UDP-4-hexulose. Meanwhile, the N-terminal domain catalyses the NADPH-dependent reduction of the intermediate species generated by the cupin domain. Analysis by ITC (isothermal titration calorimetry) revealed a fascinating thermodynamic switch governing the attachment and release of the coenzyme NADPH during each catalytic cycle. These observations suggested that the binding of coenzyme to CapF facilitates a disorder-to-order transition in the catalytic loop of the reductase (N-terminal) domain. We anticipate that the present study will improve the general understanding of the synthesis of CP in S. aureus and will aid in the design of new therapeutic agents against this pathogenic bacterium.
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14
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Lawson DM, Stevenson CEM. Structural and functional dissection of aminocoumarin antibiotic biosynthesis: a review. ACTA ACUST UNITED AC 2012; 13:125-33. [DOI: 10.1007/s10969-012-9138-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 05/12/2012] [Indexed: 10/28/2022]
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15
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Development of a Streptomyces venezuelae-based combinatorial biosynthetic system for the production of glycosylated derivatives of doxorubicin and its biosynthetic intermediates. Appl Environ Microbiol 2011; 77:4912-23. [PMID: 21602397 DOI: 10.1128/aem.02527-10] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Doxorubicin, one of the most widely used anticancer drugs, is composed of a tetracyclic polyketide aglycone and l-daunosamine as a deoxysugar moiety, which acts as an important determinant of its biological activity. This is exemplified by the fewer side effects of semisynthetic epirubicin (4'-epi-doxorubicin). An efficient combinatorial biosynthetic system that can convert the exogenous aglycone ε-rhodomycinone into diverse glycosylated derivatives of doxorubicin or its biosynthetic intermediates, rhodomycin D and daunorubicin, was developed through the use of Streptomyces venezuelae mutants carrying plasmids that direct the biosynthesis of different nucleotide deoxysugars and their transfer onto aglycone, as well as the postglycosylation modifications. This system improved epirubicin production from ε-rhodomycinone by selecting a substrate flexible glycosyltransferase, AknS, which was able to transfer the unnatural sugar donors and a TDP-4-ketohexose reductase, AvrE, which efficiently supported the biosynthesis of TDP-4-epi-l-daunosamine. Furthermore, a range of doxorubicin analogs containing diverse deoxysugar moieties, seven of which are novel rhodomycin D derivatives, were generated. This provides new insights into the functions of deoxysugar biosynthetic enzymes and demonstrates the potential of the S. venezuelae-based combinatorial biosynthetic system as a simple biological tool for modifying structurally complex sugar moieties attached to anthracyclines as an alternative to chemical syntheses for improving anticancer agents.
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16
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Tello M, Rejzek M, Wilkinson B, Lawson DM, Field RA. Tyl1a, a TDP-6-deoxy-D-xylo-4-hexulose 3,4-isomerase from Streptomyces fradiae: structure prediction, mutagenesis and solvent isotope incorporation experiments to investigate reaction mechanism. Chembiochem 2008; 9:1295-302. [PMID: 18425854 DOI: 10.1002/cbic.200800021] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Understanding the structure and mechanism of sugar nucleotide processing enzymes is invaluable in the generation of designer enzymes for biotransformation, for instance, in connection with engineering antibiotic glycosylation. In this study, homology modelling and mechanistic comparison to the structurally related RmlC epimerase family has been used to identify and assign functions to active-site residues in the Tyl1a-catalysed keto-sugar nucleotide isomerisation process. Tyl1a His63 is implicated as the base that initiates the isomerisation process by substrate C-3 deprotonation, with Arg109 stabilising the resulting enolate. Subsequent O-3 deprotonation (potentially by His65) and C-4 protonation (potentially by Tyr49) complete the isomerisation process.
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Affiliation(s)
- Mónica Tello
- School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich, NR4 7TJ, UK
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17
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Anthracycline Biosynthesis: Genes, Enzymes and Mechanisms. ANTHRACYCLINE CHEMISTRY AND BIOLOGY I 2007. [DOI: 10.1007/128_2007_14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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18
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Dong C, Major LL, Srikannathasan V, Errey JC, Giraud MF, Lam JS, Graninger M, Messner P, McNeil MR, Field RA, Whitfield C, Naismith JH. RmlC, a C3' and C5' carbohydrate epimerase, appears to operate via an intermediate with an unusual twist boat conformation. J Mol Biol 2006; 365:146-59. [PMID: 17046787 PMCID: PMC1805628 DOI: 10.1016/j.jmb.2006.09.063] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Revised: 09/21/2006] [Accepted: 09/22/2006] [Indexed: 11/27/2022]
Abstract
The striking feature of carbohydrates is their constitutional, conformational and configurational diversity. Biology has harnessed this diversity and manipulates carbohydrate residues in a variety of ways, one of which is epimerization. RmlC catalyzes the epimerization of the C3' and C5' positions of dTDP-6-deoxy-D-xylo-4-hexulose, forming dTDP-6-deoxy-L-lyxo-4-hexulose. RmlC is the third enzyme of the rhamnose pathway, and represents a validated anti-bacterial drug target. Although several structures of the enzyme have been reported, the mechanism and the nature of the intermediates have remained obscure. Despite its relatively small size (22 kDa), RmlC catalyzes four stereospecific proton transfers and the substrate undergoes a major conformational change during the course of the transformation. Here we report the structure of RmlC from several organisms in complex with product and product mimics. We have probed site-directed mutants by assay and by deuterium exchange. The combination of structural and biochemical data has allowed us to assign key residues and identify the conformation of the carbohydrate during turnover. Clear knowledge of the chemical structure of RmlC reaction intermediates may offer new opportunities for rational drug design.
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Affiliation(s)
- Changjiang Dong
- Centre for Biomolecular Sciences, The University, St. Andrews KY16 9ST, UK
| | - Louise L. Major
- Centre for Biomolecular Sciences, The University, St. Andrews KY16 9ST, UK
| | | | - James C. Errey
- School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, UK
| | | | - Joseph S. Lam
- Department of Molecular & Cellular Biology, University of Guelph, Ontario N1G 2W1, Canada
| | - Michael Graninger
- Zentrum für NanoBiotechnologie, Universität für Bodenkultur Wien, A-1180, Vienna, Austria
| | - Paul Messner
- Zentrum für NanoBiotechnologie, Universität für Bodenkultur Wien, A-1180, Vienna, Austria
| | - Michael R. McNeil
- Department of Microbiology, Colorado State University, Fort Collins, CO 80523, USA
| | - Robert A. Field
- School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, UK
| | - Chris Whitfield
- Department of Molecular & Cellular Biology, University of Guelph, Ontario N1G 2W1, Canada
| | - James H. Naismith
- Centre for Biomolecular Sciences, The University, St. Andrews KY16 9ST, UK
- Address Correspondence to James H Naismith, Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, UK. Phone 44-1334-463792 Fax 44-1334-462595 Email
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19
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Freitag A, Li SM, Heide L. Biosynthesis of the unusual 5,5-gem-dimethyl-deoxysugar noviose: investigation of the C-methyltransferase gene cloU. MICROBIOLOGY-SGM 2006; 152:2433-2442. [PMID: 16849806 DOI: 10.1099/mic.0.28931-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The aminocoumarin antibiotic clorobiocin contains an unusual branched deoxysugar with a 5,5-gem-dimethyl structure. Inactivation of the putative C-methyltransferase gene cloU was carried out, which led to the loss of the axial methyl group at C-5 of this deoxysugar moiety. This result establishes the function of cloU, and at the same time it proves that the biosynthesis of the deoxysugar moiety of clorobiocin proceeds via a 3,5-epimerization of the dTDP-4-keto-6-deoxyglucose intermediate. The inactivation was carried out on a cosmid which contained the entire clorobiocin biosynthetic gene cluster. Expression of the modified cluster in a heterologous host led to the formation of desmethyl-clorobiocin and a structural isomer thereof. Both compounds were isolated on a preparative scale, their structures were elucidated by 1H-NMR and mass spectroscopy and their antibacterial activity was assayed.
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Affiliation(s)
- Anja Freitag
- Pharmazeutische Biologie, Pharmazeutisches Institut, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Shu-Ming Li
- Pharmazeutische Biologie, Pharmazeutisches Institut, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Lutz Heide
- Pharmazeutische Biologie, Pharmazeutisches Institut, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
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20
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Jakimowicz P, Tello M, Meyers CLF, Walsh CT, Buttner MJ, Field RA, Lawson DM. The 1.6-A resolution crystal structure of NovW: a 4-keto-6-deoxy sugar epimerase from the novobiocin biosynthetic gene cluster of Streptomyces spheroides. Proteins 2006; 63:261-5. [PMID: 16411240 DOI: 10.1002/prot.20818] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Piotr Jakimowicz
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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21
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Tello M, Jakimowicz P, Errey JC, Freel Meyers CL, Walsh CT, Buttner MJ, Lawson DM, Field RA. Characterisation of Streptomyces spheroides NovW and revision of its functional assignment to a dTDP-6-deoxy-d-xylo-4-hexulose 3-epimerase. Chem Commun (Camb) 2006:1079-81. [PMID: 16514445 DOI: 10.1039/b515763c] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Characterisation of recombinant Streptomyces spheroides NovW in vitro suggests that it is not a kinetically competent dual action dTDP-6-deoxy-d-xylo-4-hexulose 3,5-epimerase, but possesses only significant 3-epimerase activity.
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Affiliation(s)
- Mónica Tello
- Centre for Carbohydrate Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
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22
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Salas JA, Méndez C. Biosynthesis Pathways for Deoxysugars in Antibiotic-Producing Actinomycetes: Isolation, Characterization and Generation of Novel Glycosylated Derivatives. J Mol Microbiol Biotechnol 2005; 9:77-85. [PMID: 16319497 DOI: 10.1159/000088838] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Many bioactive natural products synthesized by actinomycetes are glycosylated compounds in which the appended sugars contribute to specific interactions with their biological target. Most of these sugars are 6-deoxyhexoses, of which more than 70 different forms have been identified, and an increasing number of gene clusters involved in 6-deoxyhexoses biosynthesis are being characterized from antibiotic-producing actinomycetes. Novel glycosylated compounds have been generated by modifying natural deoxysugar biosynthesis pathways in the producer organisms, and/or the simultaneous expression in these strains of selected deoxysugar biosynthesis genes from other strains. Non-producing strains endowed with the capacity to synthesize novel deoxysugars through the expression of engineered deoxysugar biosynthesis clusters can also be used as alternative hosts. Transfer of these deoxysugars to a multiplicity of aglycones relies upon the existence of glycosyltransferases with an inherent degree of 'relaxed substrate specificity'. In this review, we analyze how the knowledge coming out from isolation and characterization of deoxysugar biosynthesis pathways from actinomycetes is being used to produce novel glycosylated derivatives of natural products.
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Affiliation(s)
- José A Salas
- Departamento de Biología Funcional e Instituto Universitario de Oncología de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain.
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23
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Elling L, Rupprath C, Günther N, Römer U, Verseck S, Weingarten P, Dräger G, Kirschning A, Piepersberg W. An enzyme module system for the synthesis of dTDP-activated deoxysugars from dTMP and sucrose. Chembiochem 2005; 6:1423-30. [PMID: 15977277 DOI: 10.1002/cbic.200500037] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A flexible enzyme module system is presented that allows preparative access to important dTDP-activated deoxyhexoses from dTMP and sucrose. The strategic combination of the recombinant enzymes dTMP-kinase and sucrose synthase (SuSy), and the enzymes RmlB (4,6-dehydratase), RmlC (3,5-epimerase) and RmlD (4-ketoreductase) from the biosynthetic pathway of dTDP-beta-L-rhamnose was optimized. The SuSy module (dTMP-kinase, SuSy, +/-RmlB) yielded the precursor dTDP-alpha-D-glucose (2) or the biosynthetic intermediate dTDP-6-deoxy-4-keto-alpha-D-glucose (3) on a 0.2-0.6 g scale with overall yields of 62 % and 72 %, respectively. A two-step strategy in which the SuSy module was followed by the deoxysugar module (RmlC and RmlD) resulted in the synthesis of dTDP-beta-L-rhamnose (4; 24.1 micromol, overall yield: 35.9 %). Substitution of RmlC by DnmU from the dTDP-beta-L-daunosamine pathway of Streptomyces peucetius in this module demonstrated that DnmU acts in vitro as a 3,5-epimerase with 3 as substrate to yield 4 (32.2 mumol, overall yield: 44.7 %). Chemical reduction of 3 with NaBH4 gave a mixture of the C-4 epimers dTDP-alpha-D-quinovose (6) and dTDP-alpha-D-fucose (7) in a ratio of 2:1. In summary, the modular character of the presented enzyme system provides valuable compounds for the biochemical characterization of deoxysugar pathways playing a major role in microbial producers of antibiotic and antitumour agents.
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Affiliation(s)
- Lothar Elling
- Department of Biotechnology/Biomaterial Sciences and Helmholtz Institute for Biomedical Engineering, RWTH Aachen, Worringerweg 1, 52056 Aachen, Germany.
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24
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Mulrooney EF, Poon KKH, McNally DJ, Brisson JR, Lam JS. Biosynthesis of UDP-N-acetyl-L-fucosamine, a precursor to the biosynthesis of lipopolysaccharide in Pseudomonas aeruginosa serotype O11. J Biol Chem 2005; 280:19535-42. [PMID: 15778500 DOI: 10.1074/jbc.m500612200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
UDP-N-acetyl-L-fucosamine is a precursor to l-fucosamine in the lipopolysaccharide of Pseudomonas aeruginosa serotype O11 and the capsule of Staphylococcus aureus type 5. We have demonstrated previously the involvement of three enzymes, WbjB, WbjC, and WbjD, in the biosynthesis of UDP-2-acetamido-2,6-dideoxy-L-galactose or UDP-N-acetyl-L-fucosamine (UDP-l-FucNAc). An intermediate compound from the coupled-reaction of WbjB-WbjC with the initial substrate UDP-2-acetamido-2-deoxy-alpha-D-glucose or UDP-N-acetyl-D-glucosamine (UDP-GlcNAc) was purified, and the structure was determined by NMR spectroscopy to be UDP-2-acetamido-2,6-dideoxy-L-talose (UDP-L-PneNAc). WbjD could then convert this intermediate into a new product with the same mass, consistent with a C-2 epimerization reaction. Those results led us to propose a pathway for the biosynthesis of UDP-L-FucNAc; however, the exact enzymatic activity of each of these proteins has not been defined. Here, we describe a fast protein liquid chromatography (FPLC)-based anion-exchange procedure, which allowed the separation and purification of the products of C-2 epimerization due to WbjD. Also, the application of a cryogenically cooled probe in NMR spectrometry offers the greatest sensitivity for determining the structures of minute quantities of materials, allowing the identification of the final product of the pathway. Our results showed that WbjB is bifunctional, catalyzing firstly C-4, C-6 dehydration and secondly C-5 epimerization in the reaction with the substrate UDP-D-GlcNAc, producing two intermediates. WbjC is also bifunctional, catalyzing C-3 epimerization of the second intermediate followed by reduction at C-4. The FPLC-based procedure provided good resolution of the final product of WbjD reaction from its epimer/substrate UDP-l-PneNAc, and the use of the cryogenically cooled probe in NMR revealed unequivocally that the final product is UDP-L-FucNAc.
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Affiliation(s)
- Erin F Mulrooney
- Department of Microbiology, University of Guelph, Ontario, Canada
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