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Tang Q, Petchey M, Rowlinson B, Burden TJ, Fairlamb IJS, Grogan G. Broad Spectrum Enantioselective Amide Bond Synthetase from Streptoalloteichus hindustanus. ACS Catal 2024; 14:1021-1029. [PMID: 38269041 PMCID: PMC10804368 DOI: 10.1021/acscatal.3c05656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/19/2023] [Accepted: 12/26/2023] [Indexed: 01/26/2024]
Abstract
The synthesis of amide bonds is one of the most frequently performed reactions in pharmaceutical synthesis, but the requirement for stoichiometric quantities of coupling agents and activated substrates in established methods has prompted interest in biocatalytic alternatives. Amide Bond Synthetases (ABSs) actively catalyze both the ATP-dependent adenylation of carboxylic acid substrates and their subsequent amidation using an amine nucleophile, both within the active site of the enzyme, enabling the use of only a small excess of the amine partner. We have assessed the ability of an ABS from Streptoalloteichus hindustanus (ShABS) to couple a range of carboxylic acid substrates and amines to form amine products. ShABS displayed superior activity to a previously studied ABS, McbA, and a remarkable complementary substrate specificity that included the enantioselective formation of a library of amides from racemic acid and amine coupling partners. The X-ray crystallographic structure of ShABS has permitted mutational mapping of the carboxylic acid and amine binding sites, revealing key roles for L207 and F246 in determining the enantioselectivity of the enzyme with respect to chiral acid and amine substrates. ShABS was applied to the synthesis of pharmaceutical amides, including ilepcimide, lazabemide, trimethobenzamide, and cinepazide, the last with 99% conversion and 95% isolated yield. These findings provide a blueprint for enabling a contemporary pharmaceutical synthesis of one of the most significant classes of small molecule drugs using biocatalysis.
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Affiliation(s)
- Qingyun Tang
- Department of Chemistry, University of York, Heslington, York YO10
5DD, U.K.
| | - Mark Petchey
- Department of Chemistry, University of York, Heslington, York YO10
5DD, U.K.
| | - Benjamin Rowlinson
- Department of Chemistry, University of York, Heslington, York YO10
5DD, U.K.
| | - Thomas J. Burden
- Department of Chemistry, University of York, Heslington, York YO10
5DD, U.K.
| | - Ian J. S. Fairlamb
- Department of Chemistry, University of York, Heslington, York YO10
5DD, U.K.
| | - Gideon Grogan
- Department of Chemistry, University of York, Heslington, York YO10
5DD, U.K.
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2
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Affiliation(s)
- Mark R. Petchey
- York Structural Biology Laboratory, Department of Chemistry University of York Heslington, York YO10 5DD U.K
| | - Gideon Grogan
- York Structural Biology Laboratory, Department of Chemistry University of York Heslington, York YO10 5DD U.K
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Buttner MJ, Schäfer M, Lawson DM, Maxwell A. Structural insights into simocyclinone as an antibiotic, effector ligand and substrate. FEMS Microbiol Rev 2018; 42:4604775. [PMID: 29126195 PMCID: PMC5812520 DOI: 10.1093/femsre/fux055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/07/2017] [Indexed: 12/25/2022] Open
Abstract
Simocyclinones are antibiotics produced by Streptomyces and Kitasatospora species that inhibit the validated drug target DNA gyrase in a unique way, and they are thus of therapeutic interest. Structural approaches have revealed their mode of action, the inducible-efflux mechanism in the producing organism, and given insight into one step in their biosynthesis. The crystal structures of simocyclinones bound to their target (gyrase), the transcriptional repressor SimR and the biosynthetic enzyme SimC7 reveal fascinating insight into how molecular recognition is achieved with these three unrelated proteins.
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Affiliation(s)
- Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Martin Schäfer
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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Bilyk O, Brötz E, Tokovenko B, Bechthold A, Paululat T, Luzhetskyy A. New Simocyclinones: Surprising Evolutionary and Biosynthetic Insights. ACS Chem Biol 2016; 11:241-50. [PMID: 26566170 DOI: 10.1021/acschembio.5b00669] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Simocyclinone D8 (1, SD8) has attracted attention due to its highly complex hybrid structure and the unusual way it inhibits bacterial DNA gyrase by preventing DNA binding to the enzyme. Although a hypothesis explaining simocyclinone biosynthesis has been previously proposed, little was proven in vivo due to the genetic inaccessibility of the producer strain. Herein, we report discovery of three new D-type simocyclinones (D9, D10, and D11) produced by Kitasatospora sp. and Streptomyces sp. NRRL B-24484, as well as the identification and annotation of their biosynthetic gene clusters. Unexpectedly, the arrangement of the newly discovered biosynthetic gene clusters is starkly different from the previously published one, despite the nearly identical structures of D8 and D9 simocyclinones. The gene inactivation and expression studies have disproven the role of a modular polyketide synthase (PKS) system in the assembly of the linear dicarboxylic acid. Instead, the new stand-alone ketosynthase genes were shown to be involved in the biosynthesis of the tetraene chain. Additionally, we identified the gene responsible for the conversion of simocyclinone D9 (2, SD9) into D8.
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Affiliation(s)
- Oksana Bilyk
- Helmholtz-Institute
for Pharmaceutical Research Saarland, Saarland University Campus, Building
C2.3, 66123 Saarbrücken, Germany
| | - Elke Brötz
- Helmholtz-Institute
for Pharmaceutical Research Saarland, Saarland University Campus, Building
C2.3, 66123 Saarbrücken, Germany
| | - Bogdan Tokovenko
- Helmholtz-Institute
for Pharmaceutical Research Saarland, Saarland University Campus, Building
C2.3, 66123 Saarbrücken, Germany
| | - Andreas Bechthold
- University of Freiburg, Institute for Pharmaceutical
Sciences, Department for Pharmaceutical Biology and Biotechnology, Stefan-Meier-Straße 14, 79104 Freiburg, Germany
| | - Thomas Paululat
- University of Siegen, Faculty 4, Organic Chemistry
2, Adolf-Reichwein-Straße
2, 57068 Siegen, Germany
| | - Andriy Luzhetskyy
- Helmholtz-Institute
for Pharmaceutical Research Saarland, Saarland University Campus, Building
C2.3, 66123 Saarbrücken, Germany
- Universität des Saarlandes, Pharmazeutische Biotechnologie, Building C2.3, 66123 Saarbrücken, Germany
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5
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Schäfer M, Le TBK, Hearnshaw SJ, Maxwell A, Challis GL, Wilkinson B, Buttner MJ. SimC7 Is a Novel NAD(P)H-Dependent Ketoreductase Essential for the Antibiotic Activity of the DNA Gyrase Inhibitor Simocyclinone. J Mol Biol 2015; 427:2192-204. [PMID: 25861759 PMCID: PMC4451461 DOI: 10.1016/j.jmb.2015.03.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 03/30/2015] [Accepted: 03/31/2015] [Indexed: 01/02/2023]
Abstract
Simocyclinone D8 (SD8) is a potent DNA gyrase inhibitor produced by Streptomyces antibioticus Tü6040. The simocyclinone (sim) biosynthetic gene cluster has been sequenced and a hypothetical biosynthetic pathway has been proposed. The tetraene linker in SD8 was suggested to be the product of a modular type I polyketide synthase working in trans with two monofunctional enzymes. One of these monofunctional enzymes, SimC7, was proposed to supply a dehydratase activity missing from two modules of the polyketide synthase. In this study, we report the function of SimC7. We isolated the entire ~ 72-kb sim cluster on a single phage artificial chromosome clone and produced simocyclinone heterologously in a Streptomyces coelicolor strain engineered for improved antibiotic production. Deletion of simC7 resulted in the production of a novel simocyclinone, 7-oxo-SD8, which unexpectedly carried a normal tetraene linker but was altered in the angucyclinone moiety. We demonstrate that SimC7 is an NAD(P)H-dependent ketoreductase that catalyzes the conversion of 7-oxo-SD8 into SD8. 7-oxo-SD8 was essentially inactive as a DNA gyrase inhibitor, and the reduction of the keto group by SimC7 was shown to be crucial for high-affinity binding to the enzyme. Thus, SimC7 is an angucyclinone ketoreductase that is essential for the biological activity of simocyclinone. The ~ 75-kb simocyclinone biosynthetic cluster was expressed in a heterologous system. SimC7 is a novel NAD(P)H-dependent ketoreductase. SimC7 function is essential for the antibiotic activity of the DNA gyrase inhibitor simocyclinone.
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Affiliation(s)
- Martin Schäfer
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Stephen J Hearnshaw
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Gregory L Challis
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom.
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Dunn ZD, Wever WJ, Economou NJ, Bowers AA, Li B. Enzymatic basis of "hybridity" in thiomarinol biosynthesis. Angew Chem Int Ed Engl 2015; 54:5137-41. [PMID: 25726835 DOI: 10.1002/anie.201411667] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Indexed: 11/07/2022]
Abstract
Thiomarinol is a naturally occurring double-headed antibiotic that is highly potent against methicillin-resistant Staphylococcus aureus. Its structure comprises two antimicrobial subcomponents, pseudomonic acid analogue and holothin, linked by an amide bond. TmlU was thought to be the sole enzyme responsible for this amide-bond formation. In contrast to this idea, we show that TmlU acts as a CoA ligase that activates pseudomonic acid as a thioester that is processed by the acetyltransferase HolE to catalyze the amidation. TmlU prefers complex acyl acids as substrates, whereas HolE is relatively promiscuous, accepting a range of acyl-CoA and amine substrates. Our results provide detailed biochemical information on thiomarinol biosynthesis, and evolutionary insight regarding how the pseudomonic acid and holothin pathways converge to generate this potent hybrid antibiotic. This work also demonstrates the potential of TmlU/HolE enzymes as engineering tools to generate new "hybrid" molecules.
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Affiliation(s)
- Zachary D Dunn
- Department of Chemistry, University of North Carolina at Chapel Hill, Carolina Center for Genome Sciences, Chapel Hill, NC, 27599 (USA)
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7
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Dunn ZD, Wever WJ, Economou NJ, Bowers AA, Li B. Enzymatic Basis of “Hybridity” in Thiomarinol Biosynthesis. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201411667] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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8
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Qin Z, Huang S, Yu Y, Deng H. Dithiolopyrrolone natural products: isolation, synthesis and biosynthesis. Mar Drugs 2013; 11:3970-97. [PMID: 24141227 PMCID: PMC3826145 DOI: 10.3390/md11103970] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/25/2013] [Accepted: 09/26/2013] [Indexed: 12/24/2022] Open
Abstract
Dithiolopyrrolones are a class of antibiotics that possess the unique pyrrolinonodithiole (4H-[1,2] dithiolo [4,3-b] pyrrol-5-one) skeleton linked to two variable acyl groups. To date, there are approximately 30 naturally occurring dithiolopyrrolone compounds, including holomycin, thiolutin, and aureothricin, and more recently thiomarinols, a unique class of hybrid marine bacterial natural products containing a dithiolopyrrolone framework linked by an amide bridge with an 8-hydroxyoctanoyl chain linked to a monic acid. Generally, dithiolopyrrolone antibiotics have broad-spectrum antibacterial activity against various microorganisms, including Gram-positive and Gram-negative bacteria, and even parasites. Holomycin appeared to be active against rifamycin-resistant bacteria and also inhibit the growth of the clinical pathogen methicillin-resistant Staphylococcus aureus N315. Its mode of action is believed to inhibit RNA synthesis although the exact mechanism has yet to be established in vitro. A recent work demonstrated that the fish pathogen Yersinia ruckeri employs an RNA methyltransferase for self-resistance during the holomycin production. Moreover, some dithiolopyrrolone derivatives have demonstrated promising antitumor activities. The biosynthetic gene clusters of holomycin have recently been identified in S. clavuligerus and characterized biochemically and genetically. The biosynthetic gene cluster of thiomarinol was also identified from the marine bacterium Pseudoalteromonas sp. SANK 73390, which was uniquely encoded by two independent pathways for pseudomonic acid and pyrrothine in a novel plasmid. The aim of this review is to give an overview about the isolations, characterizations, synthesis, biosynthesis, bioactivities and mode of action of this unique family of dithiolopyrrolone natural products, focusing on the period from 1940s until now.
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Affiliation(s)
- Zhiwei Qin
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; E-Mails: (Z.Q.); (S.H.)
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, Scotland, UK
| | - Sheng Huang
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; E-Mails: (Z.Q.); (S.H.)
| | - Yi Yu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; E-Mails: (Z.Q.); (S.H.)
| | - Hai Deng
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, Scotland, UK
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9
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A high-throughput screen for directed evolution of aminocoumarin amide synthetases. Anal Biochem 2011; 419:61-6. [DOI: 10.1016/j.ab.2011.07.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2011] [Revised: 07/25/2011] [Accepted: 07/31/2011] [Indexed: 01/15/2023]
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10
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A natural plasmid uniquely encodes two biosynthetic pathways creating a potent anti-MRSA antibiotic. PLoS One 2011; 6:e18031. [PMID: 21483852 PMCID: PMC3069032 DOI: 10.1371/journal.pone.0018031] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 02/18/2011] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Understanding how complex antibiotics are synthesised by their producer bacteria is essential for creation of new families of bioactive compounds. Thiomarinols, produced by marine bacteria belonging to the genus Pseudoalteromonas, are hybrids of two independently active species: the pseudomonic acid mixture, mupirocin, which is used clinically against MRSA, and the pyrrothine core of holomycin. METHODOLOGY/PRINCIPAL FINDINGS High throughput DNA sequencing of the complete genome of the producer bacterium revealed a novel 97 kb plasmid, pTML1, consisting almost entirely of two distinct gene clusters. Targeted gene knockouts confirmed the role of these clusters in biosynthesis of the two separate components, pseudomonic acid and the pyrrothine, and identified a putative amide synthetase that joins them together. Feeding mupirocin to a mutant unable to make the endogenous pseudomonic acid created a novel hybrid with the pyrrothine via "mutasynthesis" that allows inhibition of mupirocin-resistant isoleucyl-tRNA synthetase, the mupirocin target. A mutant defective in pyrrothine biosynthesis was also able to incorporate alternative amine substrates. CONCLUSIONS/SIGNIFICANCE Plasmid pTML1 provides a paradigm for combining independent antibiotic biosynthetic pathways or using mutasynthesis to develop a new family of hybrid derivatives that may extend the effective use of mupirocin against MRSA.
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11
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Boll B, Hennig S, Xie C, Sohng JK, Heide L. Adenylate-Forming Enzymes of Rubradirin Biosynthesis: RubC1 Is a Bifunctional Enzyme with Aminocoumarin Acyl Ligase and Tyrosine-Activating Domains. Chembiochem 2011; 12:1105-14. [DOI: 10.1002/cbic.201000778] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Indexed: 11/09/2022]
Affiliation(s)
- Björn Boll
- Pharmazeutisches Institut, Universität Tübingen, Germany
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12
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Murphy AC, Fukuda D, Song Z, Hothersall J, Cox RJ, Willis CL, Thomas CM, Simpson TJ. Engineered thiomarinol antibiotics active against MRSA are generated by mutagenesis and mutasynthesis of Pseudoalteromonas SANK73390. Angew Chem Int Ed Engl 2011; 50:3271-4. [PMID: 21381163 DOI: 10.1002/anie.201007029] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 01/17/2011] [Indexed: 11/06/2022]
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13
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Murphy AC, Fukuda D, Song Z, Hothersall J, Cox RJ, Willis CL, Thomas CM, Simpson TJ. Engineered Thiomarinol Antibiotics Active against MRSA Are Generated by Mutagenesis and Mutasynthesis of Pseudoalteromonas SANK73390. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007029] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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14
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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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Rui Z, Petrícková K, Skanta F, Pospísil S, Yang Y, Chen CY, Tsai SF, Floss HG, Petrícek M, Yu TW. Biochemical and genetic insights into asukamycin biosynthesis. J Biol Chem 2010; 285:24915-24. [PMID: 20522559 DOI: 10.1074/jbc.m110.128850] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Asukamycin, a member of the manumycin family metabolites, is an antimicrobial and potential antitumor agent isolated from Streptomyces nodosus subsp. asukaensis. The entire asukamycin biosynthetic gene cluster was cloned, assembled, and expressed heterologously in Streptomyces lividans. Bioinformatic analysis and mutagenesis studies elucidated the biosynthetic pathway at the genetic and biochemical level. Four gene sets, asuA-D, govern the formation and assembly of the asukamycin building blocks: a 3-amino-4-hydroxybenzoic acid core component, a cyclohexane ring, two triene polyketide chains, and a 2-amino-3-hydroxycyclopent-2-enone moiety to form the intermediate protoasukamycin. AsuE1 and AsuE2 catalyze the conversion of protoasukamycin to 4-hydroxyprotoasukamycin, which is epoxidized at C5-C6 by AsuE3 to the final product, asukamycin. Branched acyl CoA starter units, derived from Val, Leu, and Ile, can be incorporated by the actions of the polyketide synthase III (KSIII) AsuC3/C4 as well as the cellular fatty acid synthase FabH to produce the asukamycin congeners A2-A7. In addition, the type II thioesterase AsuC15 limits the cellular level of omega-cyclohexyl fatty acids and likely maintains homeostasis of the cellular membrane.
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Affiliation(s)
- Zhe Rui
- Department of Biological Science, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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Walsh CT, Fischbach MA. Natural products version 2.0: connecting genes to molecules. J Am Chem Soc 2010; 132:2469-93. [PMID: 20121095 DOI: 10.1021/ja909118a] [Citation(s) in RCA: 323] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Natural products have played a prominent role in the history of organic chemistry, and they continue to be important as drugs, biological probes, and targets of study for synthetic and analytical chemists. In this Perspective, we explore how connecting Nature's small molecules to the genes that encode them has sparked a renaissance in natural product research, focusing primarily on the biosynthesis of polyketides and non-ribosomal peptides. We survey monomer biogenesis, coupling chemistries from templated and non-templated pathways, and the broad set of tailoring reactions and hybrid pathways that give rise to the diverse scaffolds and functionalization patterns of natural products. We conclude by considering two questions: What would it take to find all natural product scaffolds? What kind of scientists will be studying natural products in the future?
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Affiliation(s)
- Christopher T Walsh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA.
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Olano C, Méndez C, Salas JA. Post-PKS tailoring steps in natural product-producing actinomycetes from the perspective of combinatorial biosynthesis. Nat Prod Rep 2010; 27:571-616. [DOI: 10.1039/b911956f] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Gómez García I, Stevenson CEM, Usón I, Freel Meyers CL, Walsh CT, Lawson DM. The crystal structure of the novobiocin biosynthetic enzyme NovP: the first representative structure for the TylF O-methyltransferase superfamily. J Mol Biol 2009; 395:390-407. [PMID: 19857499 DOI: 10.1016/j.jmb.2009.10.045] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Revised: 10/14/2009] [Accepted: 10/19/2009] [Indexed: 12/19/2022]
Abstract
NovP is an S-adenosyl-l-methionine-dependent O-methyltransferase that catalyzes the penultimate step in the biosynthesis of the aminocoumarin antibiotic novobiocin. Specifically, it methylates at 4-OH of the noviose moiety, and the resultant methoxy group is important for the potency of the mature antibiotic: previous crystallographic studies have shown that this group interacts directly with the target enzyme DNA gyrase, which is a validated drug target. We have determined the high-resolution crystal structure of NovP from Streptomyces spheroides as a binary complex with its desmethylated cosubstrate S-adenosyl-l-homocysteine. The structure displays a typical class I methyltransferase fold, in addition to motifs that are consistent with a divalent-metal-dependent mechanism. This is the first representative structure of a methyltransferase from the TylF superfamily, which includes a number of enzymes implicated in the biosynthesis of antibiotics and other therapeutics. The NovP structure reveals a number of distinctive structural features that, based on sequence conservation, are likely to be characteristic of the superfamily. These include a helical 'lid' region that gates access to the cosubstrate binding pocket and an active center that contains a 3-Asp putative metal binding site. A further conserved Asp likely acts as the general base that initiates the reaction by deprotonating the 4-OH group of the noviose unit. Using in silico docking, we have generated models of the enzyme-substrate complex that are consistent with the proposed mechanism. Furthermore, these models suggest that NovP is unlikely to tolerate significant modifications at the noviose moiety, but could show increasing substrate promiscuity as a function of the distance of the modification from the methylation site. These observations could inform future attempts to utilize NovP for methylating a range of glycosylated compounds.
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The evolution of gene collectives: How natural selection drives chemical innovation. Proc Natl Acad Sci U S A 2008; 105:4601-8. [PMID: 18216259 DOI: 10.1073/pnas.0709132105] [Citation(s) in RCA: 201] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA sequencing has become central to the study of evolution. Comparing the sequences of individual genes from a variety of organisms has revolutionized our understanding of how single genes evolve, but the challenge of analyzing polygenic phenotypes has complicated efforts to study how genes evolve when they are part of a group that functions collectively. We suggest that biosynthetic gene clusters from microbes are ideal candidates for the evolutionary study of gene collectives; these selfish genetic elements evolve rapidly, they usually comprise a complete pathway, and they have a phenotype-a small molecule-that is easy to identify and assay. Because these elements are transferred horizontally as well as vertically, they also provide an opportunity to study the effects of horizontal transmission on gene evolution. We discuss known examples to begin addressing two fundamental questions about the evolution of biosynthetic gene clusters: How do they propagate by horizontal transfer? How do they change to create new molecules?
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Anderle C, Hennig S, Kammerer B, Li SM, Wessjohann L, Gust B, Heide L. Improved mutasynthetic approaches for the production of modified aminocoumarin antibiotics. ACTA ACUST UNITED AC 2007; 14:955-67. [PMID: 17719494 DOI: 10.1016/j.chembiol.2007.07.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Revised: 07/23/2007] [Accepted: 07/24/2007] [Indexed: 11/24/2022]
Abstract
This study reports improved mutasynthetic approaches for the production of aminocoumarin antibiotics. Previously, the mutasynthetic production of aminocoumarins with differently substituted benzoyl moieties was limited by the substrate specificity of the amide synthetase CloL. We expressed two amide synthetases with different substrate specificity, CouL and SimL, in appropriately engineered producer strains. After feeding of precursor analogs that were not accepted by CloL, but by SimL or CouL, a range of aminocoumarins, unattainable in our previous experiments, was produced and isolated in preparative amounts. Further, we developed a two-stage mutasynthesis procedure for the production of hybrid antibiotics that showed the substitution pattern of novobiocin in the aminocoumarin moiety and that of clorobiocin in the deoxysugar moiety. The substitution pattern of the benzoyl moiety was determined by external addition of an appropriate precursor. Twenty-five aminocoumarin compounds were prepared by these methods, and their structures were elucidated with mass and 1H-NMR spectroscopy.
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Affiliation(s)
- Christine Anderle
- Pharmazeutische Biologie, Pharmazeutisches Institut, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
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Bililign T, Griffith BR, Thorson JS. Structure, activity, synthesis and biosynthesis of aryl-C-glycosides. Nat Prod Rep 2005; 22:742-60. [PMID: 16311633 DOI: 10.1039/b407364a] [Citation(s) in RCA: 220] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The focus of this review is to highlight the structure, bioactivity and biosynthesis of naturally occurring aryl-C-glycosides. General synthetic methods and their relevance to proposed biochemical mechanisms for the aryl-C-glycoside bond formation are also presented.
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Affiliation(s)
- Tsion Bililign
- Chemistry Department, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA.
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