1
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Zhukrovska K, Binda E, Fedorenko V, Marinelli F, Yushchuk O. The Impact of Heterologous Regulatory Genes from Lipodepsipeptide Biosynthetic Gene Clusters on the Production of Teicoplanin and A40926. Antibiotics (Basel) 2024; 13:115. [PMID: 38391501 PMCID: PMC10886168 DOI: 10.3390/antibiotics13020115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
StrR-like pathway-specific transcriptional regulators (PSRs) function as activators in the biosynthesis of various antibiotics, including glycopeptides (GPAs), aminoglycosides, aminocoumarins, and ramoplanin-like lipodepsipeptides (LDPs). In particular, the roles of StrR-like PSRs have been previously investigated in the biosynthesis of streptomycin, novobiocin, GPAs like balhimycin, teicoplanin, and A40926, as well as LDP enduracidin. In the current study, we focused on StrR-like PSRs from the ramoplanin biosynthetic gene cluster (BGC) in Actinoplanes ramoplaninifer ATCC 33076 (Ramo5) and the chersinamycin BGC in Micromonospora chersina DSM 44151 (Chers28). Through the analysis of the amino acid sequences of Ramo5 and Chers28, we discovered that these proteins are phylogenetically distant from other experimentally investigated StrR PSRs, although all StrR-like PSRs found in BGCs for different antibiotics share a conserved secondary structure. To investigate whether Ramo5 and Chers28, given their phylogenetic positions, might influence the biosynthesis of other antibiotic pathways governed by StrR-like PSRs, the corresponding genes (ramo5 and chers28) were heterologously expressed in Actinoplanes teichomyceticus NRRL B-16726 and Nonomuraea gerenzanensis ATCC 39727, which produce the clinically-relevant GPAs teicoplanin and A40926, respectively. Recombinant strains of NRRL B-16726 and ATCC 39727 expressing chers28 exhibited improved antibiotic production, although the expression of ramo5 did not yield the same effect. These results demonstrate that some StrR-like PSRs can "cross-talk" between distant biosynthetic pathways and might be utilized as tools for the activation of silent BGCs regulated by StrR-like PSRs.
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Affiliation(s)
- Kseniia Zhukrovska
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Elisa Binda
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
| | - Oleksandr Yushchuk
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
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2
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Adhikari A, Shakya S, Shrestha S, Aryal D, Timalsina KP, Dhakal D, Khatri Y, Parajuli N. Biocatalytic role of cytochrome P450s to produce antibiotics: A review. Biotechnol Bioeng 2023; 120:3465-3492. [PMID: 37691185 DOI: 10.1002/bit.28548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 08/15/2023] [Accepted: 08/26/2023] [Indexed: 09/12/2023]
Abstract
Cytochrome P450s belong to a family of heme-binding monooxygenases, which catalyze regio- and stereospecific functionalisation of C-H, C-C, and C-N bonds, including heteroatom oxidation, oxidative C-C bond cleavages, and nitrene transfer. P450s are considered useful biocatalysts for the production of pharmaceutical products, fine chemicals, and bioremediating agents. Despite having tremendous biotechnological potential, being heme-monooxygenases, P450s require either autologous or heterologous redox partner(s) to perform chemical transformations. Randomly distributed P450s throughout a bacterial genome and devoid of particular redox partners in natural products biosynthetic gene clusters (BGCs) showed an extra challenge to reveal their pharmaceutical potential. However, continuous efforts have been made to understand their involvement in antibiotic biosynthesis and their modification, and this review focused on such BGCs. Here, particularly, we have discussed the role of P450s involved in the production of macrolides and aminocoumarin antibiotics, nonribosomal peptide (NRPSs) antibiotics, ribosomally synthesized and post-translationally modified peptide (RiPPs) antibiotics, and others. Several reactions catalyzed by P450s, as well as the role of their redox partners involved in the BGCs of various antibiotics and their derivatives, have been primarily addressed in this review, which would be useful in further exploration of P450s for the biosynthesis of new therapeutics.
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Affiliation(s)
- Anup Adhikari
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Sajan Shakya
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Shreesti Shrestha
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Dipa Aryal
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Kavi Prasad Timalsina
- Department of Biotechnology, National College, Tribhuvan University, Kathmandu, Nepal
| | - Dipesh Dhakal
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida, USA
| | | | - Niranjan Parajuli
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
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3
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Salman M, Sharma P, Kumar M, Ethayathulla AS, Kaur P. Targeting novel sites in DNA gyrase for development of anti-microbials. Brief Funct Genomics 2022; 22:180-194. [PMID: 36064602 DOI: 10.1093/bfgp/elac029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/28/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance in bacteria poses major challenges in selection of the therapeutic regime for managing the infectious disease. There is currently an upsurge in the appearance of multiple drug resistance in bacterial pathogens and a decline in the discovery of novel antibiotics. DNA gyrase is an attractive target used for antibiotic discovery due to its vital role in bacterial DNA replication and segregation in addition to its absence in mammalian organisms. Despite the presence of successful antibiotics targeting this enzyme, there is a need to bypass the resistance against this validated drug target. Hence, drug development in DNA gyrase is a highly active research area. In addition to the conventional binding sites for the novobiocin and fluoroquinolone antibiotics, several novel sites are being exploited for drug discovery. The binding sites for novel bacterial type II topoisomerase inhibitor (NBTI), simocyclinone, YacG, Thiophene and CcdB are structurally and biochemically validated active sites, which inhibit the supercoiling activity of topoisomerases. The novel chemical moieties with varied scaffolds have been identified to target DNA gyrase. Amongst them, the NBTI constitutes the most advanced DNA gyrase inhibitor which are in phase III trial of drug development. The present review aims to classify the novel binding sites other than the conventional novobiocin and quinolone binding pocket to bypass the resistance due to mutations in the DNA gyrase enzyme. These sites can be exploited for the identification of new scaffolds for the development of novel antibacterial compounds.
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Affiliation(s)
- Mohd Salman
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Priyanka Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Mukesh Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - A S Ethayathulla
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
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4
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Morshed MT, Lacey E, Vuong D, Lacey AE, Lean SS, Moggach SA, Karuso P, Chooi YH, Booth TJ, Piggott AM. Chlorinated metabolites from Streptomyces sp. highlight the role of biosynthetic mosaics and superclusters in the evolution of chemical diversity. Org Biomol Chem 2021; 19:6147-6159. [PMID: 34180937 DOI: 10.1039/d1ob00600b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
LCMS-guided screening of a library of biosynthetically talented bacteria and fungi identified Streptomyces sp. MST- as a prolific producer of chlorinated metabolites. We isolated and characterised six new and nine reported compounds from MST-, belonging to three discrete classes - the depsipeptide svetamycins, the indolocarbazole borregomycins and the aromatic polyketide anthrabenzoxocinones. Following genome sequencing of MST-, we describe, for the first time, the svetamycin biosynthetic gene cluster (sve), its mosaic structure and its relationship to several distantly related gene clusters. Our analysis of the sve cluster suggested that the reported stereostructures of the svetamycins may be incorrect. This was confirmed by single-crystal X-ray diffraction analysis, allowing us to formally revise the absolute configurations of svetamycins A-G. We also show that the borregomycins and anthrabenzoxocinones are encoded by a single supercluster (bab) implicating superclusters as potential nucleation points for the evolution of biosynthetic gene clusters. These clusters highlight how individual enzymes and functional subclusters can be co-opted during the formation of biosynthetic gene clusters, providing a rare insight into the poorly understood mechanisms underpinning the evolution of chemical diversity.
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Affiliation(s)
- Mahmud T Morshed
- Department of Molecular Sciences, Macquarie University, NSW 2109, Australia.
| | - Ernest Lacey
- Department of Molecular Sciences, Macquarie University, NSW 2109, Australia. and Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - Daniel Vuong
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - Alastair E Lacey
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - Soo Sum Lean
- School of Molecular Sciences, University of Western Australia, Perth, WA 6009, Australia.
| | - Stephen A Moggach
- School of Molecular Sciences, University of Western Australia, Perth, WA 6009, Australia.
| | - Peter Karuso
- Department of Molecular Sciences, Macquarie University, NSW 2109, Australia.
| | - Yit-Heng Chooi
- School of Molecular Sciences, University of Western Australia, Perth, WA 6009, Australia.
| | - Thomas J Booth
- School of Molecular Sciences, University of Western Australia, Perth, WA 6009, Australia.
| | - Andrew M Piggott
- Department of Molecular Sciences, Macquarie University, NSW 2109, Australia.
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5
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Vargas Hoyos HA, Chiaramonte JB, Barbosa-Casteliani AG, Fernandez Morais J, Perez-Jaramillo JE, Nobre Santos S, Nascimento Queiroz SC, Soares Melo I. An Actinobacterium Strain From Soil of Cerrado Promotes Phosphorus Solubilization and Plant Growth in Soybean Plants. Front Bioeng Biotechnol 2021; 9:579906. [PMID: 33968908 PMCID: PMC8100043 DOI: 10.3389/fbioe.2021.579906] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 03/03/2021] [Indexed: 11/28/2022] Open
Abstract
The huge biological diversity of the Brazilian Cerrado is an important source of economically interesting microbial agents. The phylum Actinobacteria plays an important role in nutrient cycling, potentially improving their availability to plants. In this study, we isolated an actinobacteria (strain 3AS4) from wheat rhizospheres of crops cultivated in the Cerrado biome. Strain 3AS4 was identified as belonging to the genus Streptomyces and had phosphorus mobilization ability, mineralizing approximately 410 μg ml–1 from phytate, 300 μg ml–1 from calcium phosphate, and 200 μg ml–1 from rock phosphate. The analysis of the actinobacteria crude extract by spectrometric techniques revealed the presence of gluconic and 2-ketogluconic acid, and a greenhouse experiment was carried out to evaluate its plant growth promotion activity in soybean. Soil in its natural condition (with no phosphorus addition), 40 kg ha–1 rock phosphate from Bayovar (RP) added to soil, and triple super phosphate (SPT) added to soil were used. Significant differences in plant height were observed at 6 weeks when the plants were inoculated with the 3AS4 strain. The growth of inoculated plants in natural condition was promoted in 17% compared with the RP and SPT non-inoculated conditions, suggesting that inoculation can enable plants to grow with lower chemical P fertilizers. In the plants that were inoculated with the 3AS4 strain in the RP condition, the plant height increased by approximately 80% and the shoot:root ratio was approximately 30% higher compared to control conditions (non-inoculated plants in natural conditions). 3AS4 has P-solubilizing potential and can be exploited as an inoculant for soybean cultivation. These results suggest that this actinobacterium is a valuable resource for sustainable agriculture and will allow the reduction of phosphate fertilization in the future.
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Affiliation(s)
- Harold Alexander Vargas Hoyos
- Program for the Study and Control of Tropical Diseases-PECET, School of Medicine, University of Antioquia, Medellín, Colombia.,Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna, Brazil
| | | | | | | | - Juan Esteban Perez-Jaramillo
- Program for the Study and Control of Tropical Diseases-PECET, School of Medicine, University of Antioquia, Medellín, Colombia
| | | | | | - Itamar Soares Melo
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna, Brazil
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6
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Yan Y, Liu N, Tang Y. Recent developments in self-resistance gene directed natural product discovery. Nat Prod Rep 2020; 37:879-892. [PMID: 31912842 PMCID: PMC7340575 DOI: 10.1039/c9np00050j] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: 2000 to 2019Natural products (NPs) are important sources of human therapeutic agents and pesticides. To prevent self-harm from bioactive NPs, some microbial producers employ self-resistance genes to protect themselves. One effective strategy is to employ a self-resistance enzyme (SRE), which is a slightly mutated version of the original metabolic enzyme, and is resistant to the toxic NP but is still functional. The presence of a SRE in a gene cluster can serve as a predictive window to the biological activity of the NPs synthesized by the pathway. In this highlight, we summarize representative examples of NP biosynthetic pathways that utilize self-resistance genes for protection. Recent discoveries based on self-resistance gene identification have helped in bridging the gap between activity-guided and genome-driven approaches for NP discovery and functional assignment.
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Affiliation(s)
- Yan Yan
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA.
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7
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Jaremko MJ, Davis TD, Corpuz JC, Burkart MD. Type II non-ribosomal peptide synthetase proteins: structure, mechanism, and protein-protein interactions. Nat Prod Rep 2020; 37:355-379. [PMID: 31593192 PMCID: PMC7101270 DOI: 10.1039/c9np00047j] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Covering: 1990 to 2019 Many medicinally-relevant compounds are derived from non-ribosomal peptide synthetase (NRPS) products. Type I NRPSs are organized into large modular complexes, while type II NRPS systems contain standalone or minimal domains that often encompass specialized tailoring enzymes that produce bioactive metabolites. Protein-protein interactions and communication between the type II biosynthetic machinery and various downstream pathways are critical for efficient metabolite production. Importantly, the architecture of type II NRPS proteins makes them ideal targets for combinatorial biosynthesis and metabolic engineering. Future investigations exploring the molecular basis or protein-protein recognition in type II NRPS pathways will guide these engineering efforts. In this review, we consolidate the broad range of NRPS systems containing type II proteins and focus on structural investigations, enzymatic mechanisms, and protein-protein interactions important to unraveling pathways that produce unique metabolites, including dehydrogenated prolines, substituted benzoic acids, substituted amino acids, and cyclopropanes.
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Affiliation(s)
- Matt J Jaremko
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, USA.
| | - Tony D Davis
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, USA.
| | - Joshua C Corpuz
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, USA.
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, USA.
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8
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Ogawara H. Comparison of Antibiotic Resistance Mechanisms in Antibiotic-Producing and Pathogenic Bacteria. Molecules 2019; 24:E3430. [PMID: 31546630 PMCID: PMC6804068 DOI: 10.3390/molecules24193430] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance poses a tremendous threat to human health. To overcome this problem, it is essential to know the mechanism of antibiotic resistance in antibiotic-producing and pathogenic bacteria. This paper deals with this problem from four points of view. First, the antibiotic resistance genes in producers are discussed related to their biosynthesis. Most resistance genes are present within the biosynthetic gene clusters, but some genes such as paromomycin acetyltransferases are located far outside the gene cluster. Second, when the antibiotic resistance genes in pathogens are compared with those in the producers, resistance mechanisms have dependency on antibiotic classes, and, in addition, new types of resistance mechanisms such as Eis aminoglycoside acetyltransferase and self-sacrifice proteins in enediyne antibiotics emerge in pathogens. Third, the relationships of the resistance genes between producers and pathogens are reevaluated at their amino acid sequence as well as nucleotide sequence levels. Pathogenic bacteria possess other resistance mechanisms than those in antibiotic producers. In addition, resistance mechanisms are little different between early stage of antibiotic use and the present time, e.g., β-lactam resistance in Staphylococcus aureus. Lastly, guanine + cytosine (GC) barrier in gene transfer to pathogenic bacteria is considered. Now, the resistance genes constitute resistome composed of complicated mixture from divergent environments.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, 33-9, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, 522-1, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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9
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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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10
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Namiganda V, Mina Y, Meklat A, Touati D, Bouras N, Barakate M, Sabaou N. Antibiotic Resistance Pattern of Acinetobacter baumannii Strains Isolated from Different Clinical Specimens and Their Sensibility Against Bioactive Molecules Produced by Actinobacteria. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2019. [DOI: 10.1007/s13369-019-03893-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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O'Neill EC, Schorn M, Larson CB, Millán-Aguiñaga N. Targeted antibiotic discovery through biosynthesis-associated resistance determinants: target directed genome mining. Crit Rev Microbiol 2019; 45:255-277. [PMID: 30985219 DOI: 10.1080/1040841x.2019.1590307] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Intense competition between microbes in the environment has directed the evolution of antibiotic production in bacteria. Humans have harnessed these natural molecules for medicinal purposes, magnifying them from environmental concentrations to industrial scale. This increased exposure to antibiotics has amplified antibiotic resistance across bacteria, spurring a global antimicrobial crisis and a search for antibiotics with new modes of action. Genetic insights into these antibiotic-producing microbes reveal that they have evolved several resistance strategies to avoid self-toxicity, including product modification, substrate transport and binding, and target duplication or modification. Of these mechanisms, target duplication or modification will be highlighted in this review, as it uniquely links an antibiotic to its mode of action. We will further discuss and propose a strategy to mine microbial genomes for these genes and their associated biosynthetic gene clusters to discover novel antibiotics using target directed genome mining.
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Affiliation(s)
- Ellis C O'Neill
- a Department of Plant Sciences, University of Oxford , Oxford , Oxfordshire , UK
| | - Michelle Schorn
- b Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California , San Diego , CA , USA
| | - Charles B Larson
- b Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California , San Diego , CA , USA
| | - Natalie Millán-Aguiñaga
- c Universidad Autónoma de Baja California, Facultad de Ciencias Marinas , Ensenada , Baja California , México
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12
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Vanden Broeck A, McEwen AG, Chebaro Y, Potier N, Lamour V. Structural Basis for DNA Gyrase Interaction with Coumermycin A1. J Med Chem 2019; 62:4225-4231. [PMID: 30920824 DOI: 10.1021/acs.jmedchem.8b01928] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Coumermycin A1 is a natural aminocoumarin that inhibits bacterial DNA gyrase, a member of the GHKL proteins superfamily. We report here the first cocrystal structures of gyrase B bound to coumermycin A1, revealing that one coumermycin A1 molecule traps simultaneously two ATP-binding sites. The inhibited dimers from different species adopt distinct sequence-dependent conformations, alternative to the ATP-bound form. These structures provide a basis for the rational development of coumermycin A1 derivatives for antibiotherapy and biotechnology applications.
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Affiliation(s)
- Arnaud Vanden Broeck
- Integrated Structural Biology Department, IGBMC, UMR7104 CNRS, U1258 Inserm, University of Strasbourg, Illkirch 67404 , France
| | - Alastair G McEwen
- Integrated Structural Biology Department, IGBMC, UMR7104 CNRS, U1258 Inserm, University of Strasbourg, Illkirch 67404 , France
| | - Yassmine Chebaro
- Integrated Structural Biology Department, IGBMC, UMR7104 CNRS, U1258 Inserm, University of Strasbourg, Illkirch 67404 , France
| | - Noëlle Potier
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes, UMR 7140 CNRS, University of Strasbourg, Strasbourg 67000 , France
| | - Valérie Lamour
- Integrated Structural Biology Department, IGBMC, UMR7104 CNRS, U1258 Inserm, University of Strasbourg, Illkirch 67404 , France.,Hôpitaux Universitaires de Strasbourg , Strasbourg 67000 , France
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13
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Mori S, Green KD, Choi R, Buchko GW, Fried MG, Garneau-Tsodikova S. Using MbtH-Like Proteins to Alter the Substrate Profile of a Nonribosomal Peptide Adenylation Enzyme. Chembiochem 2018; 19:2186-2194. [PMID: 30134012 DOI: 10.1002/cbic.201800240] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 08/21/2018] [Indexed: 01/19/2023]
Abstract
MbtH-like proteins (MLPs) are required for soluble expression and/or optimal activity of some adenylation (A) domains of nonribosomal peptide synthetases. Because A domains can interact with noncognate MLP partners, how the function of an A domain, TioK, involved in the biosynthesis of the bisintercalator thiocoraline, is altered by noncognate MLPs has been investigated. Measuring TioK activity with 12 different MLPs from a variety of bacterial species by using a radiometric assay suggested that the A domain substrate promiscuity could be altered by foreign MLPs. Kinetic studies and bioinformatics analysis expanded the complexity of MLP functions and interactions.
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Affiliation(s)
- Shogo Mori
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone St., Lexington, KY, 40536-0596, USA
| | - Keith D Green
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone St., Lexington, KY, 40536-0596, USA
| | - Ryan Choi
- University of Washington, Center for Emerging and Re-emerging Infectious Diseases, 750 Republican St., Seattle, WA, 98109, USA.,University of Washington, Seattle Structural Genomics Center for Infectious Diseases, 307 Westlake Avenue N, Seattle, WA, 98109, USA
| | - Garry W Buchko
- University of Washington, Seattle Structural Genomics Center for Infectious Diseases, 307 Westlake Avenue N, Seattle, WA, 98109, USA.,Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, P. O. Box 999, Richmond, WA, 99352, USA.,School of Molecular Biosciences, Washington State University, P. O. Box 647520, Pullman, WA, 99164, USA
| | - Michael G Fried
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Biological Sciences Research Bldg, 741 South Limestone St., Lexington, KY, 40536-0509, USA
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone St., Lexington, KY, 40536-0596, USA
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14
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Petchey M, Cuetos A, Rowlinson B, Dannevald S, Frese A, Sutton PW, Lovelock S, Lloyd RC, Fairlamb IJS, Grogan G. The Broad Aryl Acid Specificity of the Amide Bond Synthetase McbA Suggests Potential for the Biocatalytic Synthesis of Amides. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804592] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mark Petchey
- Department of Chemistry; University of York; York YO10 5DD UK
| | - Anibal Cuetos
- Department of Chemistry; University of York; York YO10 5DD UK
| | | | | | - Amina Frese
- Department of Chemistry; University of York; York YO10 5DD UK
| | - Peter W. Sutton
- GSK Medicines Research Centre; Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
- Current address: Department of Chemical, Biological and Environmental Engineering; Bioprocess Engineering and Applied Biocatalysis Group; Engineering School; Campus de la UAB 08193 Bellaterra (Cerdanyola del Vallés) Barcelona Spain
| | - Sarah Lovelock
- GSK Medicines Research Centre; Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
- Current address: School of Chemistry; University of Manchester; Manchester Institute of Biotechnology; 131 Princess Street Manchester M1 7DN UK
| | - Richard C. Lloyd
- GSK Medicines Research Centre; Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | | | - Gideon Grogan
- Department of Chemistry; University of York; York YO10 5DD UK
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15
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Petchey M, Cuetos A, Rowlinson B, Dannevald S, Frese A, Sutton PW, Lovelock S, Lloyd RC, Fairlamb IJS, Grogan G. The Broad Aryl Acid Specificity of the Amide Bond Synthetase McbA Suggests Potential for the Biocatalytic Synthesis of Amides. Angew Chem Int Ed Engl 2018; 57:11584-11588. [PMID: 30035356 PMCID: PMC6282839 DOI: 10.1002/anie.201804592] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 05/22/2018] [Indexed: 11/08/2022]
Abstract
Amide bond formation is one of the most important reactions in pharmaceutical synthetic chemistry. The development of sustainable methods for amide bond formation, including those that are catalyzed by enzymes, is therefore of significant interest. The ATP-dependent amide bond synthetase (ABS) enzyme McbA, from Marinactinospora thermotolerans, catalyzes the formation of amides as part of the biosynthetic pathway towards the marinacarboline secondary metabolites. The reaction proceeds via an adenylate intermediate, with both adenylation and amidation steps catalyzed within one active site. In this study, McbA was applied to the synthesis of pharmaceutical-type amides from a range of aryl carboxylic acids with partner amines provided at 1-5 molar equivalents. The structure of McbA revealed the structural determinants of aryl acid substrate tolerance and differences in conformation associated with the two half reactions catalyzed. The catalytic performance of McbA, coupled with the structure, suggest that this and other ABS enzymes may be engineered for applications in the sustainable synthesis of pharmaceutically relevant (chiral) amides.
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Affiliation(s)
- Mark Petchey
- Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Anibal Cuetos
- Department of Chemistry, University of York, York, YO10 5DD, UK
| | | | | | - Amina Frese
- Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Peter W Sutton
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK.,Current address: Department of Chemical, Biological and Environmental Engineering, Bioprocess Engineering and Applied Biocatalysis Group, Engineering School, Campus de la UAB, 08193 Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| | - Sarah Lovelock
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK.,Current address: School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M1 7DN, UK
| | - Richard C Lloyd
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | | | - Gideon Grogan
- Department of Chemistry, University of York, York, YO10 5DD, UK
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16
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Ogawara H. Comparison of Strategies to Overcome Drug Resistance: Learning from Various Kingdoms. Molecules 2018; 23:E1476. [PMID: 29912169 PMCID: PMC6100412 DOI: 10.3390/molecules23061476] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/13/2018] [Accepted: 06/15/2018] [Indexed: 11/16/2022] Open
Abstract
Drug resistance, especially antibiotic resistance, is a growing threat to human health. To overcome this problem, it is significant to know precisely the mechanisms of drug resistance and/or self-resistance in various kingdoms, from bacteria through plants to animals, once more. This review compares the molecular mechanisms of the resistance against phycotoxins, toxins from marine and terrestrial animals, plants and fungi, and antibiotics. The results reveal that each kingdom possesses the characteristic features. The main mechanisms in each kingdom are transporters/efflux pumps in phycotoxins, mutation and modification of targets and sequestration in marine and terrestrial animal toxins, ABC transporters and sequestration in plant toxins, transporters in fungal toxins, and various or mixed mechanisms in antibiotics. Antibiotic producers in particular make tremendous efforts for avoiding suicide, and are more flexible and adaptable to the changes of environments. With these features in mind, potential alternative strategies to overcome these resistance problems are discussed. This paper will provide clues for solving the issues of drug resistance.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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17
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Rudolf JD, Chang CY, Ma M, Shen B. Cytochromes P450 for natural product biosynthesis in Streptomyces: sequence, structure, and function. Nat Prod Rep 2017; 34:1141-1172. [PMID: 28758170 PMCID: PMC5585785 DOI: 10.1039/c7np00034k] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: up to January 2017Cytochrome P450 enzymes (P450s) are some of the most exquisite and versatile biocatalysts found in nature. In addition to their well-known roles in steroid biosynthesis and drug metabolism in humans, P450s are key players in natural product biosynthetic pathways. Natural products, the most chemically and structurally diverse small molecules known, require an extensive collection of P450s to accept and functionalize their unique scaffolds. In this review, we survey the current catalytic landscape of P450s within the Streptomyces genus, one of the most prolific producers of natural products, and comprehensively summarize the functionally characterized P450s from Streptomyces. A sequence similarity network of >8500 P450s revealed insights into the sequence-function relationships of these oxygen-dependent metalloenzymes. Although only ∼2.4% and <0.4% of streptomycete P450s have been functionally and structurally characterized, respectively, the study of streptomycete P450s involved in the biosynthesis of natural products has revealed their diverse roles in nature, expanded their catalytic repertoire, created structural and mechanistic paradigms, and exposed their potential for biomedical and biotechnological applications. Continued study of these remarkable enzymes will undoubtedly expose their true complement of chemical and biological capabilities.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
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18
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Mechanistic insights into class B radical-S-adenosylmethionine methylases: ubiquitous tailoring enzymes in natural product biosynthesis. Curr Opin Chem Biol 2016; 35:73-79. [PMID: 27632683 DOI: 10.1016/j.cbpa.2016.08.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 08/23/2016] [Indexed: 01/06/2023]
Abstract
Class B radical S-adenosylmethionine (SAM) methylases are notable for their ability to catalyse methylation reactions in the biosynthesis of a wide variety of natural products, including polyketides, ribosomally biosynthesised and post-translationally modified peptides (RiPPs), nonribosomal peptides (NRPs), aminoglycosides, β-lactams, phosphonates, enediynes, aminocoumarins and terpenes. Here, we discuss the diversity of substrates and catalytic mechanism utilised by such enzymes, highlighting the stereochemical course of methylation reactions at un-activated carbon centres and the ability of some members of the family to catalyse multiple methylations.
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19
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Ding W, Li Q, Jia Y, Ji X, Qianzhu H, Zhang Q. Emerging Diversity of the Cobalamin-Dependent Methyltransferases Involving Radical-Based Mechanisms. Chembiochem 2016; 17:1191-7. [PMID: 27028019 DOI: 10.1002/cbic.201600107] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Indexed: 11/10/2022]
Abstract
Cobalamins comprise a group of cobalt-containing organometallic cofactors that play important roles in cellular metabolism. Although many cobalamin-dependent methyltransferases (e.g., methionine synthase MetH) have been extensively studied, a new group of methyltransferases that are cobalamin-dependent and utilize radical chemistry in catalysis is just beginning to be appreciated. In this Concept article, we summarize recent advances in the understanding of the radical-based and cobalamin-dependent methyltransferases and discuss the functional and mechanistic diversity of this emerging class of enzymes.
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Affiliation(s)
- Wei Ding
- Key Laboratory of Cell Activities and Stress Adaptations, (Ministry of Education), School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Qien Li
- Key Laboratory of Cell Activities and Stress Adaptations, (Ministry of Education), School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Youli Jia
- Key Laboratory of Cell Activities and Stress Adaptations, (Ministry of Education), School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xinjian Ji
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Haocheng Qianzhu
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
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20
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Zou H, Chen N, Shi M, Xian M, Song Y, Liu J. The metabolism and biotechnological application of betaine in microorganism. Appl Microbiol Biotechnol 2016; 100:3865-76. [PMID: 27005411 DOI: 10.1007/s00253-016-7462-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 03/08/2016] [Accepted: 03/09/2016] [Indexed: 11/29/2022]
Abstract
Glycine betaine (betaine) is widely distributed in nature and can be found in many microorganisms, including bacteria, archaea, and fungi. Due to its particular functions, many microorganisms utilize betaine as a functional chemical and have evolved different metabolic pathways for the biosynthesis and catabolism of betaine. As in animals and plants, the principle role of betaine is to protect microbial cells against drought, osmotic stress, and temperature stress. In addition, the role of betaine in methyl group metabolism has been observed in a variety of microorganisms. Recent studies have shown that betaine supplementation can improve the performance of microbial strains used for the fermentation of lactate, ethanol, lysine, pyruvate, and vitamin B12, during which betaine can act as stress protectant or methyl donor for the biosynthesis of structurally complex compounds. In this review, we summarize the transport, synthesis, catabolism, and functions of betaine in microorganisms and discuss potential engineering strategies that employ betaine as a methyl donor for the biosynthesis of complex secondary metabolites such as a variety of vitamins, coenzymes, and antibiotics. In conclusion, the biocompatibility, C/N ratio, abundance, and comprehensive metabolic information of betaine collectively indicate that this molecule has great potential for broad applications in microbial biotechnology.
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Affiliation(s)
- Huibin Zou
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China. .,CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.
| | - Ningning Chen
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Mengxun Shi
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Mo Xian
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Yimin Song
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Junhong Liu
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
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21
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Tengg M, Stecher H, Offner L, Plasch K, Anderl F, Weber H, Schwab H, Gruber-Khadjawi M. Methyltransferases: Green Catalysts for Friedel-Crafts Alkylations. ChemCatChem 2016. [DOI: 10.1002/cctc.201501306] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Martin Tengg
- ACIB, Austrian Centre of Industrial Biotechnology GmbH; Petersgasse 14 8010 Graz Austria
- Institute of Molecular Biotechnology; Graz University of Technology; Petersgasse 14 8010 Graz Austria
| | - Harald Stecher
- ACIB, Austrian Centre of Industrial Biotechnology GmbH; Petersgasse 14 8010 Graz Austria
- Institute of Organic Chemistry; Graz University of Technology; Stremayrgasse 9 8010 Graz Austria
| | - Lisa Offner
- ACIB, Austrian Centre of Industrial Biotechnology GmbH; Petersgasse 14 8010 Graz Austria
- Institute of Organic Chemistry; Graz University of Technology; Stremayrgasse 9 8010 Graz Austria
| | - Katharina Plasch
- ACIB, Austrian Centre of Industrial Biotechnology GmbH; Petersgasse 14 8010 Graz Austria
- Institute of Organic Chemistry; Graz University of Technology; Stremayrgasse 9 8010 Graz Austria
| | - Felix Anderl
- Institute of Organic Chemistry; Graz University of Technology; Stremayrgasse 9 8010 Graz Austria
| | - Hansjörg Weber
- Institute of Organic Chemistry; Graz University of Technology; Stremayrgasse 9 8010 Graz Austria
| | - Helmut Schwab
- ACIB, Austrian Centre of Industrial Biotechnology GmbH; Petersgasse 14 8010 Graz Austria
- Institute of Molecular Biotechnology; Graz University of Technology; Petersgasse 14 8010 Graz Austria
| | - Mandana Gruber-Khadjawi
- ACIB, Austrian Centre of Industrial Biotechnology GmbH; Petersgasse 14 8010 Graz Austria
- Institute of Organic Chemistry; Graz University of Technology; Stremayrgasse 9 8010 Graz Austria
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22
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Bernard SM, Akey DL, Tripathi A, Park SR, Konwerski JR, Anzai Y, Li S, Kato F, Sherman DH, Smith JL. Structural basis of substrate specificity and regiochemistry in the MycF/TylF family of sugar O-methyltransferases. ACS Chem Biol 2015; 10:1340-51. [PMID: 25692963 DOI: 10.1021/cb5009348] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Sugar moieties in natural products are frequently modified by O-methylation. In the biosynthesis of the macrolide antibiotic mycinamicin, methylation of a 6'-deoxyallose substituent occurs in a stepwise manner first at the 2'- and then the 3'-hydroxyl groups to produce the mycinose moiety in the final product. The timing and placement of the O-methylations impact final stage C-H functionalization reactions mediated by the P450 monooxygenase MycG. The structural basis of pathway ordering and substrate specificity is unknown. A series of crystal structures of MycF, the 3'-O-methyltransferase, including the free enzyme and complexes with S-adenosyl homocysteine (SAH), substrate, product, and unnatural substrates, show that SAM binding induces substantial ordering that creates the binding site for the natural substrate, and a bound metal ion positions the substrate for catalysis. A single amino acid substitution relaxed the 2'-methoxy specificity but retained regiospecificity. The engineered variant produced a new mycinamicin analog, demonstrating the utility of structural information to facilitate bioengineering approaches for the chemoenzymatic synthesis of complex small molecules containing modified sugars. Using the MycF substrate complex and the modeled substrate complex of a 4'-specific homologue, active site residues were identified that correlate with the 3' or 4' specificity of MycF family members and define the protein and substrate features that direct the regiochemistry of methyltransfer. This classification scheme will be useful in the annotation of new secondary metabolite pathways that utilize this family of enzymes.
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Affiliation(s)
- Steffen M. Bernard
- Chemical
Biology Doctoral Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - David L. Akey
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ashootosh Tripathi
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sung Ryeol Park
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jamie R. Konwerski
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yojiro Anzai
- Faculty
of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Shengying Li
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Fumio Kato
- Faculty
of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - David H. Sherman
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Departments of Medicinal Chemistry, Chemistry, and Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Janet L. Smith
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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23
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Chen JM, Hou C, Wang G, Tsodikov OV, Rohr J. Structural insight into MtmC, a bifunctional ketoreductase-methyltransferase involved in the assembly of the mithramycin trisaccharide chain. Biochemistry 2015; 54:2481-9. [PMID: 25587924 DOI: 10.1021/bi501462g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
More and more post-PKS tailoring enzymes are recognized as being multifunctional and codependent on other tailoring enzymes. One of the recently discovered intriguing examples is MtmC, a bifunctional TDP-4-keto-d-olivose ketoreductase-methyltransferase, which-in codependence with glycosyltransferase MtmGIV-is a key contributor to the biosynthesis of the critical trisaccharide chain of the antitumor antibiotic mithramycin (MTM), produced by Streptomyces argillaceus. We report crystal structures of three binary complexes of MtmC with its methylation cosubstrate SAM, its coproduct SAH, and a nucleotide TDP as well as crystal structures of two ternary complexes, MtmC-SAH-TDP-4-keto-d-olivose and MtmC-SAM-TDP, in the range of 2.2-2.7 Å resolution. The structures reveal general and sugar-specific recognition and catalytic structural features of MtmC. Depending on the catalytic function that is conducted by MtmC, it must bind either NADPH or SAM in the same cofactor binding pocket. A tyrosine residue (Tyr79) appears as a lid covering the sugar moiety of the substrate during the methyl transfer reaction. This residue swings out of the active site by ~180° in the absence of the substrate. This unique conformational change likely serves to release the methylated product and, possibly, to open the active site for binding the bulkier cosubstrate NADPH prior to the reduction reaction.
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Affiliation(s)
- Jhong-Min Chen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Caixia Hou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Guojun Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Jürgen Rohr
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
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24
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Abstract
DNA topoisomerases are enzymes that control the topology of DNA in all cells. There are two types, I and II, classified according to whether they make transient single- or double-stranded breaks in DNA. Their reactions generally involve the passage of a single- or double-strand segment of DNA through this transient break, stabilized by DNA-protein covalent bonds. All topoisomerases can relax DNA, but DNA gyrase, present in all bacteria, can also introduce supercoils into DNA. Because of their essentiality in all cells and the fact that their reactions proceed via DNA breaks, topoisomerases have become important drug targets; the bacterial enzymes are key targets for antibacterial agents. This article discusses the structure and mechanism of topoisomerases and their roles in the bacterial cell. Targeting of the bacterial topoisomerases by inhibitors, including antibiotics in clinical use, is also discussed.
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25
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Zettler J, Xia H, Burkard N, Kulik A, Grond S, Heide L, Apel AK. New aminocoumarins from the rare actinomycete Catenulispora acidiphila DSM 44928: identification, structure elucidation, and heterologous production. Chembiochem 2014; 15:612-21. [PMID: 24554531 DOI: 10.1002/cbic.201300712] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Indexed: 11/08/2022]
Abstract
Genome mining led to the discovery of a novel aminocoumarin gene cluster in the rare actinomycete Catenulispora acidiphila DSM 44928. Sequence analysis revealed the presence of genes putatively involved in export/resistance, regulation, and biosynthesis of the aminocoumarin moiety and its halogenation, as well as several genes with so far unknown function. Two new aminocoumarins, cacibiocin A and B, were identified in the culture broth of C. acidiphila. Heterologous expression of the putative gene cluster in Streptomyces coelicolor M1152 confirmed that this cluster is responsible for cacibiocin biosynthesis. Furthermore, total production levels of cacibiocins could be increased by heterologous expression and screening of different culture media from an initial yield of 4.9 mg L(-1) in C. acidiphila to 60 mg L(-1) in S. coelicolor M1152. By HR-MS and NMR analysis, cacibiocin A was found to contain a 3-amino-4,7-dihydroxycoumarin moiety linked by an amide bond to a pyrrole-2,5-dicarboxylic acid. The latter structural motif has not been identified previously in any natural compound. Additionally, cacibiocin B contains two chlorine atoms at positions 6' and 8' of the aminocoumarin moiety.
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Affiliation(s)
- Judith Zettler
- Eberhard-Karls-Universität Tübingen, Pharmazeutische Biologie, Auf der Morgenstelle 8, 72076 Tübingen (Germany); German Centre for Infection Research (DZIF), Partner site Tübingen (Germany)
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26
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Baltz RH. MbtH homology codes to identify gifted microbes for genome mining. ACTA ACUST UNITED AC 2014; 41:357-69. [DOI: 10.1007/s10295-013-1360-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Accepted: 09/30/2013] [Indexed: 11/24/2022]
Abstract
Abstract
Advances in DNA sequencing technologies have made it possible to sequence large numbers of microbial genomes rapidly and inexpensively. In recent years, genome sequencing initiatives have demonstrated that actinomycetes with large genomes generally have the genetic potential to produce many secondary metabolites, most of which remain cryptic. Since the numbers of new and novel pathways vary considerably among actinomycetes, and the correct assembly of secondary metabolite pathways containing type I polyketide synthase or nonribosomal peptide synthetase (NRPS) genes is costly and time consuming, it would be advantageous to have simple genetic predictors for the number and potential novelty of secondary metabolite pathways in targeted microorganisms. For secondary metabolite pathways that utilize NRPS mechanisms, the small chaperone-like proteins related to MbtH encoded by Mycobacterium tuberculosis offer unique probes or beacons to identify gifted microbes encoding large numbers of diverse NRPS pathways because of their unique function(s) and small size. The small size of the mbtH-homolog genes makes surveying large numbers of genomes straight-forward with less than ten-fold sequencing coverage. Multiple MbtH orthologs and paralogs have been coupled to generate a 24-mer multiprobe to assign numerical codes to individual MbtH homologs by BLASTp analysis. This multiprobe can be used to identify gifted microbes encoding new and novel secondary metabolites for further focused exploration by extensive DNA sequencing, pathway assembly and annotation, and expression studies in homologous or heterologous hosts.
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Affiliation(s)
- Richard H Baltz
- CognoGen Biotechnology Consulting 7636 Andora Drive 34238 Sarasota FL USA
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27
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28
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Kadlčík S, Kučera T, Chalupská D, Gažák R, Koběrská M, Ulanová D, Kopecký J, Kutejová E, Najmanová L, Janata J. Adaptation of an L-proline adenylation domain to use 4-propyl-L-proline in the evolution of lincosamide biosynthesis. PLoS One 2013; 8:e84902. [PMID: 24386435 PMCID: PMC3874040 DOI: 10.1371/journal.pone.0084902] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 11/27/2013] [Indexed: 11/18/2022] Open
Abstract
Clinically used lincosamide antibiotic lincomycin incorporates in its structure 4-propyl-L-proline (PPL), an unusual amino acid, while celesticetin, a less efficient related compound, makes use of proteinogenic L-proline. Biochemical characterization, as well as phylogenetic analysis and homology modelling combined with the molecular dynamics simulation were employed for complex comparative analysis of the orthologous protein pair LmbC and CcbC from the biosynthesis of lincomycin and celesticetin, respectively. The analysis proved the compared proteins to be the stand-alone adenylation domains strictly preferring their own natural substrate, PPL or L-proline. The LmbC substrate binding pocket is adapted to accomodate a rare PPL precursor. When compared with L-proline specific ones, several large amino acid residues were replaced by smaller ones opening a channel which allowed the alkyl side chain of PPL to be accommodated. One of the most important differences, that of the residue corresponding to V306 in CcbC changing to G308 in LmbC, was investigated in vitro and in silico. Moreover, the substrate binding pocket rearrangement also allowed LmbC to effectively adenylate 4-butyl-L-proline and 4-pentyl-L-proline, substrates with even longer alkyl side chains, producing more potent lincosamides. A shift of LmbC substrate specificity appears to be an integral part of biosynthetic pathway adaptation to the PPL acquisition. A set of genes presumably coding for the PPL biosynthesis is present in the lincomycin - but not in the celesticetin cluster; their homologs are found in biosynthetic clusters of some pyrrolobenzodiazepines (PBD) and hormaomycin. Whereas in the PBD and hormaomycin pathways the arising precursors are condensed to another amino acid moiety, the LmbC protein is the first functionally proved part of a unique condensation enzyme connecting PPL to the specialized amino sugar building unit.
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Affiliation(s)
- Stanislav Kadlčík
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Tomáš Kučera
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Dominika Chalupská
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Radek Gažák
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Markéta Koběrská
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Dana Ulanová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jan Kopecký
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Eva Kutejová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Department of Biochemistry and Structural Biology, Institute of Molecular Biology, Slovac Academy of Sciences, Bratislava, Slovakia
| | - Lucie Najmanová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jiří Janata
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- * E-mail:
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29
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Fujimori DG. Radical SAM-mediated methylation reactions. Curr Opin Chem Biol 2013; 17:597-604. [PMID: 23835516 DOI: 10.1016/j.cbpa.2013.05.032] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 05/28/2013] [Indexed: 10/26/2022]
Abstract
A subset of enzymes that belong to the radical S-adenosylmethionine (SAM) superfamily is able to catalyze methylation reactions. Substrates of these enzymes are distinct from the nucleophilic substrates that undergo methylation by a polar mechanism. Recently, activities of several radical SAM methylating enzymes have been reconstituted in vitro and their mechanisms of catalysis investigated. The RNA modifying enzymes RlmN and Cfr catalyze methylation via a methyl synthase mechanism. These enzymes use SAM in two distinct roles: as a source of a methyl group transferred to a conserved cysteine and as a source of 5'-deoxyadenosyl radical (5'-dA). Hydrogen atom abstraction by this species generates a thiomethylene radical which adds into the RNA substrate, forming an enzyme-substrate covalent adduct. In another recent study, methylation of the indole moiety of tryptophan by the radical SAM and cobalamin-binding domain enzyme TsrM has been reconstituted. Methylcobalamin serves as an intermediate methyl donor in TsrM, and is proposed to transfer the methyl group as a methyl radical. Interestingly, despite the presence of the radical SAM motif, no reductive cleavage of SAM has been observed in this methylation. These important reconstitutions set the stage for further studies on mechanisms of radical methylation.
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Affiliation(s)
- Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158-2280, USA.
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Tengg M, Stecher H, Remler P, Eiteljörg I, Schwab H, Gruber-Khadjawi M. Molecular characterization of the C-methyltransferase NovO of Streptomyces spheroides, a valuable enzyme for performing Friedel–Crafts alkylation. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.molcatb.2012.03.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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31
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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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Abstract
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Methylation is an essential and ubiquitous reaction that plays an important role in a wide range of biological processes. Most biological methylations use S-adenosylmethionine (SAM) as the methyl donor and proceed via an SN2 displacement mechanism. However, researchers have discovered an increasing number of methylations that involve radical chemistry. The enzymes known to catalyze these reactions all belong to the radical SAM superfamily. This family of enzymes utilizes a specialized [4Fe-4S] cluster for reductive cleavage of SAM to yield a highly reactive 5'-deoxyadenosyl (dAdo) radical. Radical chemistry is then imposed on a variety of organic substrates, leading to a diverse array of transformations. Until recently, researchers had not fully understood how these enzymes employ radical chemistry to mediate a methyl transfer reaction. Sequence analyses reveal that the currently identified radical SAM methyltransferases (RSMTs) can be grouped into three classes, which appear distinct in protein architecture and mechanism. Class A RSMTs mainly include the rRNA methyltransferases RlmN and Cfr from various origins. As exemplified by Escherichia coli RlmN, these proteins have a single canonical radical SAM core domain that includes an (βα)6 partial barrel most similar to that of pyruvate formate lyase-activase. The exciting recent studies on RlmN and Cfr are beginning to provide insights into the intriguing chemistry of class A RSMTs. These enzymes utilize a methylene radical generated on a unique methylated cysteine residue. However, based on the variety of substrates used by the other classes of RSMTs, alternative mechanisms are likely to be discovered. Class B RSMTs contain a proposed N-terminal cobalamin binding domain in addition to a radical SAM domain at the C-terminus. This class of proteins methylates diverse substrates at inert sp3 carbons, aromatic heterocycles, and phosphinates, possibly involving a cobalamin-mediated methyl transfer process. Class C RSMTs share significant sequence similarity with coproporphyrinogen III oxidase HemN. Despite methylating similar substrates (aromatic heterocycles), class C RSMTs likely employ a mechanism distinct from that of class A because two conserved cysteines that are required for class A are typically not found in class C RSMTs. Class A and class B enzymes probably share the use of two molecules of SAM: one to generate a dAdo radical and one to provide the methyl group to the substrate. In class A, a cysteine would act as a conduit of the methyl group whereas in class B cobalamin may serve this purpose. Currently no clues are available regarding the mechanism of class C RSMTs, but the sequence similarities between its members and HemN and the observation that HemN binds two SAM molecules suggest that class C enzymes could use two SAM molecules for catalysis. The diverse strategies for using two SAM molecules reflect the rich chemistry of radical-mediated methylation reactions and the remarkable versatility of the radical SAM superfamily.
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Affiliation(s)
- Qi Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | | | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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A ketosynthase homolog uses malonyl units to form esters in cervimycin biosynthesis. Nat Chem Biol 2011; 8:154-61. [DOI: 10.1038/nchembio.746] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 10/05/2011] [Indexed: 02/08/2023]
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Siebenberg S, Burkard N, Knuplesch A, Gust B, Grond S, Heide L. Two Pathways for Pyrrole Formation in Coumermycin A1 Biosynthesis: The Central Pyrrole Moiety Is Formed From L-Threonine. Chembiochem 2011; 12:2677-85. [DOI: 10.1002/cbic.201100494] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Indexed: 12/13/2022]
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Maharjan S, Aryal N, Bhattarai S, Koju D, Lamichhane J, Sohng JK. Biosynthesis of the nargenicin A1 pyrrole moiety from Nocardia sp. CS682. Appl Microbiol Biotechnol 2011; 93:687-96. [PMID: 21927992 DOI: 10.1007/s00253-011-3567-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 08/11/2011] [Accepted: 08/29/2011] [Indexed: 12/23/2022]
Abstract
A number of structurally diverse natural products harboring pyrrole moieties possess a wide range of biological activities. Studies on biosynthesis of pyrrole ring have shown that pyrrole moieties are derived from L-proline. Nargenicin A(1), a saturated alicyclic polyketide from Nocardia sp. CS682, is a pyrrole-2-carboxylate ester of nodusmicin. We cloned and identified a set of four genes from Nocardia sp. CS682 that show sequence similarity to the respective genes involved in the biosynthesis of the pyrrole moieties of pyoluteorin in Pseudomonas fluorescens, clorobiocin in Streptomyces roseochromogenes subsp. Oscitans, coumermycin A(1) in Streptomyces rishiriensis, one of the pyrrole rings of undecylprodigiosin in Streptomyces coelicolor, and leupyrrins in Sorangium cellulosum. These genes were designated as ngnN4, ngnN5, ngnN3, and ngnN2. In this study, we presented the evidences that the pyrrole moiety of nargenicin A(1) was also derived from L-proline by the coordinated action of three proteins, NgnN4 (proline adenyltransferase), NgnN5 (proline carrier protein), and NgnN3 (flavine-dependent acyl-coenzyme A dehydrogenases). Biosynthesis of pyrrole moiety in nargenicin A(1) is initiated by NgnN4 that catalyzes ATP-dependent activation of L-proline into L-prolyl-AMP, and the latter is transferred to NgnN5 to create prolyl-S-peptidyl carrier protein (PCP). Later, NgnN3 catalyzes the two-step oxidation of prolyl-S-PCP into pyrrole-2-carboxylate. Thus, this study presents another example of a pyrrole moiety biosynthetic pathway that uses a set of three genes to convert L-proline into pyrrole-2-carboxylic acid moiety.
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Affiliation(s)
- Sushila Maharjan
- Institute of Biomolecule Reconstruction, Sun Moon University, 100 Kalsan-ri, Tangjeonmyun, Asansi, Chungnam, 336-708, South Korea
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Function of MbtH homologs in nonribosomal peptide biosynthesis and applications in secondary metabolite discovery. J Ind Microbiol Biotechnol 2011; 38:1747-60. [PMID: 21826462 DOI: 10.1007/s10295-011-1022-8] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 07/20/2011] [Indexed: 10/17/2022]
Abstract
Mycobacterium tuberculosis encodes mycobactin, a peptide siderophore that is biosynthesized by a nonribosomal peptide synthetase (NRPS) mechanism. Within the mycobactin biosynthetic gene cluster is a gene that encodes a 71-amino-acid protein MbtH. Many other NRPS gene clusters harbor mbtH homologs, and recent genetic, biochemical, and structural studies have begun to shed light on the function(s) of these proteins. In some cases, MbtH-like proteins are required for biosynthesis of their cognate peptides, and non-cognate MbtH-like proteins have been shown to be partially complementary. Biochemical studies revealed that certain MbtH-like proteins participate in tight binding to NRPS proteins containing adenylation (A) domains where they stimulate adenylation reactions. Expression of MbtH-like proteins is important for a number of applications, including optimal production of native and genetically engineered secondary metabolites produced by mechanisms that employ NRPS enzymes. They also may serve as beacons to identify gifted actinomycetes and possibly other bacteria that encode multiple functional NRPS pathways for discovery of novel secondary metabolites by genome mining.
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Mann S, Lombard B, Loew D, Méjean A, Ploux O. Insights into the Reaction Mechanism of the Prolyl–Acyl Carrier Protein Oxidase Involved in Anatoxin-a and Homoanatoxin-a Biosynthesis. Biochemistry 2011; 50:7184-97. [DOI: 10.1021/bi200892a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stéphane Mann
- Laboratoire
Charles Friedel,
Chimie ParisTech, ENSCP, 11 rue Pierre
et Marie Curie, 75231 Paris Cedex 05, France
- CNRS, UMR 7223, 75005
Paris, France
| | - Bérangère Lombard
- Laboratory of Proteomic Mass
Spectrometry, Centre de Recherche, Institut Curie, 26 rue d'Ulm 75248, Paris Cedex 05, France
| | - Damarys Loew
- Laboratory of Proteomic Mass
Spectrometry, Centre de Recherche, Institut Curie, 26 rue d'Ulm 75248, Paris Cedex 05, France
| | - Annick Méjean
- Laboratoire
Charles Friedel,
Chimie ParisTech, ENSCP, 11 rue Pierre
et Marie Curie, 75231 Paris Cedex 05, France
- CNRS, UMR 7223, 75005
Paris, France
- Université Paris Diderot-Paris 7, 75013 Paris, France
| | - Olivier Ploux
- Laboratoire
Charles Friedel,
Chimie ParisTech, ENSCP, 11 rue Pierre
et Marie Curie, 75231 Paris Cedex 05, France
- CNRS, UMR 7223, 75005
Paris, France
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38
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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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Galm U, Wendt-Pienkowski E, Wang L, Huang SX, Unsin C, Tao M, Coughlin JM, Shen B. Comparative analysis of the biosynthetic gene clusters and pathways for three structurally related antitumor antibiotics: bleomycin, tallysomycin, and zorbamycin. JOURNAL OF NATURAL PRODUCTS 2011; 74:526-536. [PMID: 21210656 PMCID: PMC3064724 DOI: 10.1021/np1008152] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The biosynthetic gene clusters for the glycopeptide antitumor antibiotics bleomycin (BLM), tallysomycin (TLM), and zorbamycin (ZBM) have been recently cloned and characterized from Streptomyces verticillus ATCC15003, Streptoalloteichus hindustanus E465-94 ATCC31158, and Streptomyces flavoviridis ATCC21892, respectively. The striking similarities and differences among the biosynthetic gene clusters for the three structurally related glycopeptide antitumor antibiotics prompted us to compare and contrast their respective biosynthetic pathways and to investigate various enzymatic elements. The presence of different numbers of isolated nonribosomal peptide synthetase (NRPS) domains in all three clusters does not result in major structural differences of the respective compounds. The seemingly identical domain organization of the NRPS modules responsible for heterocycle formation, on the other hand, is contrasted by the biosynthesis of two different structural entities, bithiazole and thiazolinyl-thiazole, for BLM/TLM and ZBM, respectively. Variations in sugar biosynthesis apparently dictate the glycosylation patterns distinct for each of the BLM, TLM, and ZBM glycopeptide scaffolds. These observations demonstrate nature's ingenuity and flexibility in achieving structural differences and similarities via various mechanisms and will surely inspire combinatorial biosynthesis efforts to expand on natural product structural diversity.
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Affiliation(s)
- Ute Galm
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53705-2222, USA
| | - Evelyn Wendt-Pienkowski
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53705-2222, USA
| | - Liyan Wang
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53705-2222, USA
| | - Sheng-Xiong Huang
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53705-2222, USA
| | - Claudia Unsin
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53705-2222, USA
| | - Meifeng Tao
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53705-2222, USA
| | - Jane M. Coughlin
- University of Wisconsin National Cooperative Drug Discovery Group, Madison, Wisconsin 53705-2222, USA
| | - Ben Shen
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53705-2222, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53705-2222, USA
- University of Wisconsin National Cooperative Drug Discovery Group, Madison, Wisconsin 53705-2222, USA
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Cryle MJ, Staaden J, Schlichting I. Structural characterization of CYP165D3, a cytochrome P450 involved in phenolic coupling in teicoplanin biosynthesis. Arch Biochem Biophys 2011; 507:163-73. [DOI: 10.1016/j.abb.2010.10.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2010] [Revised: 10/19/2010] [Accepted: 10/19/2010] [Indexed: 11/26/2022]
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Characterization of the biosynthesis gene cluster for the pyrrole polyether antibiotic calcimycin (A23187) in Streptomyces chartreusis NRRL 3882. Antimicrob Agents Chemother 2010; 55:974-82. [PMID: 21173184 DOI: 10.1128/aac.01130-10] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The pyrrole polyether antibiotic calcimycin (A23187) is a rare ionophore that is specific for divalent cations. It is widely used as a biochemical and pharmacological tool because of its multiple, unique biological effects. Here we report on the cloning, sequencing, and mutational analysis of the 64-kb biosynthetic gene cluster from Streptomyces chartreusis NRRL 3882. Gene replacements confirmed the identity of the gene cluster, and in silico analysis of the DNA sequence revealed 27 potential genes, including 3 genes for the biosynthesis of the α-ketopyrrole moiety, 5 genes that encode modular type I polyketide synthases for the biosynthesis of the spiroketal ring, 4 genes for the biosynthesis of 3-hydroxyanthranilic acid, an N-methyltransferase tailoring gene, a resistance gene, a type II thioesterase gene, 3 regulatory genes, 4 genes with other functions, and 5 genes of unknown function. We propose a pathway for the biosynthesis of calcimycin and assign the genes to the biosynthesis steps. Our findings set the stage for producing much desired calcimycin derivatives using genetic modification instead of chemical synthesis.
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Abstract
The cytochromes P450 (P450s) are a superfamily of oxidative haemoproteins that are capable of catalysing a vast range of oxidative transformations, including the oxidation of unactivated alkanes, often with high stereo- and regio-selectivity. Fatty acid hydroxylation by P450s is widespread across both bacteria and higher organisms, with the sites of oxidation and specificity of oxidation varying from system to system. Several key examples are discussed in the present article, with the focus on P450(BioI) (CYP107H1), a biosynthetic P450 found in the biotin operon of Bacillus subtilis. The biosynthetic function of P450(BioI) is the formation of pimelic acid, a biotin precursor, via a multiple-step oxidative cleavage of long-chain fatty acids. P450(BioI) is a member of an important subgroup of P450s that accept their substrates not free in solution, but rather presented by a separate carrier protein. Structural characterization of the P450(BioI)-ACP (acyl-carrier protein) complex has recently been performed, which has revealed the basis for the oxidation of the centre of the fatty acid chain. The P450(BioI)-ACP structure is the first such P450-carrier protein complex to be characterized structurally, with important implications for other biosynthetically intriguing P450-carrier protein complexes.
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Cryle MJ, Meinhart A, Schlichting I. Structural characterization of OxyD, a cytochrome P450 involved in beta-hydroxytyrosine formation in vancomycin biosynthesis. J Biol Chem 2010; 285:24562-74. [PMID: 20519494 PMCID: PMC2915692 DOI: 10.1074/jbc.m110.131904] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Revised: 05/19/2010] [Indexed: 11/06/2022] Open
Abstract
The cytochrome P450 OxyD from the balhimycin glycopeptide antibiotic biosynthetic operon of Amycolatopsis mediterranei is involved in the biosynthesis of the modified amino acid beta-R-hydroxytyrosine, an essential precursor for biosynthesis of the vancomycin-type aglycone. OxyD binds the substrate tyrosine not free in solution, but rather covalently linked to the carrier protein (CP) domain of the non-ribosomal peptide synthase BpsD, exhibiting micromolar binding affinity to a tyrosine-loaded carrier protein construct. The crystal structure of OxyD was determined to 2.1-A resolution, revealing a potential binding site for the carrier protein-bound substrate in a different orientation to that seen with the acyl carrier protein-bound P450(BioI) (Cryle, M. J., and Schlichting, I. (2008) Proc. Natl. Acad. Sci. U.S.A. 105, 15696-15701). A series of residues were identified across known aminoacyl-CP-oxidizing P450s that are highly conserved and cluster in the active site or potential CP binding site of OxyD. These residues appear to be characteristic for aminoacyl-CP-oxidizing P450s, allowing sequence based identification of P450 function for this subgroup of P450s that play vital roles in the biosyntheses of many important natural products in addition to the vancomycin-type antibiotics. The ability to analyze such P450 function based upon sequence data alone should prove an important tool in the analysis and identification of new medicinally relevant biomolecules.
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Affiliation(s)
- Max J Cryle
- Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
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45
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Flinspach K, Westrich L, Kaysser L, Siebenberg S, Gomez-Escribano JP, Bibb M, Gust B, Heide L. Heterologous expression of the biosynthetic gene clusters of coumermycin A1, clorobiocin and caprazamycins in genetically modified Streptomyces coelicolor strains. Biopolymers 2010; 93:823-32. [DOI: 10.1002/bip.21493] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Cundliffe E, Demain AL. Avoidance of suicide in antibiotic-producing microbes. J Ind Microbiol Biotechnol 2010; 37:643-72. [PMID: 20446033 DOI: 10.1007/s10295-010-0721-x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Accepted: 03/30/2010] [Indexed: 11/29/2022]
Abstract
Many microbes synthesize potentially autotoxic antibiotics, mainly as secondary metabolites, against which they need to protect themselves. This is done in various ways, ranging from target-based strategies (i.e. modification of normal drug receptors or de novo synthesis of the latter in drug-resistant form) to the adoption of metabolic shielding and/or efflux strategies that prevent drug-target interactions. These self-defence mechanisms have been studied most intensively in antibiotic-producing prokaryotes, of which the most prolific are the actinomycetes. Only a few documented examples pertain to lower eukaryotes while higher organisms have hardly been addressed in this context. Thus, many plant alkaloids, variously described as herbivore repellents or nitrogen excretion devices, are truly antibiotics-even if toxic to humans. As just one example, bulbs of Narcissus spp. (including the King Alfred daffodil) accumulate narciclasine that binds to the larger subunit of the eukaryotic ribosome and inhibits peptide bond formation. However, ribosomes in the Amaryllidaceae have not been tested for possible resistance to narciclasine and other alkaloids. Clearly, the prevalence of suicide avoidance is likely to extend well beyond the remit of the present article.
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Affiliation(s)
- Eric Cundliffe
- Department of Biochemistry, University of Leicester, Leicester, LE1 9HN, UK.
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Méjean A, Mann S, Vassiliadis G, Lombard B, Loew D, Ploux O. In Vitro Reconstitution of the First Steps of Anatoxin-a Biosynthesis in Oscillatoria PCC 6506: From Free l-Proline to Acyl Carrier Protein Bound Dehydroproline. Biochemistry 2009; 49:103-13. [DOI: 10.1021/bi9018785] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Annick Méjean
- Biochimie des micro-organismes, Laboratoire Charles Friedel, UMR CNRS 7223, ENSCP, 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05, France
- Université Paris Diderot-Paris 7, 75013 Paris, France
| | - Stéphane Mann
- Biochimie des micro-organismes, Laboratoire Charles Friedel, UMR CNRS 7223, ENSCP, 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05, France
| | - Gaëlle Vassiliadis
- Biochimie des micro-organismes, Laboratoire Charles Friedel, UMR CNRS 7223, ENSCP, 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05, France
- Université Paris Diderot-Paris 7, 75013 Paris, France
| | - Bérangère Lombard
- Laboratory of Proteomic Mass Spectrometry, Centre de Recherche, Institut Curie, 26 rue d'Ulm, 75248 Paris, France
| | - Damarys Loew
- Laboratory of Proteomic Mass Spectrometry, Centre de Recherche, Institut Curie, 26 rue d'Ulm, 75248 Paris, France
| | - Olivier Ploux
- Biochimie des micro-organismes, Laboratoire Charles Friedel, UMR CNRS 7223, ENSCP, 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05, France
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48
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Stecher H, Tengg M, Ueberbacher B, Remler P, Schwab H, Griengl H, Gruber-Khadjawi M. Biocatalytic Friedel-Crafts Alkylation Using Non-natural Cofactors. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200905095] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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49
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Stecher H, Tengg M, Ueberbacher B, Remler P, Schwab H, Griengl H, Gruber-Khadjawi M. Biocatalytic Friedel-Crafts Alkylation Using Non-natural Cofactors. Angew Chem Int Ed Engl 2009; 48:9546-8. [DOI: 10.1002/anie.200905095] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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50
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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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