1
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Lai HE, Kennedy A, Tanner L, Bartram EA, Mei Chee S, Freemont PS, Moore SJ. Biosynthesis of Arcyriaflavin F from Streptomyces venezuelae ATCC 10712. Chembiochem 2024; 25:e202400357. [PMID: 39036938 DOI: 10.1002/cbic.202400357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/12/2024] [Accepted: 07/22/2024] [Indexed: 07/23/2024]
Abstract
Indolocarbazoles are natural products with a broad spectrum of bioactivity. A distinct feature of indolocarbazole biosynthesis is the modification of the indole and maleimide rings by regioselective tailoring enzymes. Here, we study a new indolocarbazole variant, which is encoded by the acfXODCP genes from Streptomyces venezuelae ATCC 10712. We characterise the pathway by expressing the acfXODCP genes in Streptomyces coelicolor, which led to the production of a C-5/C-5'-dihydroxylated indolocarbazole, which we assign as arcyriaflavin F. We also show that a flavin-dependent monooxygenase AcfX catalyses the C-5/C-5' dihydroxylation of the unsubstituted arcyriaflavin A into arcyriaflavin F. Interestingly, AcfX shares homology to EspX from erdasporine A biosynthesis, which instead catalyses a single C-6 indolocarbazole hydroxylation. In summary, we report a new indolocarbazole biosynthetic pathway and a regioselective C-5 indole ring tailoring enzyme AcfX.
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Affiliation(s)
- Hung-En Lai
- Section of Structural and Synthetic Biology, Centre for Synthetic Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK
| | - Agata Kennedy
- School of Biosciences, University of Kent, Canterbury, CT7 2NJ, UK
| | - Lewis Tanner
- School of Biological and Behavioural Science, Queen Mary University of London, London, E1 4NS, UK
| | - Emma A Bartram
- School of Biological and Behavioural Science, Queen Mary University of London, London, E1 4NS, UK
| | - Soo Mei Chee
- Section of Structural and Synthetic Biology, Centre for Synthetic Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK
| | - Paul S Freemont
- Section of Structural and Synthetic Biology, Centre for Synthetic Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK
- UK Dementia Research Institute Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
- UK Innovation and Knowledge Centre for Synthetic Biology (SynbiCITE) and the London Biofoundry, Imperial College Translation & Innovation Hub, Imperial College London, White City Campus 80 Wood Lane, London, W12 0BZ, UK
| | - Simon J Moore
- School of Biological and Behavioural Science, Queen Mary University of London, London, E1 4NS, UK
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2
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Launay R, Chobert SC, Abby SS, Pierrel F, André I, Esque J. Structural Reconstruction of E. coli Ubi Metabolon Using an AlphaFold2-Based Computational Framework. J Chem Inf Model 2024; 64:5175-5193. [PMID: 38710096 DOI: 10.1021/acs.jcim.4c00304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Ubiquinone (UQ) is a redox polyisoprenoid lipid found in the membranes of bacteria and eukaryotes that has important roles, notably one in respiratory metabolism, which sustains cellular bioenergetics. In Escherichia coli, several steps of the UQ biosynthesis take place in the cytosol. To perform these reactions, a supramolecular assembly called Ubi metabolon is involved. This latter is composed of seven proteins (UbiE, UbiG, UbiF, UbiH, UbiI, UbiJ, and UbiK), and its structural organization is unknown as well as its protein stoichiometry. In this study, a computational framework has been designed to predict the structure of this macromolecular assembly. In several successive steps, we explored the possible protein interactions as well as the protein stoichiometry, to finally obtain a structural organization of the complex. The use of AlphaFold2-based methods combined with evolutionary information enabled us to predict several models whose quality and confidence were further analyzed using different metrics and scores. Our work led to the identification of a "core assembly" that will guide functional and structural characterization of the Ubi metabolon.
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Affiliation(s)
- Romain Launay
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| | - Sophie-Carole Chobert
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Sophie S Abby
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Fabien Pierrel
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Isabelle André
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| | - Jérémy Esque
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
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3
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Daniel-Ivad P, Ryan KS. An imine reductase that captures reactive intermediates in the biosynthesis of the indolocarbazole reductasporine. J Biol Chem 2024; 300:105642. [PMID: 38199566 PMCID: PMC10851217 DOI: 10.1016/j.jbc.2024.105642] [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: 09/11/2023] [Revised: 12/21/2023] [Accepted: 12/31/2023] [Indexed: 01/12/2024] Open
Abstract
Imine reductases (IREDs) and reductive aminases have been used in the synthesis of chiral amine products for drug manufacturing; however, little is known about their biological contexts. Here we employ structural studies and site-directed mutagenesis to interrogate the mechanism of the IRED RedE from the biosynthetic pathway to the indolocarbazole natural product reductasporine. Cocrystal structures with the substrate-mimic arcyriaflavin A reveal an extended active site cleft capable of binding two indolocarbazole molecules. Site-directed mutagenesis of a conserved aspartate in the primary binding site reveals a new role for this residue in anchoring the substrate above the NADPH cofactor. Variants targeting the secondary binding site greatly reduce catalytic efficiency, while accumulating oxidized side-products. As indolocarbazole biosynthetic intermediates are susceptible to spontaneous oxidation, we propose the secondary site acts to protect against autooxidation, and the primary site drives catalysis through precise substrate orientation and desolvation effects. The structure of RedE with its extended active site can be the starting point as a new scaffold for engineering IREDs and reductive aminases to intercept large substrates relevant to industrial applications.
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Affiliation(s)
- Phillip Daniel-Ivad
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Katherine S Ryan
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada.
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4
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Feng KN, Zhang Y, Zhang M, Yang YL, Liu JK, Pan L, Zeng Y. A flavin-monooxygenase catalyzing oxepinone formation and the complete biosynthesis of vibralactone. Nat Commun 2023; 14:3436. [PMID: 37301868 PMCID: PMC10257657 DOI: 10.1038/s41467-023-39108-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Oxepinone rings represent one of structurally unusual motifs of natural products and the biosynthesis of oxepinones is not fully understood. 1,5-Seco-vibralactone (3) features an oxepinone motif and is a stable metabolite isolated from mycelial cultures of the mushroom Boreostereum vibrans. Cyclization of 3 forms vibralactone (1) whose β-lactone-fused bicyclic core originates from 4-hydroxybenzoate, yet it remains elusive how 4-hydroxybenzoate is converted to 3 especially for the oxepinone ring construction in the biosynthesis of 1. In this work, using activity-guided fractionation together with proteomic analyses, we identify an NADPH/FAD-dependent monooxygenase VibO as the key enzyme performing a crucial ring-expansive oxygenation on the phenol ring to generate the oxepin-2-one structure of 3. The crystal structure of VibO reveals that it forms a dimeric phenol hydroxylase-like architecture featured with a unique substrate-binding pocket adjacent to the bound FAD. Computational modeling and solution studies provide insight into the likely VibO active site geometry, and suggest possible involvement of a flavin-C4a-OO(H) intermediate.
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Affiliation(s)
- Ke-Na Feng
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yue Zhang
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Mingfang Zhang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yan-Long Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Ji-Kai Liu
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, 430074, China
| | - Lifeng Pan
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Ying Zeng
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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5
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Williford EE, DeAngelo CM, Blake KS, Kumar H, Lam KK, Jones KV, Tolia NH, Dantas G, Wencewicz TA. Structure-Based Design of Bisubstrate Tetracycline Destructase Inhibitors That Block Flavin Redox Cycling. J Med Chem 2023; 66:3917-3933. [PMID: 36877173 PMCID: PMC10099279 DOI: 10.1021/acs.jmedchem.2c01629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Tetracyclines (TCs) are an important class of antibiotics threatened by an emerging new resistance mechanism─enzymatic inactivation. These TC-inactivating enzymes, also known as tetracycline destructases (TDases), inactivate all known TC antibiotics, including drugs of last resort. Combination therapies consisting of a TDase inhibitor and a TC antibiotic represent an attractive strategy for overcoming this type of antibiotic resistance. Here, we report the structure-based design, synthesis, and evaluation of bifunctional TDase inhibitors derived from anhydrotetracycline (aTC). By appending a nicotinamide isostere to the C9 position of the aTC D-ring, we generated bisubstrate TDase inhibitors. The bisubstrate inhibitors have extended interactions with TDases by spanning both the TC and presumed NADPH binding pockets. This simultaneously blocks TC binding and the reduction of FAD by NADPH while "locking" TDases in an unproductive FAD "out" conformation.
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Affiliation(s)
- Emily E. Williford
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
| | - Caitlin M. DeAngelo
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
| | - Kevin S. Blake
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4513 Clayton Ave., St. Louis, MO, 63108, USA
| | - Hirdesh Kumar
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institute of Health, 9000 Rockville Pike, BG 29B Rm 4NN08, Bethesda, MD, 20814, USA
| | - Kendrick K. Lam
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
| | - Katherine V. Jones
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
| | - Niraj H. Tolia
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institute of Health, 9000 Rockville Pike, BG 29B Rm 4NN08, Bethesda, MD, 20814, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4513 Clayton Ave., St. Louis, MO, 63108, USA
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, 4515 McKinley Ave., St. Louis, MO, 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
| | - Timothy A. Wencewicz
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
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6
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Toplak M, Teufel R. Three Rings to Rule Them All: How Versatile Flavoenzymes Orchestrate the Structural Diversification of Natural Products. Biochemistry 2021; 61:47-56. [PMID: 34962769 PMCID: PMC8772269 DOI: 10.1021/acs.biochem.1c00763] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
The structural diversification
of natural products is instrumental
to their versatile bioactivities. In this context, redox tailoring
enzymes are commonly involved in the modification and functionalization
of advanced pathway intermediates en route to the mature natural products.
In recent years, flavoprotein monooxygenases have been shown to mediate
numerous redox tailoring reactions that include not only (aromatic)
hydroxylation, Baeyer–Villiger oxidation, or epoxidation reactions
but also oxygenations that are coupled to extensive remodeling of
the carbon backbone, which are often central to the installment of
the respective pharmacophores. In this Perspective, we will highlight
recent developments and discoveries in the field of flavoenzyme catalysis
in bacterial natural product biosynthesis and illustrate how the flavin
cofactor can be fine-tuned to enable chemo-, regio-, and stereospecific
oxygenations via distinct flavin-C4a-peroxide and flavin-N5-(per)oxide
species. Open questions remain, e.g., regarding the breadth of chemical
reactions enabled particularly by the newly discovered flavin-N5-oxygen
adducts and the role of the protein environment in steering such cascade-like
reactions. Outstanding cases involving different flavin oxygenating
species will be exemplified by the tailoring of bacterial aromatic
polyketides, including enterocin, rubromycins, rishirilides, mithramycin,
anthracyclins, chartreusin, jadomycin, and xantholipin. In addition,
the biosynthesis of tropone natural products, including tropolone
and tropodithietic acid, will be presented, which features a recently
described prototypical flavoprotein dioxygenase that may combine flavin-N5-peroxide
and flavin-N5-oxide chemistry. Finally, structural and mechanistic
features of selected enzymes will be discussed as well as hurdles
for their application in the formation of natural product derivatives
via bioengineering.
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Affiliation(s)
- Marina Toplak
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Robin Teufel
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
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7
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Toplak M, Saleem-Batcha R, Piel J, Teufel R. Catalytic Control of Spiroketal Formation in Rubromycin Polyketide Biosynthesis. Angew Chem Int Ed Engl 2021; 60:26960-26970. [PMID: 34652045 PMCID: PMC9299503 DOI: 10.1002/anie.202109384] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/07/2021] [Indexed: 12/14/2022]
Abstract
The medically important bacterial aromatic polyketide natural products typically feature a planar, polycyclic core structure. An exception is found for the rubromycins, whose backbones are disrupted by a bisbenzannulated [5,6]‐spiroketal pharmacophore that was recently shown to be assembled by flavin‐dependent enzymes. In particular, a flavoprotein monooxygenase proved critical for the drastic oxidative rearrangement of a pentangular precursor and the installment of an intermediate [6,6]‐spiroketal moiety. Here we provide structural and mechanistic insights into the control of catalysis by this spiroketal synthase, which fulfills several important functions as reductase, monooxygenase, and presumably oxidase. The enzyme hereby tightly controls the redox state of the substrate to counteract shunt product formation, while also steering the cleavage of three carbon‐carbon bonds. Our work illustrates an exceptional strategy for the biosynthesis of stable chroman spiroketals.
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Affiliation(s)
- Marina Toplak
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Raspudin Saleem-Batcha
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, 8093, Zürich, Switzerland
| | - Robin Teufel
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
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8
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Toplak M, Saleem‐Batcha R, Piel J, Teufel R. Catalytic Control of Spiroketal Formation in Rubromycin Polyketide Biosynthesis. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Marina Toplak
- Faculty of Biology University of Freiburg Schänzlestrasse 1 79104 Freiburg Germany
| | - Raspudin Saleem‐Batcha
- Institute of Pharmaceutical Sciences University of Freiburg Albertstr. 25 79104 Freiburg Germany
| | - Jörn Piel
- Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zürich 8093 Zürich Switzerland
| | - Robin Teufel
- Faculty of Biology University of Freiburg Schänzlestrasse 1 79104 Freiburg Germany
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9
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Latimer S, Keene SA, Stutts LR, Berger A, Bernert AC, Soubeyrand E, Wright J, Clarke CF, Block AK, Colquhoun TA, Elowsky C, Christensen A, Wilson MA, Basset GJ. A dedicated flavin-dependent monooxygenase catalyzes the hydroxylation of demethoxyubiquinone into ubiquinone (coenzyme Q) in Arabidopsis. J Biol Chem 2021; 297:101283. [PMID: 34626646 PMCID: PMC8559556 DOI: 10.1016/j.jbc.2021.101283] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 01/08/2023] Open
Abstract
Ubiquinone (Coenzyme Q) is a vital respiratory cofactor and liposoluble antioxidant. In plants, it is not known how the C-6 hydroxylation of demethoxyubiquinone, the penultimate step in ubiquinone biosynthesis, is catalyzed. The combination of cross-species gene network modeling along with mining of embryo-defective mutant databases of Arabidopsis thaliana identified the embryo lethal locus EMB2421 (At1g24340) as a top candidate for the missing plant demethoxyubiquinone hydroxylase. In marked contrast with prototypical eukaryotic demethoxyubiquinone hydroxylases, the catalytic mechanism of which depends on a carboxylate-bridged di-iron domain, At1g24340 is homologous to FAD-dependent oxidoreductases that instead use NAD(P)H as an electron donor. Complementation assays in Saccharomyces cerevisiae and Escherichia coli demonstrated that At1g24340 encodes a functional demethoxyubiquinone hydroxylase and that the enzyme displays strict specificity for the C-6 position of the benzoquinone ring. Laser-scanning confocal microscopy also showed that GFP-tagged At1g24340 is targeted to mitochondria. Silencing of At1g24340 resulted in 40 to 74% decrease in ubiquinone content and de novo ubiquinone biosynthesis. Consistent with the role of At1g24340 as a benzenoid ring modification enzyme, this metabolic blockage could not be bypassed by supplementation with 4-hydroxybenzoate, the immediate precursor of ubiquinone's ring. Unlike in yeast, in Arabidopsis overexpression of demethoxyubiquinone hydroxylase did not boost ubiquinone content. Phylogenetic reconstructions indicated that plant demethoxyubiquinone hydroxylase is most closely related to prokaryotic monooxygenases that act on halogenated aromatics and likely descends from an event of horizontal gene transfer between a green alga and a bacterium.
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Affiliation(s)
- Scott Latimer
- Department of Horticultural Sciences, University of Florida, Gainesville, Florida, USA.
| | - Shea A Keene
- Department of Environmental Horticulture, Plant Innovation Center, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Lauren R Stutts
- Department of Horticultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Antoine Berger
- Department of Horticultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Ann C Bernert
- Department of Horticultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Eric Soubeyrand
- Department of Horticultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Janet Wright
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Catherine F Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - Anna K Block
- Center for Medical, Agricultural and Veterinary Entomology, Chemistry Research Unit, ARS, USDA, Gainesville, Florida, USA
| | - Thomas A Colquhoun
- Department of Environmental Horticulture, Plant Innovation Center, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Christian Elowsky
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Alan Christensen
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Mark A Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Gilles J Basset
- Department of Horticultural Sciences, University of Florida, Gainesville, Florida, USA.
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10
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Ren D, Kim M, Wang SA, Liu HW. Identification of a Pyrrole Intermediate Which Undergoes C-Glycosidation and Autoxidation to Yield the Final Product in Showdomycin Biosynthesis. Angew Chem Int Ed Engl 2021; 60:17148-17154. [PMID: 34048627 DOI: 10.1002/anie.202105667] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Indexed: 02/04/2023]
Abstract
Showdomycin is a C-nucleoside bearing an electrophilic maleimide base. Herein, the biosynthetic pathway of showdomycin is presented. The initial stages of the pathway involve non-ribosomal peptide synthetase (NRPS) mediated assembly of a 2-amino-1H-pyrrole-5-carboxylic acid intermediate. This intermediate is prone to air oxidation whereupon it undergoes oxidative decarboxylation to yield an imine of maleimide, which in turn yields the maleimide upon acidification. It is also shown that this pyrrole intermediate serves as the substrate for the C-glycosidase SdmA in the pathway. After coupling with ribose 5-phosphate, the resulting C-nucleoside undergoes a similar sequence of oxidation, decarboxylation and deamination to afford showdomcyin after exposure to air. These results suggest that showdomycin could be an artifact due to aerobic isolation; however, the autoxidation may also serve to convert an otherwise inert product of the biosynthetic pathway to an electrophilic C-nucleotide thereby endowing showdomycin with its observed bioactivities.
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Affiliation(s)
- Daan Ren
- Department of Chemistry, Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX, 78712, USA
| | - Minje Kim
- Department of Chemistry, Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX, 78712, USA
| | - Shao-An Wang
- Department of Chemistry, Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX, 78712, USA
| | - Hung-Wen Liu
- Department of Chemistry, Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX, 78712, USA
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11
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Identification of a Pyrrole Intermediate Which Undergoes C‐Glycosidation and Autoxidation to Yield the Final Product in Showdomycin Biosynthesis. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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12
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An rfuABCD-like operon and its relationship to riboflavin utilization and mammalian. Infect Immun 2021; 89:e0030721. [PMID: 34310888 DOI: 10.1128/iai.00307-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Riboflavin is an essential micronutrient, but its transport and utilization has remained largely understudied among pathogenic spirochetes. Here we show that Borrelia burgdorferi, the zoonotic spirochete that causes Lyme disease, is able to import riboflavin via products of its rfuABCD-like operon as well as synthesize flavin mononucleotide and flavin adenine dinucleotide despite lacking canonical genes for their synthesis. Additionally, a mutant deficient in the rfuABCD-like operon is resistant to the antimicrobial effect of roseoflavin, a natural riboflavin analog, and is attenuated in a murine model of Lyme borreliosis. Our combined results indicate that not only are riboflavin and the maintenance of flavin pools essential for B. burgdorferi growth, but that flavin utilization and its downstream products (e.g., flavoproteins) may play a more prominent role in B. burgdorferi pathogenesis than previously appreciated.
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13
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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: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [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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14
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Beaupre BA, Reabe KR, Roman JV, Moran GR. Hydrogen movements in the oxidative half-reaction of kynurenine 3-monooxygenase from Pseudomonas fluorescens reveal the mechanism of hydroxylation. Arch Biochem Biophys 2020; 690:108474. [PMID: 32687799 DOI: 10.1016/j.abb.2020.108474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/08/2020] [Accepted: 06/17/2020] [Indexed: 11/30/2022]
Abstract
Kynurenine 3-monoxygenase (KMO) catalyzes the conversion of l-kynurenine (L-Kyn) to 3-hydroxykynurenine (3-OHKyn) in the pathway for tryptophan catabolism. We have investigated the effects of pH and deuterium substitution on the oxidative half-reaction of KMO from P. fluorescens (PfKMO). The three phases observed during the oxidative half reaction are formation of the hydroperoxyflavin, hydroxylation and product release. The measured rate constants for these phases proved largely unchanging with pH, suggesting that the KMO active site is insulated from exchange with solvent during catalysis. A solvent inventory study indicated that a solvent isotope effect of 2-3 is observed for the hydroxylation phase and that two or more protons are in flight during this step. An inverse isotope effect of 0.84 ± 0.01 on the rate constant for the hydroxylation step with ring perdeutero-L-Kyn as a substrate indicates a shift from sp2 to sp3 hybridization in the transition state leading to the formation of a non-aromatic intermediate. The pH dependence of transient state data collected for the substrate analog meta-nitrobenzoylalanine indicate that groups proximal to the hydroperoxyflavin are titrated in the range pH 5-8.5 and can be described by a pKa of 8.8. That higher pH values do not slow the rate of hydroxylation precludes that the pKa measured pertains to the proton of the hydroperoxflavin. Together, these observations indicate that the C4a-hydroperoxyflavin has a pKa ≫ 8.5, that a non-aromatic species is the immediate product of hydroxylation and that at least two solvent derived protons are in-flight during oxygen insertion to the substrate aromatic ring. A unifying mechanistic proposal for these observations is proposed.
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Affiliation(s)
- Brett A Beaupre
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Karen R Reabe
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, WI, 53211-3029, USA
| | - Joseph V Roman
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Graham R Moran
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA.
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15
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Yang CL, Zhang B, Xue WW, Li W, Xu ZF, Shi J, Shen Y, Jiao RH, Tan RX, Ge HM. Discovery, Biosynthesis, and Heterologous Production of Loonamycin, a Potent Anticancer Indolocarbazole Alkaloid. Org Lett 2020; 22:4665-4669. [DOI: 10.1021/acs.orglett.0c01456] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Cheng Long Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Bo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Wen Wen Xue
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Wu Li
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Zi Fei Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Jing Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yan Shen
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
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16
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Manenda MS, Picard MÈ, Zhang L, Cyr N, Zhu X, Barma J, Pascal JM, Couture M, Zhang C, Shi R. Structural analyses of the Group A flavin-dependent monooxygenase PieE reveal a sliding FAD cofactor conformation bridging OUT and IN conformations. J Biol Chem 2020; 295:4709-4722. [PMID: 32111738 DOI: 10.1074/jbc.ra119.011212] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/26/2020] [Indexed: 02/02/2023] Open
Abstract
Group A flavin-dependent monooxygenases catalyze the cleavage of the oxygen-oxygen bond of dioxygen, followed by the incorporation of one oxygen atom into the substrate molecule with the aid of NADPH and FAD. These flavoenzymes play an important role in many biological processes, and their most distinct structural feature is the choreographed motions of flavin, which typically adopts two distinct conformations (OUT and IN) to fulfill its function. Notably, these enzymes seem to have evolved a delicate control system to avoid the futile cycle of NADPH oxidation and FAD reduction in the absence of substrate, but the molecular basis of this system remains elusive. Using protein crystallography, size-exclusion chromatography coupled to multi-angle light scattering (SEC-MALS), and small-angle X-ray scattering (SEC-SAXS) and activity assay, we report here a structural and biochemical characterization of PieE, a member of the Group A flavin-dependent monooxygenases involved in the biosynthesis of the antibiotic piericidin A1. This analysis revealed that PieE forms a unique hexamer. Moreover, we found, to the best of our knowledge for the first time, that in addition to the classical OUT and IN conformations, FAD possesses a "sliding" conformation that exists in between the OUT and IN conformations. This observation sheds light on the underlying mechanism of how the signal of substrate binding is transmitted to the FAD-binding site to efficiently initiate NADPH binding and FAD reduction. Our findings bridge a gap currently missing in the orchestrated order of chemical events catalyzed by this important class of enzymes.
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Affiliation(s)
- Mahder S Manenda
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Marie-Ève Picard
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Liping Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Normand Cyr
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Xiaojun Zhu
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Julie Barma
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - John M Pascal
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Manon Couture
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Changsheng Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Rong Shi
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada .,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
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17
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Chenprakhon P, Wongnate T, Chaiyen P. Monooxygenation of aromatic compounds by flavin-dependent monooxygenases. Protein Sci 2020; 28:8-29. [PMID: 30311986 DOI: 10.1002/pro.3525] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/08/2018] [Accepted: 10/08/2018] [Indexed: 12/12/2022]
Abstract
Many flavoenzymes catalyze hydroxylation of aromatic compounds especially phenolic compounds have been isolated and characterized. These enzymes can be classified as either single-component or two-component flavin-dependent hydroxylases (monooxygenases). The hydroxylation reactions catalyzed by the enzymes in this group are useful for modifying the biological properties of phenolic compounds. This review aims to provide an in-depth discussion of the current mechanistic understanding of representative flavin-dependent monooxygenases including 3-hydroxy-benzoate 4-hydroxylase (PHBH, a single-component hydroxylase), 3-hydroxyphenylacetate 4-hydroxylase (HPAH, a two-component hydroxylase), and other monooxygenases which catalyze reactions in addition to hydroxylation, including 2-methyl-3-hydroxypyridine-5-carboxylate oxygenase (MHPCO, a single-component enzyme that catalyzes aromatic-ring cleavage), and HadA monooxygenase (a two-component enzyme that catalyzes additional group elimination reaction). These enzymes have different unique structural features which dictate their reactivity toward various substrates and influence their ability to stabilize flavin intermediates such as C4a-hydroperoxyflavin. Understanding the key catalytic residues and the active site environments important for governing enzyme reactivity will undoubtedly facilitate future work in enzyme engineering or enzyme redesign for the development of biocatalytic methods for the synthesis of valuable compounds.
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Affiliation(s)
- Pirom Chenprakhon
- Institute for Innovative Learning, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand.,Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, 14000, Thailand
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18
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Greule A, Stok JE, De Voss JJ, Cryle MJ. Unrivalled diversity: the many roles and reactions of bacterial cytochromes P450 in secondary metabolism. Nat Prod Rep 2019; 35:757-791. [PMID: 29667657 DOI: 10.1039/c7np00063d] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covering: 2000 up to 2018 The cytochromes P450 (P450s) are a superfamily of heme-containing monooxygenases that perform diverse catalytic roles in many species, including bacteria. The P450 superfamily is widely known for the hydroxylation of unactivated C-H bonds, but the diversity of reactions that P450s can perform vastly exceeds this undoubtedly impressive chemical transformation. Within bacteria, P450s play important roles in many biosynthetic and biodegradative processes that span a wide range of secondary metabolite pathways and present diverse chemical transformations. In this review, we aim to provide an overview of the range of chemical transformations that P450 enzymes can catalyse within bacterial secondary metabolism, with the intention to provide an important resource to aid in understanding of the potential roles of P450 enzymes within newly identified bacterial biosynthetic pathways.
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Affiliation(s)
- Anja Greule
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia. and EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Jeanette E Stok
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia. and EMBL Australia, Monash University, Clayton, Victoria 3800, Australia and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
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19
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Rodríguez Benítez A, Tweedy SE, Baker Dockrey SA, Lukowski AL, Wymore T, Khare D, Brooks CL, Palfey BA, Smith JL, Narayan ARH. Structural basis for selectivity in flavin-dependent monooxygenase-catalyzed oxidative dearomatization. ACS Catal 2019; 9:3633-3640. [PMID: 31346489 DOI: 10.1021/acscatal.8b04575] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Biocatalytic reactions embody many features of ideal chemical transformations, including the potential for impeccable selectivity, high catalytic efficiency, mild reaction conditions and the use of environmentally benign reagents. These advantages have created a demand for biocatalysts that expand the portfolio of complexity-generating reactions available to synthetic chemists. However, the tradeoff that often exists between the substrate scope of a biocatalyst and its selectivity limits the application of enzymes in synthesis. We recently demonstrated that a flavin-dependent monooxygenase, TropB, maintains high levels of site- and stereoselectivity across a range of structurally diverse substrates. Herein, we disclose the structural basis for substrate binding in TropB, which performs a synthetically challenging asymmetric oxidative dearomatization reaction with exquisite site- and stereoselectivity across a range of phenol substrates, providing a foundation for future protein engineering and reaction development efforts. Our hypothesis for substrate binding is informed by a crystal structure of TropB and molecular dynamics simulations with the corresponding computational TropB model and is supported by experimental data. In contrast to canonical class A FAD-dependent monooxygenases in which substrates bind in a protonated form, our data indicate that the phenolate form of the substrate binds in the active site. Furthermore, the substrate position is controlled through twopoint binding of the phenolate oxygen to Arg206 and Tyr239, which are shown to have distinct and essential roles in catalysis. Arg206 is involved in the reduction of the flavin cofactor, suggesting a role in flavin dynamics. Further, QM/MM simulations reveal the interactions that govern the facial selectivity that leads to a highly enantioselective transformation. Thus, the structural origins of the high levels of site-and stereoselectivity observed in reactions of TropB across a range of substrates are elucidated, providing a foundation for future protein engineering and reaction development efforts.
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20
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21
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Janosik T, Rannug A, Rannug U, Wahlström N, Slätt J, Bergman J. Chemistry and Properties of Indolocarbazoles. Chem Rev 2018; 118:9058-9128. [PMID: 30191712 DOI: 10.1021/acs.chemrev.8b00186] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The indolocarbazoles are an important class of nitrogen heterocycles which has evolved significantly in recent years, with numerous studies focusing on their diverse biological effects, or targeting new materials with potential applications in organic electronics. This review aims at providing a broad survey of the chemistry and properties of indolocarbazoles from an interdisciplinary point of view, with particular emphasis on practical synthetic aspects, as well as certain topics which have not been previously accounted for in detail, such as the occurrence, formation, biological activities, and metabolism of indolo[3,2- b]carbazoles. The literature of the past decade forms the basis of the text, which is further supplemented with older key references.
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Affiliation(s)
- Tomasz Janosik
- Research Institutes of Sweden , Bioscience and Materials, RISE Surface, Process and Formulation , SE-151 36 Södertälje , Sweden
| | - Agneta Rannug
- Institute of Environmental Medicine , Karolinska Institutet , SE-171 77 Stockholm , Sweden
| | - Ulf Rannug
- Department of Molecular Biosciences, The Wenner-Gren Institute , Stockholm University , SE-106 91 Stockholm , Sweden
| | | | - Johnny Slätt
- Department of Chemistry, Applied Physical Chemistry , KTH Royal Institute of Technology , SE-100 44 Stockholm , Sweden
| | - Jan Bergman
- Karolinska Institutet , Department of Biosciences and Nutrition , SE-141 83 Huddinge , Sweden
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22
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Bregman-Cohen A, Deri B, Maimon S, Pazy Y, Fishman A. Altering 2-Hydroxybiphenyl 3-Monooxygenase Regioselectivity by Protein Engineering for the Production of a New Antioxidant. Chembiochem 2018; 19:583-590. [DOI: 10.1002/cbic.201700648] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Almog Bregman-Cohen
- Department of Biotechnology and Food Engineering; Technion-Israel Institute of Technology; Haifa 3200003 Israel
| | - Batel Deri
- Department of Biotechnology and Food Engineering; Technion-Israel Institute of Technology; Haifa 3200003 Israel
| | - Shiran Maimon
- Department of Biotechnology and Food Engineering; Technion-Israel Institute of Technology; Haifa 3200003 Israel
| | - Yael Pazy
- Technion Center for Structural Biology; Lorry I. Lokey Center for Life Sciences and Engineering; Technion-Israel Institute of Technology; Haifa 3200003 Israel
| | - Ayelet Fishman
- Department of Biotechnology and Food Engineering; Technion-Israel Institute of Technology; Haifa 3200003 Israel
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23
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Koteva K, Cox G, Kelso JK, Surette MD, Zubyk HL, Ejim L, Stogios P, Savchenko A, Sørensen D, Wright GD. Rox, a Rifamycin Resistance Enzyme with an Unprecedented Mechanism of Action. Cell Chem Biol 2018; 25:403-412.e5. [PMID: 29398560 DOI: 10.1016/j.chembiol.2018.01.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/07/2017] [Accepted: 01/08/2018] [Indexed: 12/11/2022]
Abstract
Rifamycin monooxygenases (Rox) are present in a variety of environmental bacteria and are associated with decomposition of the clinically utilized antibiotic rifampin. Here we report the structure and function of a drug-inducible rox gene from Streptomyces venezuelae, which encodes a class A flavoprotein monooxygenase that inactivates a broad range of rifamycin antibiotics. Our findings describe a mechanism of rifamycin inactivation initiated by monooxygenation of the 2-position of the naphthyl group, which subsequently results in ring opening and linearization of the antibiotic. The result is an antibiotic that no longer adopts the basket-like structure essential for binding to the RNA exit tunnel of the target RpoB, thereby providing the molecular logic of resistance. This unique mechanism of enzymatic inactivation underpins the broad spectrum of rifamycin resistance mediated by Rox enzymes and presents a new antibiotic resistance mechanism not yet seen in microbial antibiotic detoxification.
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Affiliation(s)
- Kalinka Koteva
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Georgina Cox
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Jayne K Kelso
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Matthew D Surette
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Haley L Zubyk
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Linda Ejim
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Peter Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5G 1L6, Canada; Center for Structural Genomics of Infectious Diseases (CSGID), University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Alexei Savchenko
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Dan Sørensen
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4M1, Canada
| | - Gerard D Wright
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada.
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24
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Ma L, Zhang W, Zhu Y, Zhang G, Zhang H, Zhang Q, Zhang L, Yuan C, Zhang C. Identification and characterization of a biosynthetic gene cluster for tryptophan dimers in deep sea-derived Streptomyces sp. SCSIO 03032. Appl Microbiol Biotechnol 2017; 101:6123-6136. [PMID: 28620687 DOI: 10.1007/s00253-017-8375-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/23/2017] [Accepted: 06/01/2017] [Indexed: 01/12/2023]
Abstract
Tryptophan dimers (TDs) are an important class of natural products with diverse bioactivities and share conserved biosynthetic pathways. We report the identification of a partial gene cluster (spm) responsible for the biosynthesis of a class of unusual TDs with non-planar skeletons including spiroindimicins (SPMs), indimicins (IDMs), and lynamicins (LNMs) from the deep-sea derived Streptomyces sp. SCSIO 03032. Bioinformatics analysis, targeted gene disruptions, and heterologous expression studies confirmed the involvement of the spm gene cluster in the biosynthesis of SPM/IDM/LNMs, and revealed the indispensable roles for the halogenase/reductase pair SpmHF, the amino acid oxidase SpmO, and the chromopyrrolic acid (CPA) synthase SpmD, as well as the positive regulator SpmR and the putative transporter SpmA. However, the spm gene cluster was unable to confer a heterologous host the ability to produce SPM/IDM/LNMs. In addition, the P450 enzyme SpmP and the monooxygenase SpmX2 were found to be non-relevant to the biosynthesis of SPM/IDM/LNMs. Sequence alignment and structure modeling suggested the lack of key conserved amino acid residues in the substrate-binding pocket of SpmP. Furthermore, feeding experiments in the non-producing ΔspmO mutant revealed several biosynthetic precursors en route to SPMs, indicating that key enzymes responsible for the biosynthesis of SPMs should be encoded by genes outside of the identified spm gene cluster. Finally, the biosynthetic pathways of SPM/IDM/LNMs are proposed to lay a basis for further insights into their intriguing biosynthetic machinery.
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Affiliation(s)
- Liang Ma
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenjun Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Yiguang Zhu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Guangtao Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Haibo Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Qingbo Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Liping Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Chengshan Yuan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Changsheng Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.
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25
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Asamizu S. Biosynthesis of nitrogen-containing natural products, C7N aminocyclitols and bis-indoles, from actinomycetes. Biosci Biotechnol Biochem 2017; 81:871-881. [DOI: 10.1080/09168451.2017.1281726] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Abstract
Actinomycetes are a major source of bioactive natural products with important pharmaceutical properties. Understanding the natural enzymatic assembly of complex small molecules is important for rational metabolic pathway design to produce “artificial” natural products in bacterial cells. This review will highlight current research on the biosynthetic mechanisms of two classes of nitrogen-containing natural products, C7N aminocyclitols and bis-indoles. Validamycin A is a member of C7N aminocyclitol natural products from Streptomyces hygroscopicus. Here, two important biosynthetic steps, pseudoglycosyltranferase-catalyzed C–N bond formation, and C7-sugar phosphate cyclase-catalyzed divergent carbasugar formation, will be reviewed. In addition, the bis-indolic natural products indolocarbazole, staurosporine from Streptomyces sp. TP-A0274, and rearranged bis-indole violacein from Chromobacterium violaceum are reviewed including the oxidative course of the assembly pathway for the bis-indolic scaffold. The identified biosynthesis mechanisms will be useful to generating new biocatalytic tools and bioactive compounds.
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Affiliation(s)
- Shumpei Asamizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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26
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Koppel N, Balskus EP. Exploring and Understanding the Biochemical Diversity of the Human Microbiota. Cell Chem Biol 2016; 23:18-30. [PMID: 26933733 DOI: 10.1016/j.chembiol.2015.12.008] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 12/15/2015] [Accepted: 12/15/2015] [Indexed: 12/26/2022]
Abstract
Recent studies have illuminated a remarkable diversity and abundance of microbes living on and within the human body. While we are beginning to appreciate associations of certain bacteria and genes with particular host physiological states, considerable information is lacking about the relevant functional activities of the human microbiota. The human gut microbiome encodes tremendous potential for the biosynthesis and transformation of compounds that are important for both microbial and host physiology. Implementation of chemical knowledge and techniques will be required to improve our understanding of the biochemical diversity of the human microbiota. Such efforts include the characterization of novel microbial enzymes and pathways, isolation of microbial natural products, and development of tools to modulate biochemical functions of the gut microbiota. Ultimately, a molecular understanding of gut microbial activities will be critical for elucidating and manipulating these organisms' contributions to human health and disease.
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Affiliation(s)
- Nitzan Koppel
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
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Jackson DR, Yu X, Wang G, Patel AB, Calveras J, Barajas JF, Sasaki E, Metsä-Ketelä M, Liu HW, Rohr J, Tsai SC. Insights into Complex Oxidation during BE-7585A Biosynthesis: Structural Determination and Analysis of the Polyketide Monooxygenase BexE. ACS Chem Biol 2016; 11:1137-47. [PMID: 26813028 DOI: 10.1021/acschembio.5b00913] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cores of aromatic polyketides are essential for their biological activities. Most type II polyketide synthases (PKSs) biosynthesize these core structures involving the minimal PKS, a PKS-associated ketoreductase (KR) and aromatases/cyclases (ARO/CYCs). Oxygenases (OXYs) are rarely involved. BE-7585A is an anticancer polyketide with an angucyclic core. (13)C isotope labeling experiments suggest that its angucyclic core may arise from an oxidative rearrangement of a linear anthracyclinone. Here, we present the crystal structure and functional analysis of BexE, the oxygenase proposed to catalyze this key oxidative rearrangement step that generates the angucyclinone framework. Biochemical assays using various linear anthracyclinone model compounds combined with docking simulations narrowed down the substrate of BexE to be an immediate precursor of aklaviketone, possibly 12-deoxy-aklaviketone. The structural analysis, docking simulations, and biochemical assays provide insights into the role of BexE in BE-7585A biosynthesis and lay the groundwork for engineering such framework-modifying enzymes in type II PKSs.
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Affiliation(s)
- David R. Jackson
- Department
of Molecular Biology and Biochemistry, Department of Chemistry, and
Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| | - Xia Yu
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Guojung Wang
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Avinash B. Patel
- Department
of Molecular Biology and Biochemistry, Department of Chemistry, and
Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| | - Jordi Calveras
- Division
of Medicinal Chemistry, College of Pharmacy and Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jesus F. Barajas
- Department
of Molecular Biology and Biochemistry, Department of Chemistry, and
Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| | - Eita Sasaki
- Division
of Medicinal Chemistry, College of Pharmacy and Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | | | - Hung-wen Liu
- Division
of Medicinal Chemistry, College of Pharmacy and Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jürgen Rohr
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Shiou-Chuan Tsai
- Department
of Molecular Biology and Biochemistry, Department of Chemistry, and
Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
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28
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Du YL, Ryan KS. Catalytic repertoire of bacterial bisindole formation. Curr Opin Chem Biol 2016; 31:74-81. [DOI: 10.1016/j.cbpa.2016.01.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/19/2016] [Accepted: 01/19/2016] [Indexed: 12/19/2022]
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Kanteev M, Bregman-Cohen A, Deri B, Shahar A, Adir N, Fishman A. A crystal structure of 2-hydroxybiphenyl 3-monooxygenase with bound substrate provides insights into the enzymatic mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1906-1913. [PMID: 26275805 DOI: 10.1016/j.bbapap.2015.08.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 08/06/2015] [Accepted: 08/09/2015] [Indexed: 11/16/2022]
Abstract
2-Hydroxybiphenyl 3-monooxygenase (HbpA) is an FAD dependent monooxygenase which catalyzes the ortho-hydroxylation of a broad range of 2-substituted phenols in the presence of NADH and molecular oxygen. We have determined the structure of HbpA from the soil bacterium Pseudomonas azelaica HBP1 with bound 2-hydroxybiphenyl, as well as several variants, at a resolution of 2.3-2.5Å to investigate structure function correlations of the enzyme. An observed hydrogen bond between 2-hydroxybiphenyl and His48 in the active site confirmed the previously suggested role of this residue in substrate deprotonation. The entrance to the active site was confirmed by generating variant G255F which exhibited only 7% of the wild-type's specific activity of product formation, suggesting inhibition of substrate entrance into the active site by the large aromatic residue. Residue Arg242 is suggested to facilitate FAD movement and reduction as was previously reported in studies on the homologous protein para-hydroxybenzoate hydroxylase. In addition, it is suggested that Trp225, which is located in the active site, facilitates proper substrate entrance into the binding pocket in contrast to aklavinone-11-hydroxylase and para-hydroxybenzoate hydroxylase in which a residue at a similar position is responsible for substrate deprotonation. Structure function correlations described in this work will aid in the design of variants with improved activity and altered selectivity for potential industrial applications.
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Affiliation(s)
- Margarita Kanteev
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Almog Bregman-Cohen
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Batel Deri
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Anat Shahar
- Macromolecular Crystallography Research Center (MCRC), Department of Life Sciences & NIBN, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Noam Adir
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ayelet Fishman
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel.
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Spolitak T, Ballou DP. Evidence for catalytic intermediates involved in generating the chromopyrrolic acid scaffold of rebeccamycin by RebO and RebD. Arch Biochem Biophys 2015; 573:111-9. [DOI: 10.1016/j.abb.2015.03.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 03/23/2015] [Accepted: 03/24/2015] [Indexed: 10/23/2022]
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31
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Jensen CN, Mielke T, Farrugia JE, Frank A, Man H, Hart S, Turkenburg JP, Grogan G. Structures of the Apo and FAD-bound forms of 2-hydroxybiphenyl 3-monooxygenase (HbpA) locate activity hotspots identified by using directed evolution. Chembiochem 2015; 16:968-76. [PMID: 25737306 PMCID: PMC4515095 DOI: 10.1002/cbic.201402701] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Indexed: 11/09/2022]
Abstract
The FAD-dependent monooxygenase HbpA from Pseudomonas azelaica HBP1 catalyses the hydroxylation of 2-hydroxybiphenyl (2HBP) to 2,3-dihydroxybiphenyl (23DHBP). HbpA has been used extensively as a model for studying flavoprotein hydroxylases under process conditions, and has also been subjected to directed-evolution experiments that altered its catalytic properties. The structure of HbpA has been determined in its apo and FAD-complex forms to resolutions of 2.76 and 2.03 Å, respectively. Comparisons of the HbpA structure with those of homologues, in conjunction with a model of the reaction product in the active site, reveal His48 as the most likely acid/base residue to be involved in the hydroxylation mechanism. Mutation of His48 to Ala resulted in an inactive enzyme. The structures of HbpA also provide evidence that mutants achieved by directed evolution that altered activity are comparatively remote from the substrate-binding site.
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Affiliation(s)
- Chantel N Jensen
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD (UK)
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32
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Aldemir H, Richarz R, Gulder TAM. Das biokatalytische Repertoire natürlicher Biarylbildung. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201401075] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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33
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Aldemir H, Richarz R, Gulder TAM. The Biocatalytic Repertoire of Natural Biaryl Formation. Angew Chem Int Ed Engl 2014; 53:8286-93. [DOI: 10.1002/anie.201401075] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Indexed: 02/04/2023]
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Biosynthesis of Indolocarbazole and Goadsporin, Two Different Heterocyclic Antibiotics Produced by Actinomycetes. Biosci Biotechnol Biochem 2014; 73:2149-55. [DOI: 10.1271/bbb.90263] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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35
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Armacost K, Musila J, Gathiaka S, Ellis HR, Acevedo O. Exploring the Catalytic Mechanism of Alkanesulfonate Monooxygenase Using Molecular Dynamics. Biochemistry 2014; 53:3308-17. [DOI: 10.1021/bi5002085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kira Armacost
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Jonathan Musila
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Symon Gathiaka
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Holly R. Ellis
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Orlando Acevedo
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
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36
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Chang FY, Brady SF. Characterization of an environmental DNA-derived gene cluster that encodes the bisindolylmaleimide methylarcyriarubin. Chembiochem 2014; 15:815-21. [PMID: 24648189 DOI: 10.1002/cbic.201300756] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Indexed: 01/11/2023]
Abstract
Bisindolylmaleimides represent a naturally occurring class of metabolites that are of interest because of their protein kinase inhibition activity. From a metagenomic library constructed with soil DNA, we identified the four gene mar cluster, a bisindolylmaleimide gene cluster that encodes for methylarcyriarubin (1) production. Heterologous expression of the mar gene cluster in E. coli revealed that the Rieske dioxygenase MarC facilitates the oxidative decarboxylation of a chromopyrrolic acid (CPA) intermediate to yield the bisindolylmaleimide core. The characterization of the mar cluster defines a new role for CPA in the biosynthesis of structurally diverse bacterial tryptophan dimers.
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Affiliation(s)
- Fang-Yuan Chang
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065 (USA)
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37
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Abstract
Enzymes involved in natural product biosynthesis employ a variety of cofactors, reaction mechanisms, and substrate preferences to achieve remarkable chemical diversity found in nature. In this issue of Chemistry & Biology, Goldman and colleagues show how cofactor (FAD) binding affinity impacts the reaction mechanism and outcome of two related proteins, RebC and StaC, involved in indolocarbazoles biosynthesis.
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Goldman PJ, Ryan KS, Hamill MJ, Howard-Jones AR, Walsh CT, Elliott SJ, Drennan CL. An unusual role for a mobile flavin in StaC-like indolocarbazole biosynthetic enzymes. ACTA ACUST UNITED AC 2014; 19:855-65. [PMID: 22840773 DOI: 10.1016/j.chembiol.2012.05.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Revised: 05/10/2012] [Accepted: 05/15/2012] [Indexed: 11/15/2022]
Abstract
The indolocarbazole biosynthetic enzymes StaC, InkE, RebC, and AtmC mediate the degree of oxidation of chromopyrrolic acid on route to the natural products staurosporine, K252a, rebeccamycin, and AT2433-A1, respectively. Here, we show that StaC and InkE, which mediate a net 4-electron oxidation, bind FAD with a micromolar K(d), whereas RebC and AtmC, which mediate a net 8-electron oxidation, bind FAD with a nanomolar K(d) while displaying the same FAD redox properties. We further create RebC-10x, a RebC protein with ten StaC-like amino acid substitutions outside of previously characterized FAD-binding motifs and the complementary StaC-10x. We find that these mutations mediate both FAD affinity and product specificity, with RebC-10x displaying higher StaC activity than StaC itself. X-ray structures of this StaC catalyst identify the substrate of StaC as 7-carboxy-K252c and suggest a unique mechanism for this FAD-dependent enzyme.
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Affiliation(s)
- Peter J Goldman
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Huijbers MME, Montersino S, Westphal AH, Tischler D, van Berkel WJH. Flavin dependent monooxygenases. Arch Biochem Biophys 2013; 544:2-17. [PMID: 24361254 DOI: 10.1016/j.abb.2013.12.005] [Citation(s) in RCA: 369] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/06/2013] [Accepted: 12/09/2013] [Indexed: 11/29/2022]
Abstract
Flavin-dependent monooxygenases catalyze a wide variety of chemo-, regio- and enantioselective oxygenation reactions. As such, they are involved in key biological processes ranging from catabolism, detoxification and biosynthesis, to light emission and axon guidance. Based on fold and function, flavin-dependent monooxygenases can be distributed into eight groups. Groups A and B comprise enzymes that rely on NAD(P)H as external electron donor. Groups C-F are two-protein systems, composed of a monooxygenase and a flavin reductase. Groups G and H comprise internal monooxygenases that reduce the flavin cofactor through substrate oxidation. Recently, many new flavin-dependent monooxygenases have been discovered. In addition to posing basic enzymological questions, these proteins attract attention of pharmaceutical and fine-chemical industries, given their importance as regio- and enantioselective biocatalysts. In this review we present an update of the classification of flavin-dependent monooxygenases and summarize the latest advances in our understanding of their catalytic and structural properties.
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Affiliation(s)
- Mieke M E Huijbers
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Stefania Montersino
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Dirk Tischler
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands; Interdisciplinary Ecological Center, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany
| | - Willem J H van Berkel
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands.
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Minami A, Oguri H, Watanabe K, Oikawa H. Biosynthetic machinery of ionophore polyether lasalocid: enzymatic construction of polyether skeleton. Curr Opin Chem Biol 2013; 17:555-61. [DOI: 10.1016/j.cbpa.2013.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 05/29/2013] [Accepted: 06/01/2013] [Indexed: 02/02/2023]
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41
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Montersino S, Orru R, Barendregt A, Westphal AH, van Duijn E, Mattevi A, van Berkel WJH. Crystal structure of 3-hydroxybenzoate 6-hydroxylase uncovers lipid-assisted flavoprotein strategy for regioselective aromatic hydroxylation. J Biol Chem 2013; 288:26235-26245. [PMID: 23864660 DOI: 10.1074/jbc.m113.479303] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
3-Hydroxybenzoate 6-hydroxylase (3HB6H) from Rhodococcus jostii RHA1 is a dimeric flavoprotein that catalyzes the NADH- and oxygen-dependent para-hydroxylation of 3-hydroxybenzoate to 2,5-dihydroxybenzoate. In this study, we report the crystal structure of 3HB6H as expressed in Escherichia coli. The overall fold of 3HB6H is similar to that of p-hydroxybenzoate hydroxylase and other flavoprotein aromatic hydroxylases. Unexpectedly, a lipid ligand is bound to each 3HB6H monomer. Mass spectral analysis identified the ligand as a mixture of phosphatidylglycerol and phosphatidylethanolamine. The fatty acid chains occupy hydrophobic channels that deeply penetrate into the interior of the substrate-binding domain of each subunit, whereas the hydrophilic part is exposed on the protein surface, connecting the dimerization domains via a few interactions. Most remarkably, the terminal part of a phospholipid acyl chain is directly involved in the substrate-binding site. Co-crystallized chloride ion and the crystal structure of the H213S variant with bound 3-hydroxybenzoate provide hints about oxygen activation and substrate hydroxylation. Essential roles are played by His-213 in catalysis and Tyr-105 in substrate binding. This phospholipid-assisted strategy to control regioselective aromatic hydroxylation is of relevance for optimization of flavin-dependent biocatalysts.
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Affiliation(s)
- Stefania Montersino
- From the Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands
| | - Roberto Orru
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy, and
| | - Arjan Barendregt
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Adrie H Westphal
- From the Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands
| | - Esther van Duijn
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy, and.
| | - Willem J H van Berkel
- From the Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands,.
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Baunach M, Ding L, Bruhn T, Bringmann G, Hertweck C. Regiodivergent NC and NN Aryl Coupling Reactions of Indoloterpenes and Cycloether Formation Mediated by a Single Bacterial Flavoenzyme. Angew Chem Int Ed Engl 2013; 52:9040-3. [DOI: 10.1002/anie.201303733] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Indexed: 11/11/2022]
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Baunach M, Ding L, Bruhn T, Bringmann G, Hertweck C. Regiodivergent NC and NN Aryl Coupling Reactions of Indoloterpenes and Cycloether Formation Mediated by a Single Bacterial Flavoenzyme. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303733] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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44
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Form follows function: structural and catalytic variation in the class a flavoprotein monooxygenases. Int J Mol Sci 2012; 13:15601-39. [PMID: 23443084 PMCID: PMC3546652 DOI: 10.3390/ijms131215601] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 11/08/2012] [Accepted: 11/09/2012] [Indexed: 12/02/2022] Open
Abstract
Flavoprotein monooxygenases (FPMOs) exhibit an array of mechanistic solutions to a common chemical objective; the monooxygenation of a target substrate. Each FPMO efficiently couples reduction of a flavin cofactor by NAD(P)H to oxygenation of the target substrate via a (hydro)peroxyflavin intermediate. This purpose of this review is to describe in detail the Class A flavoprotein hydroxylases (FPMO) in the context of the other FPMO classes (B–F). Both one and two component FPMOs are found in nature. Two-component enzymes require, in addition to the monooxygenase, the involvement of a reductase that first catalyzes the reduction of the flavin by NAD(P)H. The Class A and B FPMOs are single-component and manage to orchestrate the same net reaction within a single peptide. The Class A enzymes have, by some considerable margin, the most complete research record. These enzymes use choreographed movements of the flavin ring that facilitate access of the organic substrates to the active site, provide a means for interaction of NADPH with the flavin, offer a mechanism to sequester the dioxygen reduction chemistry from solvent and a means to release the product. The majority of the discrete catalytic events of the catalytic cycle can be observed directly in exquisite detail using spectrophotometric kinetic methods and many of the key mechanistic conclusions are further supported by structural data. This review attempts to compile each of the key observations made for both paradigm and newly discovered examples of Class A FPMOs into a complete catalytic description of one enzymatic turnover.
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Asamizu S, Hirano S, Onaka H, Koshino H, Shiro Y, Nagano S. Coupling Reaction of Indolepyruvic Acid by StaD and Its Product: Implications for Biosynthesis of Indolocarbazole and Violacein. Chembiochem 2012; 13:2495-500. [DOI: 10.1002/cbic.201200535] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Indexed: 11/06/2022]
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Prokaryotic assembly factors for the attachment of flavin to complex II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:637-47. [PMID: 22985599 DOI: 10.1016/j.bbabio.2012.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 09/05/2012] [Accepted: 09/07/2012] [Indexed: 01/01/2023]
Abstract
Complex II (also known as Succinate dehydrogenase or Succinate-ubiquinone oxidoreductase) is an important respiratory enzyme that participates in both the tricarboxylic acid cycle and electron transport chain. Complex II consists of four subunits including a catalytic flavoprotein (SdhA), an iron-sulphur subunit (SdhB) and two hydrophobic membrane anchors (SdhC and SdhD). Complex II also contains a number of redox cofactors including haem, Fe-S clusters and FAD, which mediate electron transfer from succinate oxidation to the reduction of the mobile electron carrier ubiquinone. The flavin cofactor FAD is an important redox cofactor found in many proteins that participate in oxidation/reduction reactions. FAD is predominantly bound non-covalently to flavoproteins, with only a small percentage of flavoproteins, such as complex II, binding FAD covalently. Aside from a few examples, the mechanisms of flavin attachment have been a relatively unexplored area. This review will discuss the FAD cofactor and the mechanisms used by flavoproteins to covalently bind FAD. Particular focus is placed on the attachment of FAD to complex II with an emphasis on SdhE (a DUF339/SDH5 protein previously termed YgfY), the first protein identified as an assembly factor for FAD attachment to flavoproteins in prokaryotes. The molecular details of SdhE-dependent flavinylation of complex II are discussed and comparisons are made to known cofactor chaperones. Furthermore, an evolutionary hypothesis is proposed to explain the distribution of SdhE homologues in bacterial and eukaryotic species. Mechanisms for regulating SdhE function and how this may be linked to complex II function in different bacterial species are also discussed. This article is part of a Special Issue entitled: Respiratory complex II: Role in cellular physiology and disease.
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Montersino S, van Berkel WJH. Functional annotation and characterization of 3-hydroxybenzoate 6-hydroxylase from Rhodococcus jostii RHA1. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1824:433-42. [PMID: 22207056 DOI: 10.1016/j.bbapap.2011.12.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 12/09/2011] [Accepted: 12/14/2011] [Indexed: 12/11/2022]
Abstract
The genome of Rhodococcus jostii RHA1 contains an unusually large number of oxygenase encoding genes. Many of these genes have yet an unknown function, implying that a notable part of the biochemical and catabolic biodiversity of this Gram-positive soil actinomycete is still elusive. Here we present a multiple sequence alignment and phylogenetic analysis of putative R. jostii RHA1 flavoprotein hydroxylases. Out of 18 candidate sequences, three hydroxylases are absent in other available Rhodococcus genomes. In addition, we report the biochemical characterization of 3-hydroxybenzoate 6-hydroxylase (3HB6H), a gentisate-producing enzyme originally mis-annotated as salicylate hydroxylase. R. jostii RHA1 3HB6H expressed in Escherichia coli is a homodimer with each 47kDa subunit containing a non-covalently bound FAD cofactor. The enzyme has a pH optimum around pH 8.3 and prefers NADH as external electron donor. 3HB6H is active with a series of 3-hydroxybenzoate analogues, bearing substituents in ortho- or meta-position of the aromatic ring. Gentisate, the physiological product, is a non-substrate effector of 3HB6H. This compound is not hydroxylated but strongly stimulates the NADH oxidase activity of the enzyme.
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Montersino S, Tischler D, Gassner GT, van Berkel WJH. Catalytic and Structural Features of Flavoprotein Hydroxylases and Epoxidases. Adv Synth Catal 2011. [DOI: 10.1002/adsc.201100384] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Structure and Mutation Analysis of Archaeal Geranylgeranyl Reductase. J Mol Biol 2011; 409:543-57. [DOI: 10.1016/j.jmb.2011.04.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 03/26/2011] [Accepted: 04/01/2011] [Indexed: 11/19/2022]
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Groom K, Bhattacharya A, Zechel DL. Rebeccamycin and Staurosporine Biosynthesis: Insight into the Mechanisms of the Flavin-Dependent Monooxygenases RebC and StaC. Chembiochem 2011; 12:396-400. [DOI: 10.1002/cbic.201000580] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Indexed: 11/10/2022]
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