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Chen PYT, Adak S, Chekan JR, Liscombe DK, Miyanaga A, Bernhardt P, Diethelm S, Fielding EN, George JH, Miles ZD, Murray LAM, Steele TS, Winter JM, Noel JP, Moore BS. Structural Basis of Stereospecific Vanadium-Dependent Haloperoxidase Family Enzymes in Napyradiomycin Biosynthesis. Biochemistry 2022; 61:1844-1852. [PMID: 35985031 PMCID: PMC10978243 DOI: 10.1021/acs.biochem.2c00338] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Vanadium-dependent haloperoxidases (VHPOs) from Streptomyces bacteria differ from their counterparts in fungi, macroalgae, and other bacteria by catalyzing organohalogenating reactions with strict regiochemical and stereochemical control. While this group of enzymes collectively uses hydrogen peroxide to oxidize halides for incorporation into electron-rich organic molecules, the mechanism for the controlled transfer of highly reactive chloronium ions in the biosynthesis of napyradiomycin and merochlorin antibiotics sets the Streptomyces vanadium-dependent chloroperoxidases apart. Here we report high-resolution crystal structures of two homologous VHPO family members associated with napyradiomycin biosynthesis, NapH1 and NapH3, that catalyze distinctive chemical reactions in the construction of meroterpenoid natural products. The structures, combined with site-directed mutagenesis and intact protein mass spectrometry studies, afforded a mechanistic model for the asymmetric alkene and arene chlorination reactions catalyzed by NapH1 and the isomerase activity catalyzed by NapH3. A key lysine residue in NapH1 situated between the coordinated vanadate and the putative substrate binding pocket was shown to be essential for catalysis. This observation suggested the involvement of the ε-NH2, possibly through formation of a transient chloramine, as the chlorinating species much as proposed in structurally distinct flavin-dependent halogenases. Unexpectedly, NapH3 is modified post-translationally by phosphorylation of an active site His (τ-pHis) consistent with its repurposed halogenation-independent, α-hydroxyketone isomerase activity. These structural studies deepen our understanding of the mechanistic underpinnings of VHPO enzymes and their evolution as enantioselective biocatalysts.
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Affiliation(s)
- Percival Yang-Ting Chen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Sanjoy Adak
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Jonathan R Chekan
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - David K Liscombe
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Akimasa Miyanaga
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Peter Bernhardt
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Stefan Diethelm
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Elisha N Fielding
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Jonathan H George
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Zachary D Miles
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Lauren A M Murray
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Taylor S Steele
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Jaclyn M Winter
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Joseph P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
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2
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Wang J, Pang X, Chen C, Gao C, Zhou X, Liu Y, Luo X. Chemistry, Biosynthesis, and Biological Activity of Halogenated Compounds Produced by Marine Microorganisms. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202200064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jiamin Wang
- CAS Key Laboratory of Tropical Marine Bio‐resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou 510301 China
- University of Chinese Academy of Sciences 19 Yuquan Road Beijing 100049 China
| | - Xiaoyan Pang
- CAS Key Laboratory of Tropical Marine Bio‐resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou 510301 China
| | - Chunmei Chen
- CAS Key Laboratory of Tropical Marine Bio‐resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou 510301 China
- University of Chinese Academy of Sciences 19 Yuquan Road Beijing 100049 China
| | - Chenghai Gao
- Institute of Marine Drugs Guangxi University of Chinese Medicine Nanning 530200 China
| | - Xuefeng Zhou
- CAS Key Laboratory of Tropical Marine Bio‐resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458 China
- University of Chinese Academy of Sciences 19 Yuquan Road Beijing 100049 China
| | - Yonghong Liu
- CAS Key Laboratory of Tropical Marine Bio‐resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou 510301 China
- Institute of Marine Drugs Guangxi University of Chinese Medicine Nanning 530200 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458 China
- University of Chinese Academy of Sciences 19 Yuquan Road Beijing 100049 China
| | - Xiaowei Luo
- Institute of Marine Drugs Guangxi University of Chinese Medicine Nanning 530200 China
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Paul CE, Eggerichs D, Westphal AH, Tischler D, van Berkel WJH. Flavoprotein monooxygenases: Versatile biocatalysts. Biotechnol Adv 2021; 51:107712. [PMID: 33588053 DOI: 10.1016/j.biotechadv.2021.107712] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/27/2021] [Accepted: 02/06/2021] [Indexed: 12/13/2022]
Abstract
Flavoprotein monooxygenases (FPMOs) are single- or two-component enzymes that catalyze a diverse set of chemo-, regio- and enantioselective oxyfunctionalization reactions. In this review, we describe how FPMOs have evolved from model enzymes in mechanistic flavoprotein research to biotechnologically relevant catalysts that can be applied for the sustainable production of valuable chemicals. After a historical account of the development of the FPMO field, we explain the FPMO classification system, which is primarily based on protein structural properties and electron donor specificities. We then summarize the most appealing reactions catalyzed by each group with a focus on the different types of oxygenation chemistries. Wherever relevant, we report engineering strategies that have been used to improve the robustness and applicability of FPMOs.
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Affiliation(s)
- Caroline E Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Daniel Eggerichs
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dirk Tischler
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands.
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4
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Organohalide-Respiring Bacteria at the Heart of Anaerobic Metabolism in Arctic Wet Tundra Soils. Appl Environ Microbiol 2021; 87:AEM.01643-20. [PMID: 33187999 DOI: 10.1128/aem.01643-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/10/2020] [Indexed: 11/20/2022] Open
Abstract
Recent work revealed an active biological chlorine cycle in coastal Arctic tundra of northern Alaska. This raised the question of whether chlorine cycling was restricted to coastal areas or if these processes extended to inland tundra. The anaerobic process of organohalide respiration, carried out by specialized bacteria like Dehalococcoides, consumes hydrogen gas and acetate using halogenated organic compounds as terminal electron acceptors, potentially competing with methanogens that produce the greenhouse gas methane. We measured microbial community composition and soil chemistry along an ∼262-km coastal-inland transect to test for the potential of organohalide respiration across the Arctic Coastal Plain and studied the microbial community associated with Dehalococcoides to explore the ecology of this group and its potential to impact C cycling in the Arctic. Concentrations of brominated organic compounds declined sharply with distance from the coast, but the decrease in organic chlorine pools was more subtle. The relative abundances of Dehalococcoides were similar across the transect, except for being lower at the most inland site. Dehalococcoides correlated with other strictly anaerobic genera, plus some facultative ones, that had the genetic potential to provide essential resources (hydrogen, acetate, corrinoids, or organic chlorine). This community included iron reducers, sulfate reducers, syntrophic bacteria, acetogens, and methanogens, some of which might also compete with Dehalococcoides for hydrogen and acetate. Throughout the Arctic Coastal Plain, Dehalococcoides is associated with the dominant anaerobes that control fluxes of hydrogen, acetate, methane, and carbon dioxide. Depending on seasonal electron acceptor availability, organohalide-respiring bacteria could impact carbon cycling in Arctic wet tundra soils.IMPORTANCE Once considered relevant only in contaminated sites, it is now recognized that biological chlorine cycling is widespread in natural environments. However, linkages between chlorine cycling and other ecosystem processes are not well established. Species in the genus Dehalococcoides are highly specialized, using hydrogen, acetate, vitamin B12-like compounds, and organic chlorine produced by the surrounding community. We studied which neighbors might produce these essential resources for Dehalococcoides species. We found that Dehalococcoides species are ubiquitous across the Arctic Coastal Plain and are closely associated with a network of microbes that produce or consume hydrogen or acetate, including the most abundant anaerobic bacteria and methanogenic archaea. We also found organic chlorine and microbes that can produce these compounds throughout the study area. Therefore, Dehalococcoides could control the balance between carbon dioxide and methane (a more potent greenhouse gas) when suitable organic chlorine compounds are available to drive hydrogen and acetate uptake.
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Mukherjee G, Sastri CV. Eccentricities in Spectroscopy and Reactivity of Non‐Heme Metal Intermediates Contained in Bispidine Scaffolds. Isr J Chem 2020. [DOI: 10.1002/ijch.202000045] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Gourab Mukherjee
- Department of Chemistry Indian Institute of Technology Guwahati Guwahati, Assam 781039 India
| | - Chivukula V. Sastri
- Department of Chemistry Indian Institute of Technology Guwahati Guwahati, Assam 781039 India
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6
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Visser SP. Second‐Coordination Sphere Effects on Selectivity and Specificity of Heme and Nonheme Iron Enzymes. Chemistry 2020; 26:5308-5327. [DOI: 10.1002/chem.201905119] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/04/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Sam P. Visser
- The Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical ScienceThe University of Manchester 131 Princess Street Manchester M1 7DN UK
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7
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Mubarak MQE, Visser SP. Computational Study on the Catalytic Reaction Mechanism of Heme Haloperoxidase Enzymes. Isr J Chem 2019. [DOI: 10.1002/ijch.201900099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- M. Qadri E. Mubarak
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science The University of Manchester 131 Princess Street Manchester M1 7DN United Kingdom
| | - Sam P. Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science The University of Manchester 131 Princess Street Manchester M1 7DN United Kingdom
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8
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Halogenating Enzymes for Active Agent Synthesis: First Steps Are Done and Many Have to Follow. Molecules 2019; 24:molecules24214008. [PMID: 31694313 PMCID: PMC6864650 DOI: 10.3390/molecules24214008] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/28/2019] [Accepted: 10/31/2019] [Indexed: 12/22/2022] Open
Abstract
Halogens can be very important for active agents as vital parts of their binding mode, on the one hand, but are on the other hand instrumental in the synthesis of most active agents. However, the primary halogenating compound is molecular chlorine which has two major drawbacks, high energy consumption and hazardous handling. Nature bypassed molecular halogens and evolved at least six halogenating enzymes: Three kind of haloperoxidases, flavin-dependent halogenases as well as α-ketoglutarate and S-adenosylmethionine (SAM)-dependent halogenases. This review shows what is known today on these enzymes in terms of biocatalytic usage. The reader may understand this review as a plea for the usage of halogenating enzymes for fine chemical syntheses, but there are many steps to take until halogenating enzymes are reliable, flexible, and sustainable catalysts for halogenation.
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9
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China H, Ogino H. A useful propionate cofactor enhancing activity for organic solvent-tolerant recombinant metal-free bromoperoxidase (perhydrolase) from Streptomyces aureofaciens. Biochem Biophys Res Commun 2019; 516:327-332. [PMID: 31204052 DOI: 10.1016/j.bbrc.2019.06.036] [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: 06/03/2019] [Accepted: 06/07/2019] [Indexed: 11/19/2022]
Abstract
The oxidative brominating activity of an organic solvent-tolerant recombinant metal-free bromoperoxidase BPO-A1 with C-terminal His-tag (rBPO-A1), from Streptomyces aureofaciens found to depend on various additives. These included carboxylic acids, used as cofactors and alcohols, used as water-miscible organic solvents. Enzyme activity was significantly enhanced by using propanoic acid (PA) as a cofactor, which had a high Log D at pH 5.0 and ethylene glycol with a low Log P. The positional specificity of oxidative hydroxybromination for olefins, using rBPO-A1 and PA in the presence of methanol, was higher compared to a non-enzymatic reaction using peracetic acid. The oxidative bromination step, occurring after enzymatic peroxidation step, is suggested to be pseudoenzymatic.
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Affiliation(s)
- Hideyasu China
- Department of Chemical Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Nakaku, Sakai, Osaka, 599-8531, Japan; Department of Applied Chemistry, College of Life Sciences Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Hiroyasu Ogino
- Department of Chemical Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Nakaku, Sakai, Osaka, 599-8531, Japan.
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10
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Sorabad GS, Maddani MR. Metal-free, green and efficient oxidative α halogenation of enaminones by halo acid and DMSO. NEW J CHEM 2019. [DOI: 10.1039/c8nj06412a] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metal free oxidative halogenation of N-aryl enaminones has been demonstrated using a DMSO–halo acid combination under mild reaction conditions. The present method is a straightforward approach and is also applied for the synthesis of chromenone derivatives in excellent yields.
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Affiliation(s)
- Ganesh Shivayogappa Sorabad
- Department of Post-Graduate Studies and Research in Chemistry
- Mangalore University
- Mangalagangothri-574199
- India
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11
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Timmins A, Fowler NJ, Warwicker J, Straganz GD, de Visser SP. Does Substrate Positioning Affect the Selectivity and Reactivity in the Hectochlorin Biosynthesis Halogenase? Front Chem 2018; 6:513. [PMID: 30425979 PMCID: PMC6218459 DOI: 10.3389/fchem.2018.00513] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 10/04/2018] [Indexed: 12/17/2022] Open
Abstract
In this work we present the first computational study on the hectochlorin biosynthesis enzyme HctB, which is a unique three-domain halogenase that activates non-amino acid moieties tethered to an acyl-carrier, and as such may have biotechnological relevance beyond other halogenases. We use a combination of small cluster models and full enzyme structures calculated with quantum mechanics/molecular mechanics methods. Our work reveals that the reaction is initiated with a rate-determining hydrogen atom abstraction from substrate by an iron (IV)-oxo species, which creates an iron (III)-hydroxo intermediate. In a subsequent step the reaction can bifurcate to either halogenation or hydroxylation of substrate, but substrate binding and positioning drives the reaction to optimal substrate halogenation. Furthermore, several key residues in the protein have been identified for their involvement in charge-dipole interactions and induced electric field effects. In particular, two charged second coordination sphere amino acid residues (Glu223 and Arg245) appear to influence the charge density on the Cl ligand and push the mechanism toward halogenation. Our studies, therefore, conclude that nonheme iron halogenases have a chemical structure that induces an electric field on the active site that affects the halide and iron charge distributions and enable efficient halogenation. As such, HctB is intricately designed for a substrate halogenation and operates distinctly different from other nonheme iron halogenases.
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Affiliation(s)
- Amy Timmins
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, University of Manchester, Manchester, United Kingdom
| | - Nicholas J. Fowler
- The Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Jim Warwicker
- The Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Grit D. Straganz
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
- Institute of Molecular Biosciences, Graz University, Graz, Austria
| | - Sam P. de Visser
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, University of Manchester, Manchester, United Kingdom
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12
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Timmins A, Quesne MG, Borowski T, de Visser SP. Group Transfer to an Aliphatic Bond: A Biomimetic Study Inspired by Nonheme Iron Halogenases. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01673] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Amy Timmins
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Matthew G. Quesne
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Sam P. de Visser
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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13
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A Comparative Review on the Catalytic Mechanism of Nonheme Iron Hydroxylases and Halogenases. Catalysts 2018. [DOI: 10.3390/catal8080314] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Enzymatic halogenation and haloperoxidation are unusual processes in biology; however, a range of halogenases and haloperoxidases exist that are able to transfer an aliphatic or aromatic C–H bond into C–Cl/C–Br. Haloperoxidases utilize hydrogen peroxide, and in a reaction with halides (Cl−/Br−), they react to form hypohalides (OCl−/OBr−) that subsequently react with substrate by halide transfer. There are three types of haloperoxidases, namely the iron-heme, nonheme vanadium, and flavin-dependent haloperoxidases that are reviewed here. In addition, there are the nonheme iron halogenases that show structural and functional similarity to the nonheme iron hydroxylases and form an iron(IV)-oxo active species from a reaction of molecular oxygen with α-ketoglutarate on an iron(II) center. They subsequently transfer a halide (Cl−/Br−) to an aliphatic C–H bond. We review the mechanism and function of nonheme iron halogenases and hydroxylases and show recent computational modelling studies of our group on the hectochlorin biosynthesis enzyme and prolyl-4-hydroxylase as examples of nonheme iron halogenases and hydroxylases. These studies have established the catalytic mechanism of these enzymes and show the importance of substrate and oxidant positioning on the stereo-, chemo- and regioselectivity of the reaction that takes place.
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14
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Menon BRK, Latham J, Dunstan MS, Brandenburger E, Klemstein U, Leys D, Karthikeyan C, Greaney MF, Shepherd SA, Micklefield J. Structure and biocatalytic scope of thermophilic flavin-dependent halogenase and flavin reductase enzymes. Org Biomol Chem 2018; 14:9354-9361. [PMID: 27714222 DOI: 10.1039/c6ob01861k] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Flavin-dependent halogenase (Fl-Hal) enzymes have been shown to halogenate a range of synthetic as well as natural aromatic compounds. The exquisite regioselectively of Fl-Hal enzymes can provide halogenated building blocks which are inaccessible using standard halogenation chemistries. Consequently, Fl-Hal are potentially useful biocatalysts for the chemoenzymatic synthesis of pharmaceuticals and other valuable products, which are derived from haloaromatic precursors. However, the application of Fl-Hal enzymes, in vitro, has been hampered by their poor catalytic activity and lack of stability. To overcome these issues, we identified a thermophilic tryptophan halogenase (Th-Hal), which has significantly improved catalytic activity and stability, compared with other Fl-Hal characterised to date. When used in combination with a thermostable flavin reductase, Th-Hal can efficiently halogenate a number of aromatic substrates. X-ray crystal structures of Th-Hal, and the reductase partner (Th-Fre), provide insights into the factors that contribute to enzyme stability, which could guide the discovery and engineering of more robust and productive halogenase biocatalysts.
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Affiliation(s)
- Binuraj R K Menon
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Jonathan Latham
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Mark S Dunstan
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Eileen Brandenburger
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Ulrike Klemstein
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - David Leys
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Chinnan Karthikeyan
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Michael F Greaney
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Sarah A Shepherd
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Jason Micklefield
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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15
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Ma Z, Chen C. Natural products as inspiration for the development of new synthetic methods. J CHIN CHEM SOC-TAIP 2018; 65:43-59. [PMID: 29430058 PMCID: PMC5800783 DOI: 10.1002/jccs.201700134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Natural products have played an important role in shaping modern synthetic organic chemistry. In particular, their complex molecular skeletons have stimulated the development of many new synthetic methods. We highlight in this article some recent examples of synthetic design inspired by the biosynthesis of natural products.
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Affiliation(s)
- Zhiqiang Ma
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, USA
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, P. R. China
| | - Chuo Chen
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, USA
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16
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Agarwal V, Miles ZD, Winter JM, Eustáquio AS, El Gamal AA, Moore BS. Enzymatic Halogenation and Dehalogenation Reactions: Pervasive and Mechanistically Diverse. Chem Rev 2017; 117:5619-5674. [PMID: 28106994 PMCID: PMC5575885 DOI: 10.1021/acs.chemrev.6b00571] [Citation(s) in RCA: 248] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Naturally produced halogenated compounds are ubiquitous across all domains of life where they perform a multitude of biological functions and adopt a diversity of chemical structures. Accordingly, a diverse collection of enzyme catalysts to install and remove halogens from organic scaffolds has evolved in nature. Accounting for the different chemical properties of the four halogen atoms (fluorine, chlorine, bromine, and iodine) and the diversity and chemical reactivity of their organic substrates, enzymes performing biosynthetic and degradative halogenation chemistry utilize numerous mechanistic strategies involving oxidation, reduction, and substitution. Biosynthetic halogenation reactions range from simple aromatic substitutions to stereoselective C-H functionalizations on remote carbon centers and can initiate the formation of simple to complex ring structures. Dehalogenating enzymes, on the other hand, are best known for removing halogen atoms from man-made organohalogens, yet also function naturally, albeit rarely, in metabolic pathways. This review details the scope and mechanism of nature's halogenation and dehalogenation enzymatic strategies, highlights gaps in our understanding, and posits where new advances in the field might arise in the near future.
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Affiliation(s)
- Vinayak Agarwal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
| | - Zachary D. Miles
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego
| | | | - Alessandra S. Eustáquio
- College of Pharmacy, Department of Medicinal Chemistry & Pharmacognosy and Center for Biomolecular Sciences, University of Illinois at Chicago
| | - Abrahim A. El Gamal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
| | - Bradley S. Moore
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego
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17
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Süssmuth RD, Mainz A. Nonribosomal Peptide Synthesis-Principles and Prospects. Angew Chem Int Ed Engl 2017; 56:3770-3821. [PMID: 28323366 DOI: 10.1002/anie.201609079] [Citation(s) in RCA: 543] [Impact Index Per Article: 77.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Indexed: 01/05/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) are large multienzyme machineries that assemble numerous peptides with large structural and functional diversity. These peptides include more than 20 marketed drugs, such as antibacterials (penicillin, vancomycin), antitumor compounds (bleomycin), and immunosuppressants (cyclosporine). Over the past few decades biochemical and structural biology studies have gained mechanistic insights into the highly complex assembly line of nonribosomal peptides. This Review provides state-of-the-art knowledge on the underlying mechanisms of NRPSs and the variety of their products along with detailed analysis of the challenges for future reprogrammed biosynthesis. Such a reprogramming of NRPSs would immediately spur chances to generate analogues of existing drugs or new compound libraries of otherwise nearly inaccessible compound structures.
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Affiliation(s)
- Roderich D Süssmuth
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623, Berlin, Germany
| | - Andi Mainz
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623, Berlin, Germany
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18
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Süssmuth RD, Mainz A. Nicht-ribosomale Peptidsynthese - Prinzipien und Perspektiven. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609079] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Roderich D. Süssmuth
- Technische Universität Berlin; Institut für Chemie; Straße des 17. Juni 124 10623 Berlin Deutschland
| | - Andi Mainz
- Technische Universität Berlin; Institut für Chemie; Straße des 17. Juni 124 10623 Berlin Deutschland
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19
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Rugg G, Senn HM. Formation and structure of the ferryl [FeO] intermediate in the non-haem iron halogenase SyrB2: classical and QM/MM modelling agree. Phys Chem Chem Phys 2017; 19:30107-30119. [DOI: 10.1039/c7cp05937j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
All O2 activation roads for three substrates and three spin states in SyrB2 lead to the same [FeO] structure.
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Affiliation(s)
- G. Rugg
- WestCHEM and School of Chemistry
- University of Glasgow
- Glasgow G12 8QQ
- UK
| | - H. M. Senn
- WestCHEM and School of Chemistry
- University of Glasgow
- Glasgow G12 8QQ
- UK
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20
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Shepherd SA, Menon BRK, Fisk H, Struck AW, Levy C, Leys D, Micklefield J. A Structure-Guided Switch in the Regioselectivity of a Tryptophan Halogenase. Chembiochem 2016; 17:821-4. [PMID: 26840773 PMCID: PMC5071727 DOI: 10.1002/cbic.201600051] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Indexed: 12/04/2022]
Abstract
Flavin‐dependent halogenases are potentially useful biocatalysts for the regioselective halogenation of aromatic compounds. Haloaromatic compounds can be utilised in the synthesis and biosynthesis of pharmaceuticals and other valuable products. Here we report the first X‐ray crystal structure of a tryptophan 6‐halogenase (SttH), which enabled key residues that contribute to the regioselectivity in tryptophan halogenases to be identified. Structure‐guided mutagenesis resulted in a triple mutant (L460F/P461E/P462T) that exhibited a complete switch in regioselectivity; with the substrate 3‐indolepropionate 75 % 5‐chlorination was observed with the mutant in comparison to 90 % 6‐chlorination for the wild‐type SttH. This is the first clear example of how regiocomplementary halogenases can be created from a single parent enzyme. The biocatalytic repertoire of SttH was also expanded to include a range of indolic and non‐indolic substrates.
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Affiliation(s)
- Sarah A Shepherd
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Binuraj R K Menon
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Heidi Fisk
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Anna-Winona Struck
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Colin Levy
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - David Leys
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Jason Micklefield
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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21
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China H, Okada Y, Dohi T. The Multiple Reactions in the Monochlorodimedone Assay: Discovery of Unique Dehalolactonizations under Mild Conditions. ASIAN J ORG CHEM 2015. [DOI: 10.1002/ajoc.201500210] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Hideyasu China
- Department of Applied Chemistry; College of Life Sciences; Ritsumeikan University; 1-1-1 Nojihigashi Kusatsu Shiga 525-8577 Japan
| | - Yutaka Okada
- Department of Applied Chemistry; College of Life Sciences; Ritsumeikan University; 1-1-1 Nojihigashi Kusatsu Shiga 525-8577 Japan
| | - Toshifumi Dohi
- Department of Pharmaceutical Sciences; College of Pharmaceutical Sciences; Ritsumeikan University; Japan
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22
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China H, Okada Y, Ogino H. Production mechanism of active species on the oxidative bromination following perhydrolase activity. J PHYS ORG CHEM 2015. [DOI: 10.1002/poc.3490] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hideyasu China
- Department of Applied Chemistry, College of Life Sciences; Ritsumeikan University; 1-1-1 Nojihigashi Kusatsu Shiga 525-8577 Japan
- Department of Chemical Engineering; Osaka Prefecture University; 1-1 Gakuen-cho, Nakaku Sakai Osaka 599-8531 Japan
| | - Yutaka Okada
- Department of Applied Chemistry, College of Life Sciences; Ritsumeikan University; 1-1-1 Nojihigashi Kusatsu Shiga 525-8577 Japan
| | - Hiroyasu Ogino
- Department of Chemical Engineering; Osaka Prefecture University; 1-1 Gakuen-cho, Nakaku Sakai Osaka 599-8531 Japan
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23
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Enzymatic Halogenases and Haloperoxidases: Computational Studies on Mechanism and Function. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2015; 100:113-51. [PMID: 26415843 DOI: 10.1016/bs.apcsb.2015.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Despite the fact that halogenated compounds are rare in biology, a number of organisms have developed processes to utilize halogens and in recent years, a string of enzymes have been identified that selectively insert halogen atoms into, for instance, a CH aliphatic bond. Thus, a number of natural products, including antibiotics, contain halogenated functional groups. This unusual process has great relevance to the chemical industry for stereoselective and regiospecific synthesis of haloalkanes. Currently, however, industry utilizes few applications of biological haloperoxidases and halogenases, but efforts are being worked on to understand their catalytic mechanism, so that their catalytic function can be upscaled. In this review, we summarize experimental and computational studies on the catalytic mechanism of a range of haloperoxidases and halogenases with structurally very different catalytic features and cofactors. This chapter gives an overview of heme-dependent haloperoxidases, nonheme vanadium-dependent haloperoxidases, and flavin adenine dinucleotide-dependent haloperoxidases. In addition, we discuss the S-adenosyl-l-methionine fluoridase and nonheme iron/α-ketoglutarate-dependent halogenases. In particular, computational efforts have been applied extensively for several of these haloperoxidases and halogenases and have given insight into the essential structural features that enable these enzymes to perform the unusual halogen atom transfer to substrates.
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24
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Shepherd SA, Karthikeyan C, Latham J, Struck AW, Thompson ML, Menon BRK, Styles MQ, Levy C, Leys D, Micklefield J. Extending the biocatalytic scope of regiocomplementary flavin-dependent halogenase enzymes. Chem Sci 2015; 6:3454-3460. [PMID: 29511510 PMCID: PMC5659210 DOI: 10.1039/c5sc00913h] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 04/09/2015] [Indexed: 11/21/2022] Open
Abstract
Flavin-dependent halogenases are potentially valuable biocatalysts for the regioselective halogenation of aromatic compounds. These enzymes, utilising benign inorganic halides, offer potential advantages over traditional non-enzymatic halogenation chemistry that often lacks regiocontrol and requires deleterious reagents. Here we extend the biocatalytic repertoire of the tryptophan halogenases, demonstrating how these enzymes can halogenate a range of alternative aryl substrates. Using structure guided mutagenesis we also show that it is possible to alter the regioselectivity as well as increase the activity of the halogenases with non-native substrates including anthranilic acid; an important intermediate in the synthesis and biosynthesis of pharmaceuticals and other valuable products.
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Affiliation(s)
- Sarah A Shepherd
- School of Chemistry , The University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK .
- Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK
| | - Chinnan Karthikeyan
- School of Chemistry , The University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK .
- Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK
| | - Jonathan Latham
- School of Chemistry , The University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK .
- Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK
| | - Anna-Winona Struck
- School of Chemistry , The University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK .
- Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK
| | - Mark L Thompson
- School of Chemistry , The University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK .
- Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK
| | - Binuraj R K Menon
- School of Chemistry , The University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK .
- Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK
| | - Matthew Q Styles
- School of Chemistry , The University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK .
- Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK
| | - Colin Levy
- Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK
- Faculty of Life Sciences , The University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK
| | - David Leys
- Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK
- Faculty of Life Sciences , The University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK
| | - Jason Micklefield
- School of Chemistry , The University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK .
- Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK
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25
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Draksharapu A, Angelone D, Quesne MG, Padamati SK, Gómez L, Hage R, Costas M, Browne WR, de Visser SP. Identification and spectroscopic characterization of nonheme iron(III) hypochlorite intermediates. Angew Chem Int Ed Engl 2015; 54:4357-61. [PMID: 25663379 PMCID: PMC4670478 DOI: 10.1002/anie.201411995] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Revised: 01/10/2015] [Indexed: 11/18/2022]
Abstract
Fe(III)-hypohalite complexes have been implicated in a wide range of important enzyme-catalyzed halogenation reactions including the biosynthesis of natural products and antibiotics and post-translational modification of proteins. The absence of spectroscopic data on such species precludes their identification. Herein, we report the generation and spectroscopic characterization of nonheme Fe(III)-hypohalite intermediates of possible relevance to iron halogenases. We show that Fe(III)-OCl polypyridylamine complexes can be sufficiently stable at room temperature to be characterized by UV/Vis absorption, resonance Raman and EPR spectroscopies, and cryo-ESIMS. DFT methods rationalize the pathways to the formation of the Fe(III)-OCl, and ultimately Fe(IV)=O, species and provide indirect evidence for a short-lived Fe(II)-OCl intermediate. The species observed and the pathways involved offer insight into and, importantly, a spectroscopic database for the investigation of iron halogenases.
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Affiliation(s)
- Apparao Draksharapu
- Stratingh Institute for Chemistry, Faculty of Mathematics and Natural Sciences, University of GroningenNijenborgh 4, 9747 AG Groningen (The Netherlands) E-mail:
| | - Davide Angelone
- Stratingh Institute for Chemistry, Faculty of Mathematics and Natural Sciences, University of GroningenNijenborgh 4, 9747 AG Groningen (The Netherlands) E-mail:
| | - Matthew G Quesne
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester M1 7DN (UK) E-mail:
| | - Sandeep K Padamati
- Stratingh Institute for Chemistry, Faculty of Mathematics and Natural Sciences, University of GroningenNijenborgh 4, 9747 AG Groningen (The Netherlands) E-mail:
| | - Laura Gómez
- Departament de Química and Institute of Computational Chemistry and Catalysis (IQCC), University of GironaCampus de Montilivi, Girona 17071 (Spain)
- Serveis Tècnics de Recerca (STR), Universitat de GironaParc Científic i Tecnològic, E-17003 Girona, Spain
| | - Ronald Hage
- Catexel Ltd., BioPartner Center LeidenGalileiweg 8, 2333 BD Leiden (The Netherlands)
| | - Miquel Costas
- Departament de Química and Institute of Computational Chemistry and Catalysis (IQCC), University of GironaCampus de Montilivi, Girona 17071 (Spain)
| | - Wesley R Browne
- Stratingh Institute for Chemistry, Faculty of Mathematics and Natural Sciences, University of GroningenNijenborgh 4, 9747 AG Groningen (The Netherlands) E-mail:
| | - Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester M1 7DN (UK) E-mail:
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26
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Draksharapu A, Angelone D, Quesne MG, Padamati SK, Gómez L, Hage R, Costas M, Browne WR, de Visser SP. Identification and Spectroscopic Characterization of Nonheme Iron(III) Hypochlorite Intermediates. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 127:4431-4435. [PMID: 27478260 PMCID: PMC4955228 DOI: 10.1002/ange.201411995] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Revised: 01/10/2015] [Indexed: 11/07/2022]
Abstract
FeIII-hypohalite complexes have been implicated in a wide range of important enzyme-catalyzed halogenation reactions including the biosynthesis of natural products and antibiotics and post-translational modification of proteins. The absence of spectroscopic data on such species precludes their identification. Herein, we report the generation and spectroscopic characterization of nonheme FeIII-hypohalite intermediates of possible relevance to iron halogenases. We show that FeIII-OCl polypyridylamine complexes can be sufficiently stable at room temperature to be characterized by UV/Vis absorption, resonance Raman and EPR spectroscopies, and cryo-ESIMS. DFT methods rationalize the pathways to the formation of the FeIII-OCl, and ultimately FeIV=O, species and provide indirect evidence for a short-lived FeII-OCl intermediate. The species observed and the pathways involved offer insight into and, importantly, a spectroscopic database for the investigation of iron halogenases.
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Affiliation(s)
- Apparao Draksharapu
- Stratingh Institute for Chemistry, Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands)
| | - Davide Angelone
- Stratingh Institute for Chemistry, Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands)
| | - Matthew G. Quesne
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN (UK)
| | - Sandeep K. Padamati
- Stratingh Institute for Chemistry, Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands)
| | - Laura Gómez
- Departament de Química and Institute of Computational Chemistry and Catalysis (IQCC), University of Girona, Campus de Montilivi, Girona 17071 (Spain)
- Serveis Tècnics de Recerca (STR), Universitat de Girona, Parc Científic i Tecnològic, E‐17003 Girona, Spain
| | - Ronald Hage
- Catexel Ltd., BioPartner Center Leiden, Galileiweg 8, 2333 BD Leiden (The Netherlands)
| | - Miquel Costas
- Departament de Química and Institute of Computational Chemistry and Catalysis (IQCC), University of Girona, Campus de Montilivi, Girona 17071 (Spain)
| | - Wesley R. Browne
- Stratingh Institute for Chemistry, Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands)
| | - Sam P. de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN (UK)
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27
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28
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Senn HM. Insights into enzymatic halogenation from computational studies. Front Chem 2014; 2:98. [PMID: 25426489 PMCID: PMC4227530 DOI: 10.3389/fchem.2014.00098] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 10/20/2014] [Indexed: 12/15/2022] Open
Abstract
The halogenases are a group of enzymes that have only come to the fore over the last 10 years thanks to the discovery and characterization of several novel representatives. They have revealed the fascinating variety of distinct chemical mechanisms that nature utilizes to activate halogens and introduce them into organic substrates. Computational studies using a range of approaches have already elucidated many details of the mechanisms of these enzymes, often in synergistic combination with experiment. This Review summarizes the main insights gained from these studies. It also seeks to identify open questions that are amenable to computational investigations. The studies discussed herein serve to illustrate some of the limitations of the current computational approaches and the challenges encountered in computational mechanistic enzymology.
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Affiliation(s)
- Hans M. Senn
- WestCHEM School of Chemistry, University of GlasgowGlasgow, UK
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29
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Vardhaman AK, Barman P, Kumar S, Sastri CV, Kumar D, de Visser SP. Mechanistic insight into halide oxidation by non-heme iron complexes. Haloperoxidase versus halogenase activity. Chem Commun (Camb) 2014; 49:10926-8. [PMID: 24136302 DOI: 10.1039/c3cc46792a] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work presents the first detailed study on mechanistic aspects of halide oxidation by non-heme iron complexes. We show that while iron(III)-hydroperoxo complexes oxidise halides via oxygen atom transfer, the corresponding iron(IV)-oxo complex reacts via electron transfer.
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Affiliation(s)
- Anil Kumar Vardhaman
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam 781039, India.
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30
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Huang Z, Li F, Chen B, Lu T, Yuan Y, Yuan G. A sustainable process for catalytic oxidative bromination with molecular oxygen. CHEMSUSCHEM 2013; 6:1337-1340. [PMID: 23776057 DOI: 10.1002/cssc.201300289] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 05/04/2013] [Indexed: 06/02/2023]
Affiliation(s)
- Zhijun Huang
- Beijing National Laboratory of Molecular Science, Laboratory of New Materials, Institute of Chemistry, Chinese Academy of Sciences, Beijing, PR China
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31
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Maphosa F, Lieten SH, Dinkla I, Stams AJ, Smidt H, Fennell DE. Ecogenomics of microbial communities in bioremediation of chlorinated contaminated sites. Front Microbiol 2012; 3:351. [PMID: 23060869 PMCID: PMC3462421 DOI: 10.3389/fmicb.2012.00351] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 09/12/2012] [Indexed: 11/29/2022] Open
Abstract
Organohalide compounds such as chloroethenes, chloroethanes, and polychlorinated benzenes are among the most significant pollutants in the world. These compounds are often found in contamination plumes with other pollutants such as solvents, pesticides, and petroleum derivatives. Microbial bioremediation of contaminated sites, has become commonplace whereby key processes involved in bioremediation include anaerobic degradation and transformation of these organohalides by organohalide respiring bacteria and also via hydrolytic, oxygenic, and reductive mechanisms by aerobic bacteria. Microbial ecogenomics has enabled us to not only study the microbiology involved in these complex processes but also develop tools to better monitor and assess these sites during bioremediation. Microbial ecogenomics have capitalized on recent advances in high-throughput and -output genomics technologies in combination with microbial physiology studies to address these complex bioremediation problems at a system level. Advances in environmental metagenomics, transcriptomics, and proteomics have provided insights into key genes and their regulation in the environment. They have also given us clues into microbial community structures, dynamics, and functions at contaminated sites. These techniques have not only aided us in understanding the lifestyles of common organohalide respirers, for example Dehalococcoides, Dehalobacter, and Desulfitobacterium, but also provided insights into novel and yet uncultured microorganisms found in organohalide respiring consortia. In this paper, we look at how ecogenomic studies have aided us to understand the microbial structures and functions in response to environmental stimuli such as the presence of chlorinated pollutants.
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Affiliation(s)
- Farai Maphosa
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
| | | | | | - Alfons J. Stams
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
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32
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Koryakina I, Neville J, Nonaka K, Van Lanen SG, Williams GJ. A High-Throughput Screen for Directed Evolution of the Natural Product Sulfotransferase LipB. ACTA ACUST UNITED AC 2011; 16:845-51. [DOI: 10.1177/1087057111413273] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In this article, the authors describe a colorimetric, high-throughput assay suitable for optimizing the activity of the recently discovered sulfotransferase LipB, by directed evolution. Crucially, LipB uses para-nitrophenol sulfate as donor in the sulfation of the nucleoside antibiotic liposidomycin B-I and other acceptor surrogates. Thus, using a robotic liquid-handling device, crude cell extracts were prepared from an Escherichia coli strain that overproduced LipB in wells of a microplate, and production of para-nitrophenol at 405 nm was monitored spectrophotometrically. Enzyme activity could be detected only in the presence of both LipB substrates and overexpressed LipB. The screen displays a suitable standard deviation for directed evolution and importantly is not limited to the natural desulfo-liposidomycin acceptor. The authors plan to use the screen to identify LipB variants with altered acceptor specificity and promiscuity for use in sulfation of natural products and other small-molecule therapeutics.
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Affiliation(s)
- Irina Koryakina
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
| | - Jessica Neville
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
| | - Koichi Nonaka
- Biopharmaceutical Research Group I, Biopharmaceutical Technology Research Laboratories, Pharmaceutical Technology Division, Fukushima, Japan
| | - Steven G. Van Lanen
- College of Pharmacy, Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky
| | - Gavin J. Williams
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
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33
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Macheroux P, Kappes B, Ealick SE. Flavogenomics--a genomic and structural view of flavin-dependent proteins. FEBS J 2011; 278:2625-34. [PMID: 21635694 DOI: 10.1111/j.1742-4658.2011.08202.x] [Citation(s) in RCA: 215] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Riboflavin (vitamin B(2)) serves as the precursor for FMN and FAD in almost all organisms that utilize the redox-active isoalloxazine ring system as a coenzyme in enzymatic reactions. The role of flavin, however, is not limited to redox processes, as ∼ 10% of flavin-dependent enzymes catalyze nonredox reactions. Moreover, the flavin cofactor is also widely used as a signaling and sensing molecule in biological processes such as phototropism and nitrogen fixation. Here, we present a study of 374 flavin-dependent proteins analyzed with regard to their function, structure and distribution among 22 archaeal, eubacterial, protozoan and eukaryotic genomes. More than 90% of flavin-dependent enzymes are oxidoreductases, and the remaining enzymes are classified as transferases (4.3%), lyases (2.9%), isomerases (1.4%) and ligases (0.4%). The majority of enzymes utilize FAD (75%) rather than FMN (25%), and bind the cofactor noncovalently (90%). High-resolution structures are available for about half of the flavoproteins. FAD-containing proteins predominantly bind the cofactor in a Rossmann fold (∼ 50%), whereas FMN-containing proteins preferably adopt a (βα)(8)-(TIM)-barrel-like or flavodoxin-like fold. The number of genes encoding flavin-dependent proteins varies greatly in the genomes analyzed, and covers a range from ∼ 0.1% to 3.5% of the predicted genes. It appears that some species depend heavily on flavin-dependent oxidoreductases for degradation or biosynthesis, whereas others have minimized their flavoprotein arsenal. An understanding of 'flavin-intensive' lifestyles, such as in the human pathogen Mycobacterium tuberculosis, may result in valuable new intervention strategies that target either riboflavin biosynthesis or uptake.
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Affiliation(s)
- Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Graz, Austria.
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Lang A, Polnick S, Nicke T, William P, Patallo EP, Naismith JH, van Pée KH. Changing the regioselectivity of the tryptophan 7-halogenase PrnA by site-directed mutagenesis. Angew Chem Int Ed Engl 2011; 50:2951-3. [PMID: 21404376 DOI: 10.1002/anie.201007896] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Indexed: 11/07/2022]
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Exploring the links between natural products and bacterial assemblages in the sponge Aplysina aerophoba. Appl Environ Microbiol 2010; 77:862-70. [PMID: 21115701 DOI: 10.1128/aem.00100-10] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The sponge Aplysina aerophoba produces a large diversity of brominated alkaloids (BAs) and hosts a complex microbial assemblage. Although BAs are located within sponge cells, the enzymes that bind halogen elements to organic compounds have been exclusively described in algae, fungi, and bacteria. Bacterial communities within A. aerophoba could therefore be involved in the biosynthesis of these compounds. This study investigates whether changes in both the concentration of BAs and the bacterial assemblages are correlated in A. aerophoba. To do so, we quantified major natural products using high-performance liquid chromatography and analyzed bacterial assemblages using denaturing gradient gel electrophoresis on the 16S rRNA gene. We identified multiple associations between bacteria and natural products, including a strong relationship between a Chloroflexi phylotype and aplysinamisin-1 and between an unidentified bacterium and aerophobin-2 and isofistularin-3. Our results suggest that these bacteria could either be involved in the production of BAs or be directly affected by them. To our knowledge, this is one of the first reports that find a significant correlation between natural products and bacterial populations in any benthic organism. Further investigating these associations will shed light on the organization and functioning of host-endobiont systems such as Aplysina aerophoba.
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Morrison MD, Hanthorn JJ, Pratt DA. Synthesis of pyrrolnitrin and related halogenated phenylpyrroles. Org Lett 2010; 11:1051-4. [PMID: 19196161 DOI: 10.1021/ol8026957] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A general approach to halogenated arylpyrroles, including the antifungal natural product pyrrolnitrin, is described using newly synthesized halogenated pyrroles and 2,6-disubstituted nitrobenzenes or 2,6-disubstituted anilines.
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Affiliation(s)
- Matthew D Morrison
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada K7L 3N6
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37
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Affiliation(s)
- Ying Jin
- Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, University Town of Shenzhen, Xili, Nanshan District, Shenzhen, China, 518055, and Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Yuqing Liu
- Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, University Town of Shenzhen, Xili, Nanshan District, Shenzhen, China, 518055, and Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Zhuo Wang
- Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, University Town of Shenzhen, Xili, Nanshan District, Shenzhen, China, 518055, and Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Shuqin Kwong
- Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, University Town of Shenzhen, Xili, Nanshan District, Shenzhen, China, 518055, and Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Zhengshuang Xu
- Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, University Town of Shenzhen, Xili, Nanshan District, Shenzhen, China, 518055, and Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Tao Ye
- Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, University Town of Shenzhen, Xili, Nanshan District, Shenzhen, China, 518055, and Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
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Podgoršek A, Zupan M, Iskra J. Oxidative Halogenierungen mit umweltschonenden Oxidationsmitteln: Sauerstoff und Wasserstoffperoxid. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200901223] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Podgoršek A, Zupan M, Iskra J. Oxidative Halogenation with “Green” Oxidants: Oxygen and Hydrogen Peroxide. Angew Chem Int Ed Engl 2009; 48:8424-50. [DOI: 10.1002/anie.200901223] [Citation(s) in RCA: 310] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Wagner C, El Omari M, König GM. Biohalogenation: nature's way to synthesize halogenated metabolites. JOURNAL OF NATURAL PRODUCTS 2009; 72:540-553. [PMID: 19245259 DOI: 10.1021/np800651m] [Citation(s) in RCA: 156] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Halogenated natural products are widely distributed in nature, some of them showing potent biological activities. Incorporation of halogen atoms in drug leads is a common strategy to modify molecules in order to vary their bioactivities and specificities. Chemical halogenation, however, often requires harsh reaction conditions and results in unwanted byproduct formation. It is thus of great interest to investigate the biosynthesis of halogenated natural products and the biotechnological potential of halogenating enzymes. This review aims to give a comprehensive overview on the current knowledge concerning biological halogenations.
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Affiliation(s)
- Claudia Wagner
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, D-53115 Bonn, Germany
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Functional characterization of the biosynthesis of radicicol, an Hsp90 inhibitor resorcylic acid lactone from Chaetomium chiversii. ACTA ACUST UNITED AC 2009; 15:1328-38. [PMID: 19101477 DOI: 10.1016/j.chembiol.2008.10.006] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2008] [Revised: 09/05/2008] [Accepted: 10/03/2008] [Indexed: 01/17/2023]
Abstract
Fungal polyketides with the resorcylic acid lactone (RAL) scaffold are of interest for growth stimulation, the treatment of cancer, and neurodegenerative diseases. The RAL radicicol is a nanomolar inhibitor of the chaperone Hsp90, whose repression leads to a combinatorial blockade of cancer-causing pathways. Clustered genes for radicicol biosynthesis were identified and functionally characterized from the endophytic fungus Chaetomium chiversii, and compared to recently described RAL biosynthetic gene clusters. Radicicol production is abolished upon targeted inactivation of a putative cluster-specific regulator, or either of the two polyketide synthases that are predicted to collectively synthesize the radicicol polyketide core. Genomic evidence supports the existence of flavin-dependent halogenases in fungi: inactivation of such a putative halogenase from the C. chiversii radicicol locus yields dechloro-radicicol (monocillin I). Inactivation of a cytochrome P450 epoxidase furnishes pochonin D, a deepoxy-dihydro radicicol analog.
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Abstract
Simple halogen substituents frequently afford key structural features that account for the potency and selectivity of natural products, including antibiotics and hormones. For example, when a single chlorine atom on the antibiotic vancomycin is replaced by hydrogen, the resulting antibacterial activity decreases by up to 70% (HarrisC. M.; KannanR.; KopeckaH.; HarrisT. M.J. Am. Chem. Soc.1985, 107, 6652−6658). This Account analyzes how structure underlies mechanism in halogenases, the molecular machines designed by nature to incorporate halogens into diverse substrates.
Traditional synthetic methods of integrating halogens into complex molecules are often complicated by a lack of specificity and regioselectivity. Nature, however, has developed a variety of elegant mechanisms for halogenating specific substrates with both regio- and stereoselectivity. An improved understanding of the biological routes toward halogenation could lead to the development of novel synthetic methods for the creation of new compounds with enhanced functions. Already, researchers have co-opted a fluorinase from the microorganism Streptomyces cattleya to produce 18F-labeled molecules for use in positron emission tomography (PET) (DengH.; CobbS. L.; GeeA. D.; LockhartA.; MartarelloL.; McGlincheyR. P.; O’HaganD.; OnegaM.Chem. Commun.2006, 652−654). Therefore, the discovery and characterization of naturally occurring enzymatic halogenation mechanisms has become an active area of research. The catalogue of known halogenating enzymes has expanded from the familiar haloperoxidases to include oxygen-dependent enzymes and fluorinases. Recently, the discovery of a nucleophilic halogenase that catalyzes chlorinations has expanded the repertoire of biological halogenation chemistry (DongC.; HuangF.; DengH.; SchaffrathC.; SpencerJ. B.; O’HaganD.; NaismithJ. H.Nature2004, 427, 561−56514765200). Structural characterization has provided a basis toward a mechanistic understanding of the specificity and chemistry of these enzymes. In particular, the latest crystallographic snapshots of active site architecture and halide binding sites have provided key insights into enzyme catalysis. Herein is a summary of the five classes of halogenases, focusing on the three most recently discovered: flavin-dependent halogenases, non-heme iron-dependent halogenases, and nucleophilic halogenases. Further, the potential roles of halide-binding sites in determining halide selectivity are discussed, as well as whether or not binding-site composition is always a seminal factor for selectivity. Expanding our understanding of the basic chemical principles that dictate the activity of the halogenases will advance both biology and chemistry. A thorough mechanistic analysis will elucidate the biological principles that dictate specificity, and the application of those principles to new synthetic techniques will expand the utility of halogenations in small-molecule development.
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Costa R, van Aarle IM, Mendes R, van Elsas JD. Genomics of pyrrolnitrin biosynthetic loci: evidence for conservation and whole-operon mobility within gram-negative bacteria. Environ Microbiol 2008; 11:159-75. [PMID: 18793314 DOI: 10.1111/j.1462-2920.2008.01750.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pyrrolnitrin (PRN) is a tryptophan-derived secondary metabolite produced by a narrow range of gram-negative bacteria. The PRN biosynthesis by rhizobacteria presumably has a key role in their life strategies and in the biocontrol of plant diseases. The biosynthetic operon that encodes the pathway that converts tryptophan to PRN is composed of four genes, prnA through D, whose diversity, genomic context and spread over bacterial genomes are poorly understood. Therefore, we launched an endeavour aimed at retrieving, by in vitro and in silico means, diverse bacteria carrying the prnABCD biosynthetic loci in their genomes. Analysis of polymorphisms of the prnD gene sequences revealed a high level of conservation between Burkholderia, Pseudomonas and Serratia spp. derived sequences. Whole-operon- and prnD-based phylogeny resulted in tree topologies that are incongruent with the taxonomic status of the evaluated strains as predicted by 16S rRNA gene phylogeny. The genomic composition of c. 20 kb DNA fragments containing the PRN operon varied in different strains. Highly conserved and distinct transposase-encoding genes surrounding the PRN biosynthetic operons of Burkholderia pseudomallei strains were found. A prnABCD-deprived genomic region in B. pseudomallei strain K96243 contained the same gene composition as, and shared high homology with, the flanking regions of the PRN operon in B. pseudomallei strains 668, 1106a and 1710b. Our results strongly suggest that the PRN biosynthetic operon is mobile. The extent, frequency and promiscuity of this mobility remain to be understood.
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Affiliation(s)
- Rodrigo Costa
- Centre for Ecological and Evolutionary Studies, Department of Microbial Ecology, University of Groningen, Kerklaan 30 9750 AA Haren, The Netherlands
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Wagner C, Molitor IM, König GM. Critical view on the monochlorodimedone assay utilized to detect haloperoxidase activity. PHYTOCHEMISTRY 2008; 69:323-32. [PMID: 17889043 DOI: 10.1016/j.phytochem.2007.07.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Revised: 07/16/2007] [Accepted: 07/29/2007] [Indexed: 05/17/2023]
Abstract
The current study aimed to identify the halogenating enzymes involved in the biosynthesis of the ambigols A, B, C and tjipanazole D, isolated from the cyanobacterium Fischerella ambigua. Haloperoxidase (HPO) activity within F. ambigua was therefore assayed spectrophotometrically by using monochlorodimedone (MCD) during protein purification. This strategy revealed the isolation of a protein positive in the MCD-assay, but an involvement in halogenating processes could not be verified. N-terminal sequencing rather demonstrated homology to cytochrome c(6) from other cyanobacteria and green algae. From our findings it thus has to be concluded that the spectrophotometrical MCD-assay routinely used to detect HPO activity may yield false positive results, mainly since the assay focuses on the decline of the educt and not on the formation of the product. Our data indicate that the reaction of MCD with proteins of the cytochrome c- family leads to unspecific products.
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Affiliation(s)
- Claudia Wagner
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, D-53115 Bonn, Germany
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Abstract
Flavoenzymes are colourful oxidoreductases that catalyze a large variety of different types of reactions. Flavoenzymes have been extensively studied for their structural and mechanistic properties and are gaining momentum in industrial biocatalytic applications. Some of these enzymes catalyze the oxidative modification of protein substrates. New insights in oxidative flavoenzymes and in particular in novel family members point towards their potential application in the pharmaceutical, fine-chemical and food industries.
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Affiliation(s)
- Vivi Joosten
- Laboratory of Biochemistry, Wageningen University Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
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