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Baral B, Matroodi S, Siitonen V, Thapa K, Akhgari A, Yamada K, Nuutila A, Metsä-Ketelä M. Co-factor independent oxidases ncnN and actVA-3 are involved in the dimerization of benzoisochromanequinone antibiotics in naphthocyclinone and actinorhodin biosynthesis. FEMS Microbiol Lett 2023; 370:fnad123. [PMID: 37989784 PMCID: PMC10697411 DOI: 10.1093/femsle/fnad123] [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: 08/24/2023] [Revised: 10/19/2023] [Accepted: 11/20/2023] [Indexed: 11/23/2023] Open
Abstract
Streptomyces produce complex bioactive secondary metabolites with remarkable chemical diversity. Benzoisochromanequinone polyketides actinorhodin and naphthocyclinone are formed through dimerization of half-molecules via single or double carbon-carbon bonds, respectively. Here we sequenced the genome of S. arenae DSM40737 to identify the naphthocyclinone gene cluster and established heterologous production in S. albus J1074 by utilizing direct cluster capture techniques. Comparative sequence analysis uncovered ncnN and ncnM gene products as putative enzymes responsible for dimerization. Inactivation of ncnN that is homologous to atypical co-factor independent oxidases resulted in the accumulation of fogacin, which is likely a reduced shunt product of the true substrate for naphthocyclinone dimerization. In agreement, inactivation of the homologous actVA-3 in S. coelicolor M145 also led to significantly reduced production of actinorhodin. Previous work has identified the NAD(P)H-dependent reductase ActVA-4 as the key enzyme in actinorhodin dimerization, but surprisingly inactivation of the homologous ncnM did not abolish naphthocyclinone formation and the mutation may have been complemented by an endogenous gene product. Our data suggests that dimerization of benzoisochromanequinone polyketides require two-component reductase-oxidase systems.
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Affiliation(s)
- Bikash Baral
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Soheila Matroodi
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
- Laboratory of Biotechnology, Department of Marine Biology, Faculty of Marine Science and Oceanography, University of Marine Science and Technology, 64199-34619 Khorramshahr, Iran
| | - Vilja Siitonen
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Keshav Thapa
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Amir Akhgari
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Keith Yamada
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Aleksi Nuutila
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Mikko Metsä-Ketelä
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
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Single-Component and Two-Component para-Nitrophenol Monooxygenases: Structural Basis for Their Catalytic Difference. Appl Environ Microbiol 2021; 87:e0117121. [PMID: 34469195 DOI: 10.1128/aem.01171-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
para-Nitrophenol (PNP) is a hydrolytic product of organophosphate insecticides, such as parathion and methylparathion, in soil. Aerobic microbial degradation of PNP has been classically shown to proceed via the "hydroquinone (HQ) pathway" in Gram-negative degraders, whereas it proceeds via the "benzenetriol (BT) pathway" in Gram-positive ones. The "HQ pathway" is initiated by a single-component PNP 4-monooxygenase and the "BT pathway" by a two-component PNP 2-monooxygenase. Their regioselectivity intrigued us enough to investigate their catalytic difference through structural study. PnpA1 is the oxygenase component of the two-component PNP 2-monooxygenase from Gram-positive Rhodococcus imtechensis strain RKJ300. It also catalyzes the hydroxylation of 4-nitrocatechol (4NC) and 2-chloro-4-nitrophenol (2C4NP). However, the mechanisms are unknown. Here, PnpA1 was structurally determined to be a member of the group D flavin-dependent monooxygenases with an acyl coenzyme A (acyl-CoA) dehydrogenase fold. The crystal structure and site-directed mutagenesis underlined the direct involvement of Arg100 and His293 in catalysis. The bulky side chain of Val292 was proposed to push the substrate toward flavin adenine dinucleotide (FAD), hence positioning the substrate properly. An N450A variant was found with improved activity for 4NC and 2C4NP-probably because of the reduced steric hindrance. PnpA1 shows an obvious difference in substrate selectivity with its close homologues TcpA and TftD, which may be caused by the unique Thr296 and a different conformation in the loop from positions 449 to 454 (loop 449-454). Above all, our study allows structural comparison between the two types of PNP monooxygenases. An explanation that accounts for their regioselectivity was proposed: the different PNP binding manners determine their choice of ortho- or para-hydroxylation on PNP. IMPORTANCE Single-component PNP monoxygenases hydroxylate PNP at the 4 position, while two-component ones do so at the 2 position. However, their catalytic and structural differences remain elusive. The structure of single-component PNP 4-monooxygenase has previously been determined. In this study, to illustrate their catalytic difference, we resolved the crystal structure of PnpA1, a typical two-component PNP 2-monooxygenase. The roles of several key amino acid residues in substrate binding and catalysis were revealed, and a variant with improved activities toward 4NC and 2C4NP was obtained. Moreover, through comparison of the two types of PNP monooxygenases, a hypothesis was proposed to account for their catalytic difference, which gives us a better understanding of these two similar reactions at the molecular level. In addition, these results will also be of further aid in rational design of enzymes in bioremediation and biosynthesis.
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Frensch B, Lechtenberg T, Kather M, Yunt Z, Betschart M, Kammerer B, Lüdeke S, Müller M, Piel J, Teufel R. Enzymatic spiroketal formation via oxidative rearrangement of pentangular polyketides. Nat Commun 2021; 12:1431. [PMID: 33664266 PMCID: PMC7933358 DOI: 10.1038/s41467-021-21432-9] [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] [Received: 10/28/2020] [Accepted: 01/11/2021] [Indexed: 12/15/2022] Open
Abstract
The structural complexity and bioactivity of natural products often depend on enzymatic redox tailoring steps. This is exemplified by the generation of the bisbenzannulated [5,6]-spiroketal pharmacophore in the bacterial rubromycin family of aromatic polyketides, which exhibit a wide array of bioactivities such as the inhibition of HIV reverse transcriptase or DNA helicase. Here we elucidate the complex flavoenzyme-driven formation of the rubromycin pharmacophore that is markedly distinct from conventional (bio)synthetic strategies for spiroketal formation. Accordingly, a polycyclic aromatic precursor undergoes extensive enzymatic oxidative rearrangement catalyzed by two flavoprotein monooxygenases and a flavoprotein oxidase that ultimately results in a drastic distortion of the carbon skeleton. The one-pot in vitro reconstitution of the key enzymatic steps as well as the comprehensive characterization of reactive intermediates allow to unravel the intricate underlying reactions, during which four carbon-carbon bonds are broken and two CO2 become eliminated. This work provides detailed insight into perplexing redox tailoring enzymology that sets the stage for the (chemo)enzymatic production and bioengineering of bioactive spiroketal-containing polyketides. Rubromycin family of natural products belongs to aromatic polyketides with diverse bioactivities, but details of their biosynthesis are limited. Here, the authors report the complete in vitro reconstitution of enzymatic formation of the spiroketal moiety of rubromycin polyketides, driven by flavin-dependent enzymes, and characterize reaction intermediates.
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Affiliation(s)
- Britta Frensch
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Thorsten Lechtenberg
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Michel Kather
- BIOSS Center for Biological Signaling Studies, University of Freiburg, 79104, Freiburg, Germany
| | - Zeynep Yunt
- Department of Molecular Biology and Genetics, Koç University, Istanbul, 34450, Turkey
| | - Martin Betschart
- Institute of Pharmaceutical Sciences, University of Freiburg, 79104, Freiburg, Germany
| | - Bernd Kammerer
- BIOSS Center for Biological Signaling Studies, University of Freiburg, 79104, Freiburg, Germany.,Hermann Staudinger Graduate School, University of Freiburg, 79104, Freiburg, Germany
| | - Steffen Lüdeke
- Institute of Pharmaceutical Sciences, University of Freiburg, 79104, Freiburg, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, University of Freiburg, 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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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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Hashimoto M, Taguchi T, Ishikawa K, Mori R, Hotta A, Watari S, Katakawa K, Kumamoto T, Okamoto S, Ichinose K. Unveiling Two Consecutive Hydroxylations: Mechanisms of Aromatic Hydroxylations Catalyzed by Flavin‐Dependent Monooxygenases for the Biosynthesis of Actinorhodin and Related Antibiotics. Chembiochem 2019; 21:623-627. [DOI: 10.1002/cbic.201900490] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Makoto Hashimoto
- Research Institute of Pharmaceutical SciencesMusashino University 1-1-20, Shinmachi Nishitokyo-shi Tokyo 202-8585 Japan
| | - Takaaki Taguchi
- National Institute of Health Sciences 3-25-26, Tonomachi Kawasaki-ku Kawasaki-shi Kanagawa 210-9501 Japan
| | - Kazuki Ishikawa
- Research Institute of Pharmaceutical SciencesMusashino University 1-1-20, Shinmachi Nishitokyo-shi Tokyo 202-8585 Japan
| | - Ryuichiro Mori
- Research Institute of Pharmaceutical SciencesMusashino University 1-1-20, Shinmachi Nishitokyo-shi Tokyo 202-8585 Japan
| | - Akari Hotta
- Research Institute of Pharmaceutical SciencesMusashino University 1-1-20, Shinmachi Nishitokyo-shi Tokyo 202-8585 Japan
| | - Susumu Watari
- Research Institute of Pharmaceutical SciencesMusashino University 1-1-20, Shinmachi Nishitokyo-shi Tokyo 202-8585 Japan
| | - Kazuaki Katakawa
- Research Institute of Pharmaceutical SciencesMusashino University 1-1-20, Shinmachi Nishitokyo-shi Tokyo 202-8585 Japan
| | - Takuya Kumamoto
- Graduate School of Biomedical and Health SciencesHiroshima University 1-2-3 Kasumi Minami-ku Hiroshima City Hiroshima 734-8553 Japan
| | - Susumu Okamoto
- National Agriculture and Food Research Organization 2-1-12 Kannondai Tsukuba Ibaraki 305-8642 Japan
| | - Koji Ichinose
- Research Institute of Pharmaceutical SciencesMusashino University 1-1-20, Shinmachi Nishitokyo-shi Tokyo 202-8585 Japan
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Pimviriyakul P, Chaiyen P. A complete bioconversion cascade for dehalogenation and denitration by bacterial flavin-dependent enzymes. J Biol Chem 2018; 293:18525-18539. [PMID: 30282807 DOI: 10.1074/jbc.ra118.005538] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 09/29/2018] [Indexed: 12/17/2022] Open
Abstract
Halogenated phenol and nitrophenols are toxic compounds that are widely accumulated in the environment. Enzymes in the had operon from the bacterium Ralstonia pickettii DTP0602 have the potential for application as biocatalysts in the degradation of many of these toxic chemicals. HadA monooxygenase previously was identified as a two-component reduced FAD (FADH-)-utilizing monooxygenase with dual activities of dehalogenation and denitration. However, the partner enzymes of HadA, that is, the flavin reductase and quinone reductase that provide the FADH- for HadA and reduce quinone to hydroquinone, remain to be identified. In this report, we overexpressed and purified the flavin reductases, HadB and HadX, to investigate their functional and catalytic properties. Our results indicated that HadB is an FMN-dependent quinone reductase that converts the quinone products from HadA to hydroquinone compounds that are more stable and can be assimilated by downstream enzymes in the pathway. Transient kinetics indicated that HadB prefers NADH and menadione as the electron donor and acceptor, respectively. We found that HadX is an FAD-bound flavin reductase, which can generate FADH- for HadA to catalyze dehalogenation or denitration reactions. Thermodynamic and transient kinetic experiments revealed that HadX prefers to bind FAD over FADH- and that HadX can transfer FADH- from HadX to HadA via free diffusion. Moreover, HadX rapidly catalyzed NADH-mediated reduction of flavin and provided the FADH- for a monooxygenase of a different system. Combination of all three flavin-dependent enzymes, i.e. HadA/HadB/HadX, reconstituted an effective dehalogenation and denitration cascade, which may be useful for future bioremediation applications.
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Affiliation(s)
- Panu Pimviriyakul
- From the School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210 and.,the Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 14000, Thailand
| | - Pimchai Chaiyen
- From the School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210 and
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Two-Component Flavin-Dependent Riboflavin Monooxygenase Degrades Riboflavin in Devosia riboflavina. J Bacteriol 2018; 200:JB.00022-18. [PMID: 29610214 DOI: 10.1128/jb.00022-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/28/2018] [Indexed: 12/22/2022] Open
Abstract
The actinobacterium Microbacterium maritypicum splits riboflavin (vitamin B2) into lumichrome and d-ribose. However, such degradation by other bacteria and the involvement of a two-component flavin-dependent monooxygenase (FMO) in the reaction remain unknown. Here we investigated the mechanism of riboflavin degradation by the riboflavin-assimilating alphaproteobacterium Devosia riboflavina (formerly Pseudomonas riboflavina). We found that adding riboflavin to bacterial cultures induced riboflavin-degrading activity and a protein of the FMO family that had 67% amino acid identity with the predicted riboflavin hydrolase (RcaE) of M. maritypicum MF109. The D. riboflavina genome clustered genes encoding the predicted FMO, flavin reductase (FR), ribokinase, and flavokinase, and riboflavin induced their expression. This finding suggests that these genes constitute a mechanism for utilizing riboflavin as a carbon source. Recombinant FMO (rFMO) protein of D. riboflavina oxidized riboflavin in the presence of reduced flavin mononucleotide (FMN) provided by recombinant FR (rFR), oxidized FMN and NADH, and produced stoichiometric amounts of lumichrome and d-ribose. Further investigation of the enzymatic properties of D. riboflavina rFMO indicated that rFMO-rFR coupling accompanied O2 consumption and the generation of enzyme-bound hydroperoxy-FMN, which are characteristic of two-component FMOs. These results suggest that D. riboflavina FMO is involved in hydroperoxy-FMN-dependent mechanisms to oxygenize riboflavin and a riboflavin monooxygenase is necessary for the initial step of riboflavin degradation.IMPORTANCE Whether bacteria utilize either a monooxygenase or a hydrolase for riboflavin degradation has remained obscure. The present study found that a novel riboflavin monooxygenase, not riboflavin hydrolase, facilitated this process in D. riboflavina The riboflavin monooxygenase gene was clustered with flavin reductase, flavokinase, and ribokinase genes, and riboflavin induced their expression and riboflavin-degrading activity. The gene cluster is uniquely distributed in Devosia species and actinobacteria, which have exploited an environmental niche by developing adaptive mechanisms for riboflavin utilization.
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Elucidation of the trigonelline degradation pathway reveals previously undescribed enzymes and metabolites. Proc Natl Acad Sci U S A 2018; 115:E4358-E4367. [PMID: 29686076 DOI: 10.1073/pnas.1722368115] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Trigonelline (TG; N-methylnicotinate) is a ubiquitous osmolyte. Although it is known that it can be degraded, the enzymes and metabolites have not been described so far. In this work, we challenged the laboratory model soil-borne, gram-negative bacterium Acinetobacter baylyi ADP1 (ADP1) for its ability to grow on TG and we identified a cluster of catabolic, transporter, and regulatory genes. We dissected the pathway to the level of enzymes and metabolites, and proceeded to in vitro reconstruction of the complete pathway by six purified proteins. The four enzymatic steps that lead from TG to methylamine and succinate are described, and the structures of previously undescribed metabolites are provided. Unlike many aromatic compounds that undergo hydroxylation prior to ring cleavage, the first step of TG catabolism proceeds through direct cleavage of the C5-C6 bound, catalyzed by a flavin-dependent, two-component oxygenase, which yields (Z)-2-((N-methylformamido)methylene)-5-hydroxy-butyrolactone (MFMB). MFMB is then oxidized into (E)-2-((N-methylformamido) methylene) succinate (MFMS), which is split up by a hydrolase into carbon dioxide, methylamine, formic acid, and succinate semialdehyde (SSA). SSA eventually fuels up the TCA by means of an SSA dehydrogenase, assisted by a Conserved Hypothetical Protein. The cluster is conserved across marine, soil, and plant-associated bacteria. This emphasizes the role of TG as a ubiquitous nutrient for which an efficient microbial catabolic toolbox is available.
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Lv M, Zhao J, Deng Z, Yu Y. Characterization of the Biosynthetic Gene Cluster for Benzoxazole Antibiotics A33853 Reveals Unusual Assembly Logic. ACTA ACUST UNITED AC 2016; 22:1313-24. [PMID: 26496684 DOI: 10.1016/j.chembiol.2015.09.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 08/26/2015] [Accepted: 09/10/2015] [Indexed: 10/22/2022]
Abstract
A33853, which shows excellent bioactivity against Leishmania, is a benzoxazole-family compound formed from two moieties of 3-hydroxyanthranilic acid and one 3-hydroxypicolinic acid. In this study, we have identified the gene cluster responsible for the biosynthesis of A33853 in Streptomyces sp. NRRL12068 through genome mining and heterologous expression. Bioinformatics analysis and functional characterization of the orfs contained in the gene cluster revealed that the biosynthesis of A33853 is directed by a group of unusual enzymes. In particular, BomK, annotated as a ketosynthase, was found to catalyze the amide bond formation between 3-hydroxypicolinic and 3-hydroxyanthranilic acid during the assembly of A33853. BomJ, a putative ATP-dependent coenzyme A ligase, and BomN, a putative amidohydrolase, were further proposed to be involved in the benzoxazole formation in A33853 according to gene deletion experiments. Finally, we have successfully utilized mutasynthesis to generate two analogs of A33853, which were reported previously to possess excellent anti-leishmanial activity.
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Affiliation(s)
- Meinan Lv
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, P. R. China
| | - Junfeng Zhao
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, P. R. China
| | - Zixin Deng
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, P. R. China
| | - Yi Yu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, P. R. China.
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Zhang C, Sheng C, Wang W, Hu H, Peng H, Zhang X. Identification of the Lomofungin Biosynthesis Gene Cluster and Associated Flavin-Dependent Monooxygenase Gene in Streptomyces lomondensis S015. PLoS One 2015; 10:e0136228. [PMID: 26305803 PMCID: PMC4549113 DOI: 10.1371/journal.pone.0136228] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 07/30/2015] [Indexed: 01/09/2023] Open
Abstract
Streptomyces lomondensis S015 synthesizes the broad-spectrum phenazine antibiotic lomofungin. Whole genome sequencing of this strain revealed a genomic locus consisting of 23 open reading frames that includes the core phenazine biosynthesis gene cluster lphzGFEDCB. lomo10, encoding a putative flavin-dependent monooxygenase, was also identified in this locus. Inactivation of lomo10 by in-frame partial deletion resulted in the biosynthesis of a new phenazine metabolite, 1-carbomethoxy-6-formyl-4,9-dihydroxy-phenazine, along with the absence of lomofungin. This result suggests that lomo10 is responsible for the hydroxylation of lomofungin at its C-7 position. This is the first description of a phenazine hydroxylation gene in Streptomyces, and the results of this study lay the foundation for further investigation of phenazine metabolite biosynthesis in Streptomyces.
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Affiliation(s)
- Chunxiao Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Chaolan Sheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
- * E-mail:
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Huasong Peng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
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Carbon-flux distribution within Streptomyces coelicolor metabolism: a comparison between the actinorhodin-producing strain M145 and its non-producing derivative M1146. PLoS One 2013; 8:e84151. [PMID: 24376790 PMCID: PMC3871631 DOI: 10.1371/journal.pone.0084151] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 11/19/2013] [Indexed: 01/12/2023] Open
Abstract
Metabolic Flux Analysis is now viewed as essential to elucidate the metabolic pattern of cells and to design appropriate genetic engineering strategies to improve strain performance and production processes. Here, we investigated carbon flux distribution in two Streptomyces coelicolor A3 (2) strains: the wild type M145 and its derivative mutant M1146, in which gene clusters encoding the four main antibiotic biosynthetic pathways were deleted. Metabolic Flux Analysis and (13)C-labeling allowed us to reconstruct a flux map under steady-state conditions for both strains. The mutant strain M1146 showed a higher growth rate, a higher flux through the pentose phosphate pathway and a higher flux through the anaplerotic phosphoenolpyruvate carboxylase. In that strain, glucose uptake and the flux through the Krebs cycle were lower than in M145. The enhanced flux through the pentose phosphate pathway in M1146 is thought to generate NADPH enough to face higher needs for biomass biosynthesis and other processes. In both strains, the production of NADPH was higher than NADPH needs, suggesting a key role for nicotinamide nucleotide transhydrogenase for redox homeostasis. ATP production is also likely to exceed metabolic ATP needs, indicating that ATP consumption for maintenance is substantial.Our results further suggest a possible competition between actinorhodin and triacylglycerol biosynthetic pathways for their common precursor, acetyl-CoA. These findings may be instrumental in developing new strategies exploiting S. coelicolor as a platform for the production of bio-based products of industrial interest.
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Metsä-Ketelä M, Oja T, Taguchi T, Okamoto S, Ichinose K. Biosynthesis of pyranonaphthoquinone polyketides reveals diverse strategies for enzymatic carbon–carbon bond formation. Curr Opin Chem Biol 2013; 17:562-70. [DOI: 10.1016/j.cbpa.2013.06.032] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 05/30/2013] [Accepted: 06/25/2013] [Indexed: 11/26/2022]
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13
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Taguchi T, Yabe M, Odaki H, Shinozaki M, Metsä-Ketelä M, Arai T, Okamoto S, Ichinose K. Biosynthetic Conclusions from the Functional Dissection of Oxygenases for Biosynthesis of Actinorhodin and Related Streptomyces Antibiotics. ACTA ACUST UNITED AC 2013; 20:510-20. [DOI: 10.1016/j.chembiol.2013.03.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 02/25/2013] [Accepted: 03/06/2013] [Indexed: 11/28/2022]
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Hayes RP, Webb BN, Subramanian AK, Nissen M, Popchock A, Xun L, Kang C. Structural and catalytic differences between two FADH(2)-dependent monooxygenases: 2,4,5-TCP 4-monooxygenase (TftD) from Burkholderia cepacia AC1100 and 2,4,6-TCP 4-monooxygenase (TcpA) from Cupriavidus necator JMP134. Int J Mol Sci 2012; 13:9769-9784. [PMID: 22949829 PMCID: PMC3431827 DOI: 10.3390/ijms13089769] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/27/2012] [Accepted: 07/31/2012] [Indexed: 11/16/2022] Open
Abstract
2,4,5-TCP 4-monooxygenase (TftD) and 2,4,6-TCP 4-monooxygenase (TcpA) have been discovered in the biodegradation of 2,4,5-trichlorophenol (2,4,5-TCP) and 2,4,6-trichlorophenol (2,4,6-TCP). TcpA and TftD belong to the reduced flavin adenine dinucleotide (FADH2)-dependent monooxygenases and both use 2,4,6-TCP as a substrate; however, the two enzymes produce different end products. TftD catalyzes a typical monooxygenase reaction, while TcpA catalyzes a typical monooxygenase reaction followed by a hydrolytic dechlorination. We have previously reported the 3D structure of TftD and confirmed the catalytic residue, His289. Here we have determined the crystal structure of TcpA and investigated the apparent differences in specificity and catalysis between these two closely related monooxygenases through structural comparison. Our computational docking results suggest that Ala293 in TcpA (Ile292 in TftD) is possibly responsible for the differences in substrate specificity between the two monooxygenases. We have also identified that Arg101 in TcpA could provide inductive effects/charge stabilization during hydrolytic dechlorination. The collective information provides a fundamental understanding of the catalytic reaction mechanism and the parameters for substrate specificity. The information may provide guidance for designing bioremediation strategies for polychlorophenols, a major group of environmental pollutants.
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Affiliation(s)
- Robert P. Hayes
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; E-Mails: (R.P.H.); (B.N.W.); (A.K.S.); (M.N.)
| | - Brian N. Webb
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; E-Mails: (R.P.H.); (B.N.W.); (A.K.S.); (M.N.)
| | - Arun Kumar Subramanian
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; E-Mails: (R.P.H.); (B.N.W.); (A.K.S.); (M.N.)
| | - Mark Nissen
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; E-Mails: (R.P.H.); (B.N.W.); (A.K.S.); (M.N.)
| | - Andrew Popchock
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA; E-Mail:
| | - Luying Xun
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA; E-Mail:
- Authors to whom correspondence should be addressed; E-Mails: (L.X.); (C.K.); Tel.: +1-509-335-2787 (L.X.); +1-509-335-1523 (C.K.); Fax: +1-509-335-9688 (L.X.); +1-509-335-8867 (C.K.)
| | - ChulHee Kang
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; E-Mails: (R.P.H.); (B.N.W.); (A.K.S.); (M.N.)
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA; E-Mail:
- Authors to whom correspondence should be addressed; E-Mails: (L.X.); (C.K.); Tel.: +1-509-335-2787 (L.X.); +1-509-335-1523 (C.K.); Fax: +1-509-335-9688 (L.X.); +1-509-335-8867 (C.K.)
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15
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Taguchi T, Ebihara T, Furukawa A, Hidaka Y, Ariga R, Okamoto S, Ichinose K. Identification of the actinorhodin monomer and its related compound from a deletion mutant of the actVA-ORF4 gene of Streptomyces coelicolor A3(2). Bioorg Med Chem Lett 2012; 22:5041-5. [DOI: 10.1016/j.bmcl.2012.06.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 06/01/2012] [Accepted: 06/04/2012] [Indexed: 10/28/2022]
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Siitonen V, Blauenburg B, Kallio P, Mäntsälä P, Metsä-Ketelä M. Discovery of a Two-Component Monooxygenase SnoaW/SnoaL2 Involved in Nogalamycin Biosynthesis. ACTA ACUST UNITED AC 2012; 19:638-46. [DOI: 10.1016/j.chembiol.2012.04.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 03/16/2012] [Accepted: 04/04/2012] [Indexed: 11/30/2022]
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18
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Characterization of the two-component monooxygenase system AlnT/AlnH reveals early timing of quinone formation in alnumycin biosynthesis. J Bacteriol 2012; 194:2829-36. [PMID: 22467789 DOI: 10.1128/jb.00228-12] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Alnumycin A is an aromatic polyketide with a strong resemblance to related benzoisochromanequinone (BIQ) antibiotics, such as the model antibiotic actinorhodin. One intriguing difference between these metabolites is that the positions of the benzene and quinone rings are reversed in alnumycin A in comparison to the BIQ polyketides. In this paper we demonstrate that inactivation of either the monooxygenase alnT gene or the flavin reductase alnH gene results in the accumulation of a novel nonquinoid metabolite, thalnumycin A (ThA), in the culture medium. Additionally, two other previously characterized metabolites, K1115 A and 1,6-dihydroxy-8-propylanthraquinone (DHPA), were identified, which had oxidized into quinones putatively nonenzymatically at the incorrect position in the central ring. None of the compounds isolated contained correctly formed pyran rings, which suggests that on the alnumycin pathway quinone biosynthesis occurs prior to third ring cyclization. The regiochemistry of the two-component monooxygenase system AlnT/AlnH was finally confirmed in vitro by using ThA, FMN, and NADH in enzymatic synthesis, where the reaction product, thalnumycin B (ThB), was verified to contain the expected p-hydroquinone structure in the lateral ring.
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19
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Taguchi T, Okamoto S, Hasegawa K, Ichinose K. Epoxyquinone Formation Catalyzed by a Two-Component Flavin-Dependent Monooxygenase Involved in Biosynthesis of the Antibiotic Actinorhodin. Chembiochem 2011; 12:2767-73. [DOI: 10.1002/cbic.201100571] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Indexed: 11/11/2022]
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20
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Wang Y, Li H, Yao J, Wang X, Antonietti M. Synthesis of boron doped polymeric carbon nitride solids and their use as metal-free catalysts for aliphatic C–H bond oxidation. Chem Sci 2011. [DOI: 10.1039/c0sc00475h] [Citation(s) in RCA: 354] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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21
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Ruangchan N, Tongsook C, Sucharitakul J, Chaiyen P. pH-dependent studies reveal an efficient hydroxylation mechanism of the oxygenase component of p-hydroxyphenylacetate 3-hydroxylase. J Biol Chem 2010; 286:223-33. [PMID: 21030590 DOI: 10.1074/jbc.m110.163881] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
p-Hydroxyphenylacetate (HPA) 3-hydroxylase (HPAH) catalyzes the hydroxylation of HPA at the ortho-position to yield 3,4-dihydroxyphenylacetate. The enzyme is a flavin-dependent two-component monooxygenase that consists of a reductase component and an oxygenase component (C(2)). C(2) catalyzes the hydroxylation of HPA using oxygen and reduced FMN as co-substrates. To date, the effects of pH on the oxygenation of the two-component monooxygenases have never been reported. Here, we report the reaction kinetics of C(2)·FMNH(-) with oxygen at various pH values investigated by stopped-flow and rapid quenched-flow techniques. In the absence of HPA, the rate constant for the formation of C4a-hydroperoxy-FMN (∼1.1 × 10(6) m(-1)s(-1)) was unaffected at pH 6.2-9.9, which indicated that the pK(a) of the enzyme-bound reduced FMN was less than 6.2. The rate constant for the following H(2)O(2) elimination step increased with higher pH, which is consistent with a pK(a) of >9.4. In the presence of HPA, the rate constants for the formation of C4a-hydroperoxy-FMN (∼4.8 × 10(4) m(-1)s(-1)) and the ensuing hydroxylation step (15-17 s(-1)) were not significantly affected by the pH. In contrast, the following steps of C4a-hydroxy-FMN dehydration to form oxidized FMN occurred through two pathways that were dependent on the pH of the reaction. One pathway, dominant at low pH, allowed the detection of a C4a-hydroxy-FMN intermediate, whereas the pathway dominant at high pH produced oxidized FMN without an apparent accumulation of the intermediate. However, both pathways efficiently catalyzed hydroxylation without generating significant amounts of wasteful H(2)O(2) at pH 6.2-9.9. The decreased accumulation of the intermediate at higher pH was due to the greater rates of C4a-hydroxy-FMN decay caused by the abolishment of substrate inhibition in the dehydration step at high pH.
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Affiliation(s)
- Nantidaporn Ruangchan
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400, Thailand
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22
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Ellis HR. The FMN-dependent two-component monooxygenase systems. Arch Biochem Biophys 2010; 497:1-12. [PMID: 20193654 DOI: 10.1016/j.abb.2010.02.007] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Revised: 02/13/2010] [Accepted: 02/16/2010] [Indexed: 11/19/2022]
Abstract
The FMN-dependent two-component monooxygenase systems catalyze a diverse range of reactions. These two-component systems are composed of an FMN reductase enzyme and a monooxygenase enzyme that catalyze the oxidation of various substrates. The role of the reductase is to supply reduced flavin to the monooxygenase enzyme, while the monooxygenase enzyme utilizes the reduced flavin to activate molecular oxygen. Unlike flavoproteins with a tightly or covalently bound prosthetic group, these enzymes catalyze the reductive and oxidative half-reaction on two separate enzymes. An interesting feature of these enzymes is their ability to transfer reduced flavin from the reductase to the monooxygenase enzyme. This review covers the reported mechanistic and structural properties of these enzyme systems, and evaluates the mechanism of flavin transfer.
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Affiliation(s)
- Holly R Ellis
- The Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA.
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23
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Olano C, Méndez C, Salas JA. Post-PKS tailoring steps in natural product-producing actinomycetes from the perspective of combinatorial biosynthesis. Nat Prod Rep 2010; 27:571-616. [DOI: 10.1039/b911956f] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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24
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Webb BN, Ballinger JW, Kim E, Belchik SM, Lam KS, Youn B, Nissen MS, Xun L, Kang C. Characterization of chlorophenol 4-monooxygenase (TftD) and NADH:FAD oxidoreductase (TftC) of Burkholderia cepacia AC1100. J Biol Chem 2009; 285:2014-27. [PMID: 19915006 DOI: 10.1074/jbc.m109.056135] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Burkholderia cepacia AC1100 completely degrades 2,4,5-trichlorophenol, in which an FADH(2)-dependent monooxygenase (TftD) and an NADH:FAD oxidoreductase (TftC) catalyze the initial steps. TftD oxidizes 2,4,5-trichlorophenol (2,4,5-TCP) to 2,5-dichloro-p-benzoquinone, which is chemically reduced to 2,5-dichloro-p-hydroquinone (2,5-DiCHQ). Then, TftD oxidizes the latter to 5-chloro-2-hydroxy-p-benzoquinone. In those processes, TftC provides all the required FADH(2). We have determined the crystal structures of dimeric TftC and tetrameric TftD at 2.0 and 2.5 A resolution, respectively. The structure of TftC was similar to those of related flavin reductases. The stacked nicotinamide:isoalloxazine rings in TftC and sequential reaction kinetics suggest that the reduced FAD leaves TftC after NADH oxidation. The structure of TftD was also similar to the known structures of FADH(2)-dependent monooxygenases. Its His-289 residue in the re-side of the isoalloxazine ring is within hydrogen bonding distance with a hydroxyl group of 2,5-DiCHQ. An H289A mutation resulted in the complete loss of activity toward 2,5-DiCHQ and a significant decrease in catalytic efficiency toward 2,4,5-TCP. Thus, His-289 plays different roles in the catalysis of 2,4,5-TCP and 2,5-DiCHQ. The results support that free FADH(2) is generated by TftC, and TftD uses FADH(2) to separately transform 2,4,5-TCP and 2,5-DiCHQ. Additional experimental data also support the diffusion of FADH(2) between TftC and TftD without direct physical interaction between the two enzymes.
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Affiliation(s)
- Brian N Webb
- Department of Chemistry, WashingtonState University,Pullman, Washington 99164-4660, USA
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25
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Okamoto S, Taguchi T, Ochi K, Ichinose K. Biosynthesis of Actinorhodin and Related Antibiotics: Discovery of Alternative Routes for Quinone Formation Encoded in the act Gene Cluster. ACTA ACUST UNITED AC 2009; 16:226-36. [DOI: 10.1016/j.chembiol.2009.01.015] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 01/22/2009] [Accepted: 01/28/2009] [Indexed: 10/21/2022]
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26
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Oja T, Palmu K, Lehmussola H, Leppäranta O, Hännikäinen K, Niemi J, Mäntsälä P, Metsä-Ketelä M. Characterization of the alnumycin gene cluster reveals unusual gene products for pyran ring formation and dioxan biosynthesis. ACTA ACUST UNITED AC 2008; 15:1046-57. [PMID: 18940666 DOI: 10.1016/j.chembiol.2008.07.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Revised: 07/23/2008] [Accepted: 07/28/2008] [Indexed: 11/28/2022]
Abstract
Alnumycin is closely related to the benzoisochromanequinone (BIQ) polyketides such as actinorhodin. Exceptional structural features include differences in aglycone tailoring that result in the unique alnumycin chromophore and the existence of an unusual 4-hydroxymethyl-5-hydroxy-1,3-dioxan moiety. Cloning and sequencing of the alnumycin gene cluster from Streptomyces sp. CM020 revealed expected biosynthesis genes for polyketide assembly, but several genes encoding subsequent tailoring enzymes were highly atypical. Heterologous expression studies confirmed that all of the genes required for alnumycin biosynthesis resided within the sequenced clone. Inactivation of genes aln4 and aln5 showed that the mechanism of pyran ring formation differs from actinorhodin and granaticin pathways. Further inactivation studies identified two genes, alnA and alnB, involved in the synthesis and attachment of the dioxan moiety, and resulted in the production of the polyketide prealnumycin.
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Affiliation(s)
- Terhi Oja
- Department of Biochemistry and Food Chemistry, University of Turku, FIN-20014 Turku, Finland
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27
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Kim SH, Hisano T, Iwasaki W, Ebihara A, Miki K. Crystal structure of the flavin reductase component (HpaC) of 4-hydroxyphenylacetate 3-monooxygenase from Thermus thermophilus HB8: Structural basis for the flavin affinity. Proteins 2008; 70:718-30. [PMID: 17729270 DOI: 10.1002/prot.21534] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The two-component enzyme, 4-hydroxyphenylacetate 3-monooxygenase, catalyzes the conversion of 4-hydroxyphenylacetate to 3,4-dihydroxyphenylacetate. In the overall reaction, the oxygenase component (HpaB) introduces a hydroxyl group into the benzene ring of 4-hydroxyphenylacetate using molecular oxygen and reduced flavin, while the reductase component (HpaC) provides free reduced flavins for HpaB. The crystal structures of HpaC from Thermus thermophilus HB8 in the ligand-free form, the FAD-containing form, and the ternary complex with FAD and NAD(+) were determined. In the ligand-free form, two large grooves are present at the dimer interface, and are occupied by water molecules. A structural analysis of HpaC containing FAD revealed that FAD has a low occupancy, indicating that it is not tightly bound to HpaC. This was further confirmed in flavin dissociation experiments, showing that FAD can be released from HpaC. The structure of the ternary complex revealed that FAD and NAD(+) are bound in the groove in the extended and folded conformation, respectively. The nicotinamide ring of NAD(+) is sandwiched between the adenine ring of NAD(+) and the isoalloxazine ring of FAD. The distance between N5 of the isoalloxazine ring and C4 of the nicotinamide ring is about 3.3 A, sufficient to permit hydride transfer. The structures of these three states are essentially identical, however, the side chains of several residues show small conformational changes, indicating an induced fit upon binding of NADH. Inactivity with respect to NADPH can be explained as instability of the binding of NADPH with the negatively charged 2'-phosphate group buried inside the complex, as well as a possible repulsive effect by the dipole of helix alpha1. A comparison of the binding mode of FAD with that in PheA2 from Bacillus thermoglucosidasius A7, which contains FAD as a prosthetic group, reveals remarkable conformational differences in a less conserved loop region (Gly83-Gly94) involved in the binding of the AMP moiety of FAD. These data suggest that variations in the affinities for FAD in the reductases of the two-component flavin-diffusible monooxygenase family may be attributed to difference in the interaction between the AMP moiety of FAD and the less conserved loop region which possibly shows structural divergence.
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Affiliation(s)
- Seong-Hoon Kim
- SPring-8 Center, RIKEN Harima Institute, Koto 1-1-1, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
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Valton J, Mathevon C, Fontecave M, Nivière V, Ballou DP. Mechanism and regulation of the Two-component FMN-dependent monooxygenase ActVA-ActVB from Streptomyces coelicolor. J Biol Chem 2008; 283:10287-96. [PMID: 18245777 DOI: 10.1074/jbc.m709730200] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ActVA-ActVB system from Streptomyces coelicolor is a two-component flavin-dependent monooxygenase involved in the antibiotic actinorhodin biosynthesis. ActVB is a NADH:flavin oxidoreductase that provides a reduced FMN to ActVA, the monooxygenase that catalyzes the hydroxylation of dihydrokalafungin, the precursor of actinorhodin. In this work, using stopped-flow spectrophotometry, we investigated the mechanism of hydroxylation of dihydrokalafungin catalyzed by ActVA and that of the reduced FMN transfer from ActVB to ActVA. Our results show that the hydroxylation mechanism proceeds with the participation of two different reaction intermediates in ActVA active site. First, a C(4a)-FMN-hydroperoxide species is formed after binding of reduced FMN to the monooxygenase and reaction with O(2). This intermediate hydroxylates the substrate and is transformed to a second reaction intermediate, a C(4a)-FMN-hydroxy species. In addition, we demonstrate that reduced FMN can be transferred efficiently from the reductase to the monooxygenase without involving any protein.protein complexes. The rate of transfer of reduced FMN from ActVB to ActVA was found to be controlled by the release of NAD(+) from ActVB and was strongly affected by NAD(+) concentration, with an IC(50) of 40 microm. This control of reduced FMN transfer by NAD(+) was associated with the formation of a strong charge.transfer complex between NAD(+) and reduced FMN in the active site of ActVB. These results suggest that, in Streptomyces coelicolor, the reductase component ActVB can act as a regulatory component of the monooxygenase activity by controlling the transfer of reduced FMN to the monooxygenase.
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Affiliation(s)
- Julien Valton
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606, USA
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29
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Taguchi T, Okamoto S, Itoh T, Ebizuka Y, Ochi K, Ichinose K. Actinoperylone, a novel perylenequinone-type shunt product, from a deletion mutant of the actVA-ORF5 and ORF6 genes for actinorhodin biosynthesis in Streptomyces coelicolor A3(2). Tetrahedron Lett 2008. [DOI: 10.1016/j.tetlet.2007.12.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Zhan X, Carpenter RA, Ellis HR. Catalytic Importance of the Substrate Binding Order for the FMNH2-Dependent Alkanesulfonate Monooxygenase Enzyme. Biochemistry 2008; 47:2221-30. [DOI: 10.1021/bi701853w] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xuanzhi Zhan
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
| | - Russell A. Carpenter
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
| | - Holly R. Ellis
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
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31
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Kertesz MA, Fellows E, Schmalenberger A. Rhizobacteria and plant sulfur supply. ADVANCES IN APPLIED MICROBIOLOGY 2007; 62:235-68. [PMID: 17869607 DOI: 10.1016/s0065-2164(07)62008-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Michael A Kertesz
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
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32
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Kim SH, Hisano T, Takeda K, Iwasaki W, Ebihara A, Miki K. Crystal structure of the oxygenase component (HpaB) of the 4-hydroxyphenylacetate 3-monooxygenase from Thermus thermophilus HB8. J Biol Chem 2007; 282:33107-17. [PMID: 17804419 DOI: 10.1074/jbc.m703440200] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 4-hydroxyphenylacetate (4HPA) 3-monooxygenase is involved in the initial step of the 4HPA degradation pathway and catalyzes 4HPA hydroxylation to 3,4-dihydroxyphenylacetate. This enzyme consists of two components, an oxygenase (HpaB) and a reductase (HpaC). To understand the structural basis of the catalytic mechanism of HpaB, crystal structures of HpaB from Thermus thermophilus HB8 were determined in three states: a ligand-free form, a binary complex with FAD, and a ternary complex with FAD and 4HPA. Structural analysis revealed that the binding and dissociation of flavin are accompanied by conformational changes of the loop between beta5 and beta6 and of the loop between beta8 and beta9, leading to preformation of part of the substrate-binding site (Ser-197 and Thr-198). The latter loop further changes its conformation upon binding of 4HPA and obstructs the active site from the bulk solvent. Arg-100 is located adjacent to the putative oxygen-binding site and may be involved in the formation and stabilization of the C4a-hydroperoxyflavin intermediate.
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Affiliation(s)
- Seong-Hoon Kim
- SPring-8 Center, RIKEN Harima Institute, Koto 1-1-1, Sayo-cho, Sayo-gun, Hyogo, Japan
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Deng D, Li X, Fang X, Sun G. Characterization of two components of the 2-naphthoate monooxygenase system from Burkholderia sp. strain JT1500. FEMS Microbiol Lett 2007; 273:22-7. [PMID: 17559398 DOI: 10.1111/j.1574-6968.2007.00774.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
2-Naphthoate monooxygenase, a two-protein system, encoded by the nmoA and nmoB genes, was heterologously overexpressed in Escherichia coli. The proteins used for functional characterization were purified to over 90% homogeneity by affinity chromatography. The oxidative component EnmoA (47.9 kDa) lacked substrate catalysis capability on its own, and the reductive component EnmoB (33.4 kDa) and its truncated derivate EnmoB(T) (25 kDa) possessed nearly identical independent flavin reductase activities, c. 130 micromol min(-1) mg(-1) of protein. The inframe fusioned protein EnmoB(T)A (65.2 kDa), containing NmoB(T) and NmoA peptides showed a stable 2-naphthoate monooxygenase activity of 1.2 micromol min(-1) mg(-1) of protein. This is the first report on the purification of a fused form of a two-component flavoprotein monooxygenase. In the specificity experiment, FAD and NADH were shown to be preferred cosubstrates for EnmoB and EnmoB(T). All these data suggest that NmoB(T)A is a two-component flavoprotein monooxygenase, consisting of an oxygenase and a reductase component. NmoA is a member of the class D flavoprotein monooxygenase, and NmoB is an independent NADH:Flavin oxidoreductase.
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Affiliation(s)
- Daiyong Deng
- Microbiology and Environmental Biotechnology, Guangdong Institute of Microbiology, Guangdong Province, China
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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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Sucharitakul J, Chaiyen P, Entsch B, Ballou DP. Kinetic Mechanisms of the Oxygenase from a Two-component Enzyme, p-Hydroxyphenylacetate 3-Hydroxylase from Acinetobacter baumannii. J Biol Chem 2006; 281:17044-17053. [PMID: 16627482 DOI: 10.1074/jbc.m512385200] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
p-Hydroxyphenylacetate hydroxylase (HPAH) from Acinetobacter baumannii catalyzes the hydroxylation of p-hydroxyphenylacetate (HPA) to form 3,4-dihydroxyphenylacetate (DHPA). The enzyme system is composed of two proteins: an FMN reductase (C1) and an oxygenase that uses FMNH- (C2). We report detailed transient kinetics studies at 4 degrees C of the reaction mechanism of C2.C2 binds rapidly and tightly to reduced FMN (Kd, 1.2 +/- 0.2 microm), but less tightly to oxidized FMN (Kd, 250 +/- 50 microm). The complex of C -FMNH-2 reacted with oxygen to form C(4a)-hydroperoxy-FMN at 1.1 +/- 0.1 x 10(6) m(-1) s(-1), whereas the C -FMNH-2 -HPA complex reacted with oxygen to form C(4a)-hydroperoxy-FMN-HPA more slowly (k = 4.8 +/- 0.2 x 10(4) m(-1) s(-1)). The kinetic mechanism of C2 was shown to be a preferential random order type, in which HPA or oxygen can initially bind to the C -FMNH-2 complex, but the preferred path was oxygen reacting with C -FMNH-2 to form the C(4a)-hydroperoxy-FMN intermediate prior to HPA binding. Hydroxylation occurs from the ternary complex with a rate constant of 20 s(-1) to form the C2-C(4a)-hydroxy-FMN-DHPA complex. At high HPA concentrations (>0.5 mm), HPA formed a dead end complex with the C2-C(4a)-hydroxy-FMN intermediate (similar to single component flavoprotein hydroxylases), thus inhibiting the bound flavin from returning to the oxidized form. When FADH- was used, C(4a)-hydroperoxy-FAD, C(4a)-hydroxy-FAD, and product were formed at rates similar to those with FMNH-. Thus, C2 has the unusual ability to use both common flavin cofactors in catalysis.
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Affiliation(s)
- Jeerus Sucharitakul
- Department of Biochemistry and Center for Excellence in Protein Structure & Function, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein Structure & Function, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
| | - Barrie Entsch
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-06060
| | - David P Ballou
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-06060
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