1
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Li Q, Zhang S, Liu F, Su H, Sheng X. Quantum chemical modeling of enantioselective sulfoxidation and epoxidation reactions by indole monooxygenase VpIndA1. Phys Chem Chem Phys 2024; 26:16521-16528. [PMID: 38809594 DOI: 10.1039/d4cp00552j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Indole monooxygenases (IMOs) are enzymes from the family of Group E monooxygenases, requiring flavin adenine dinucleotide (FAD) for their activities. IMOs play important roles in both sulfoxidation and epoxidation reactions. The broad substrate range and high selectivity of IMOs make them promising biocatalytic tools for synthesizing chiral compounds. In the present study, quantum chemical calculations using the cluster approach were performed to investigate the reaction mechanism and the enantioselectivity of the IMO from Variovorax paradoxus EPS (VpIndA1). The sulfoxidation of methyl phenyl sulfide (MPS) and the epoxidation of indene were chosen as the representative reactions. The calculations confirmed that the FADOOH intermediate is the catalytic species in the VpIndA1 reactions. The oxidation of MPS adopts a one-step mechanism involving the direct oxygen-transfer from FADOOH to the substrate and the proton transfer from the -OH group back to FAD, while the oxidation of indene follows a stepwise mechanism involving a carbocation intermediate. It was computationally predicted that VpIndA1 prefers the formation of (S)-product for the MPS sulfoxidation and (1S,2R)-product for the indene epoxidation, consistent with the experimental observations. Importantly, the factors controlling the stereo-preference of the two reactions are identified. The findings in the present study provide valuable insights into the VpIndA1-catalyzed reactions, which are essential for the rational design of this enzyme and other IMOs for industrial applications. It is also worth emphasizing that the quantum chemical cluster approach is again demonstrated to be powerful in studying the enantioselectivity of enzymatic reactions.
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Affiliation(s)
- Qinrou Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China.
| | - Shiqing Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China.
- National Center of Technology Innovation for Synthetic Biology, National Engineering Research Center of Industrial Enzymes and Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin 300308, P. R. China
| | - Fufeng Liu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China
| | - Hao Su
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China.
- National Center of Technology Innovation for Synthetic Biology, National Engineering Research Center of Industrial Enzymes and Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin 300308, P. R. China
| | - Xiang Sheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China.
- National Center of Technology Innovation for Synthetic Biology, National Engineering Research Center of Industrial Enzymes and Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin 300308, P. R. China
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2
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Johnson S, Li H, Valentino H, Sobrado P. Mechanism of Nitrone Formation by a Flavin-Dependent Monooxygenase. Biochemistry 2024; 63:1445-1459. [PMID: 38779817 PMCID: PMC11154958 DOI: 10.1021/acs.biochem.3c00656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
OxaD is a flavin-dependent monooxygenase (FMO) responsible for catalyzing the oxidation of an indole nitrogen atom, resulting in the formation of a nitrone. Nitrones serve as versatile intermediates in complex syntheses, including challenging reactions like cycloadditions. Traditional organic synthesis methods often yield limited results and involve environmentally harmful chemicals. Therefore, the enzymatic synthesis of nitrone-containing compounds holds promise for more sustainable industrial processes. In this study, we explored the catalytic mechanism of OxaD using a combination of steady-state and rapid-reaction kinetics, site-directed mutagenesis, spectroscopy, and structural modeling. Our investigations showed that OxaD catalyzes two oxidations of the indole nitrogen of roquefortine C, ultimately yielding roquefortine L. The reductive-half reaction analysis indicated that OxaD rapidly undergoes reduction and follows a "cautious" flavin reduction mechanism by requiring substrate binding before reduction can take place. This characteristic places OxaD in class A of the FMO family, a classification supported by a structural model featuring a single Rossmann nucleotide binding domain and a glutathione reductase fold. Furthermore, our spectroscopic analysis unveiled both enzyme-substrate and enzyme-intermediate complexes. Our analysis of the oxidative-half reaction suggests that the flavin dehydration step is the slow step in the catalytic cycle. Finally, through mutagenesis of the conserved D63 residue, we demonstrated its role in flavin motion and product oxygenation. Based on our findings, we propose a catalytic mechanism for OxaD and provide insights into the active site architecture within class A FMOs.
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Affiliation(s)
- Sydney
B. Johnson
- Department
of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United
States
| | - Hao Li
- Department
of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United
States
| | - Hannah Valentino
- Department
of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United
States
| | - Pablo Sobrado
- Department
of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United
States
- Center
of Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United
States
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3
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Knaus T, Macheroux P, Mutti FG. Fus-SMO: Kinetics, Biochemical Characterisation and In Silico Modelling of a Chimeric Styrene Monooxygenase Demonstrating Quantitative Coupling Efficiency. Chembiochem 2024; 25:e202300833. [PMID: 38306174 DOI: 10.1002/cbic.202300833] [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: 12/10/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/03/2024]
Abstract
The styrene monooxygenase, a two-component enzymatic system for styrene epoxidation, was characterised through the study of Fus-SMO - a chimera resulting from the fusion of StyA and StyB using a flexible linker. Notably, it remains debated whether the transfer of FADH2 from StyB to StyA occurs through diffusion, channeling, or a combination of both. Fus-SMO was identified as a trimer with one bound FAD molecule. In silico modelling revealed a well-distanced arrangement (45-50 Å) facilitated by the flexible linker's loopy structure. Pre-steady-state kinetics elucidated the FADox reduction intricacies (kred=110 s-1 for bound FADox), identifying free FADox binding as the rate-determining step. The aerobic oxidation of FADH2 (kox=90 s-1) and subsequent decomposition to FADox and H2O2 demonstrated StyA's protective effect on the bound hydroperoxoflavin (kdec=0.2 s-1) compared to free cofactor (kdec=1.8 s-1). At varied styrene concentrations, kox for FADH2 ranged from 80 to 120 s-1. Studies on NADH consumption vs. styrene epoxidation revealed Fus-SMO's ability to achieve quantitative coupling efficiency in solution, surpassing natural two-component SMOs. The results suggest that Fus-SMO exhibits enhanced FADH2 channelling between subunits. This work contributes to comprehending FADH2 transfer mechanisms in SMO and illustrates how protein fusion can elevate catalytic efficiency for biocatalytic applications.
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Affiliation(s)
- Tanja Knaus
- Van 't Hoff Institute for Molecular Sciences, HIMS-Biocat, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
| | - Francesco G Mutti
- Van 't Hoff Institute for Molecular Sciences, HIMS-Biocat, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
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4
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Chen Q, Xiao H, Li ZP, Pei XQ, Yang W, Liu Y, Wu ZL. Stereo-complementary epoxidation of 4-vinyl-2,3-dihydrobenzofuran using mutants of SeStyA with enhanced stability and enantioselectivity. MOLECULAR CATALYSIS 2023. [DOI: 10.1016/j.mcat.2023.113055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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5
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Kratky J, Eggerichs D, Heine T, Hofmann S, Sowa P, Weiße RH, Tischler D, Sträter N. Structural and Mechanistic Studies on Substrate and Stereoselectivity of the Indole Monooxygenase VpIndA1: New Avenues for Biocatalytic Epoxidations and Sulfoxidations. Angew Chem Int Ed Engl 2023; 62:e202300657. [PMID: 36762980 DOI: 10.1002/anie.202300657] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/11/2023]
Abstract
Flavoprotein monooxygenases are a versatile group of enzymes for biocatalytic transformations. Among these, group E monooxygenases (GEMs) catalyze enantioselective epoxidation and sulfoxidation reactions. Here, we describe the crystal structure of an indole monooxygenase from the bacterium Variovorax paradoxus EPS, a GEM designated as VpIndA1. Complex structures with substrates reveal productive binding modes that, in conjunction with force-field calculations and rapid mixing kinetics, reveal the structural basis of substrate and stereoselectivity. Structure-based redesign of the substrate cavity yielded variants with new substrate selectivity (for sulfoxidation of benzyl phenyl sulfide) or with greatly enhanced stereoselectivity (from 35.1 % to 99.8 % ee for production of (1S,2R)-indene oxide). This first determination of the substrate binding mode of GEMs combined with structure-function relationships opens the door for structure-based design of these powerful biocatalysts.
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Affiliation(s)
- Julia Kratky
- Institute of Bioanalytical Chemistry, Leipzig University, Deutscher Platz 5, 04103, Leipzig, Germany
| | - Daniel Eggerichs
- Microbial Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Thomas Heine
- Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Sarah Hofmann
- Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Philipp Sowa
- Microbial Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Renato H Weiße
- Institute of Bioanalytical Chemistry, Leipzig University, Deutscher Platz 5, 04103, Leipzig, Germany
| | - Dirk Tischler
- Microbial Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany.,Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Norbert Sträter
- Institute of Bioanalytical Chemistry, Leipzig University, Deutscher Platz 5, 04103, Leipzig, Germany
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6
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Sequence-guided stereo-enhancing and -inverting of (R)-styrene monooxygenases for highly enantioselective epoxidation. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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7
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Properties and Mechanisms of Flavin-Dependent Monooxygenases and Their Applications in Natural Product Synthesis. Int J Mol Sci 2022; 23:ijms23052622. [PMID: 35269764 PMCID: PMC8910399 DOI: 10.3390/ijms23052622] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/21/2022] [Accepted: 02/25/2022] [Indexed: 11/17/2022] Open
Abstract
Natural products are usually highly complicated organic molecules with special scaffolds, and they are an important resource in medicine. Natural products with complicated structures are produced by enzymes, and this is still a challenging research field, its mechanisms requiring detailed methods for elucidation. Flavin adenine dinucleotide (FAD)-dependent monooxygenases (FMOs) catalyze many oxidation reactions with chemo-, regio-, and stereo-selectivity, and they are involved in the synthesis of many natural products. In this review, we introduce the mechanisms for different FMOs, with the classical FAD (C4a)-hydroperoxide as the major oxidant. We also summarize the difference between FMOs and cytochrome P450 (CYP450) monooxygenases emphasizing the advantages of FMOs and their specificity for substrates. Finally, we present examples of FMO-catalyzed synthesis of natural products. Based on these explanations, this review will expand our knowledge of FMOs as powerful enzymes, as well as implementation of the FMOs as effective tools for biosynthesis.
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8
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Cui CY, Chen Q, He Q, Chen C, Zhang RM, Feng Y, Sun J. Transferability of tigecycline resistance: Characterization of the expanding Tet(X) family. WIREs Mech Dis 2022; 14:e1538. [PMID: 35023325 DOI: 10.1002/wsbm.1538] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 01/13/2023]
Abstract
Tetracycline and its derivative tigecycline are clinical options against Gram-negative bacterial infections. The emergence of mobile Tet(X) enzymes that destruct tetracycline-type antibiotics is posing a big challenge to antibacterial therapy and food/environmental securities. Here, we present an update on a growing number of Tet(X) variants. We describe structure and action of Tet(X) enzyme, and discuss the evolutional origin. In addition, potential Tet(X) inhibitors are given. This mini-review might benefit better understanding of Tet(X)-mediated tigecycline resistance. This article is categorized under: Infectious Diseases > Genetics/Genomics/Epigenetics Infectious Diseases > Environmental Factors Infectious Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Chao-Yue Cui
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - Qiwei Chen
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China.,Department of Microbiology, and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qian He
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - Chong Chen
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, China
| | - Rong-Min Zhang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - Youjun Feng
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.,Department of Microbiology, and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
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9
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Simić S, Zukić E, Schmermund L, Faber K, Winkler CK, Kroutil W. Shortening Synthetic Routes to Small Molecule Active Pharmaceutical Ingredients Employing Biocatalytic Methods. Chem Rev 2021; 122:1052-1126. [PMID: 34846124 DOI: 10.1021/acs.chemrev.1c00574] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Biocatalysis, using enzymes for organic synthesis, has emerged as powerful tool for the synthesis of active pharmaceutical ingredients (APIs). The first industrial biocatalytic processes launched in the first half of the last century exploited whole-cell microorganisms where the specific enzyme at work was not known. In the meantime, novel molecular biology methods, such as efficient gene sequencing and synthesis, triggered breakthroughs in directed evolution for the rapid development of process-stable enzymes with broad substrate scope and good selectivities tailored for specific substrates. To date, enzymes are employed to enable shorter, more efficient, and more sustainable alternative routes toward (established) small molecule APIs, and are additionally used to perform standard reactions in API synthesis more efficiently. Herein, large-scale synthetic routes containing biocatalytic key steps toward >130 APIs of approved drugs and drug candidates are compared with the corresponding chemical protocols (if available) regarding the steps, reaction conditions, and scale. The review is structured according to the functional group formed in the reaction.
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Affiliation(s)
- Stefan Simić
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Erna Zukić
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Luca Schmermund
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Kurt Faber
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Christoph K Winkler
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Wolfgang Kroutil
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria.,Field of Excellence BioHealth─University of Graz, 8010 Graz, Austria.,BioTechMed Graz, 8010 Graz, Austria
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10
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Meng L, Sun C, Gao L, Saleem M, Li B, Wang C. Hydroxybenzoate hydroxylase genes underlying protocatechuic acid production in Valsa mali are required for full pathogenicity in apple trees. MOLECULAR PLANT PATHOLOGY 2021; 22:1370-1382. [PMID: 34390112 PMCID: PMC8518569 DOI: 10.1111/mpp.13119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/01/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Valsa mali is the causative agent of apple tree valsa canker, which causes significant losses in apple production. It produces various toxic compounds that kill plant cells, facilitating infection. Among these, protocatechuic acid exhibits the highest phytotoxic activity. However, those genes involved in toxin production have not been studied. In this study we identified four hydroxybenzoate hydroxylase genes (VmHbh1, VmHbh2, VmHbh3, and VmHbh4) from the transcriptome of V. mali. The VmHbh protein had high enzymatic activities of hydroxybenzoate hydroxylase, which could convert 4-hydroxybenzoate to protocatechuic acid. These four VmHbh genes all had highly elevated transcript levels during the V. mali infection process, especially VmHbh1 and VmHbh4, with 26.0- and 53.4-fold increases, respectively. Mutants of the four genes were generated to study whether VmHbhs are required for V. mali pathogenicity. Of the four genes, the VmHbh1 and VmHbh4 deletion mutants considerably attenuated V. mali virulence in apple leaves and in twigs, coupled with much reduced toxin levels. The VmHbh2 and VmHbh3 deletion mutants promoted the transcript levels of the other VmHbhs, suggesting functional redundancies of VmHbhs in V. mali virulence. The results provide insights into the functions of VmHbhs in the production of protocatechuic acid by V. mali during its infection of apple trees.
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Affiliation(s)
- Lulu Meng
- College of Plant Health and MedicineKey Laboratory of Integrated Crop Pest Management of Shandong ProvinceShandong Province Key Laboratory of Applied MycologyQingdao Agricultural UniversityQingdaoChina
| | - Cuicui Sun
- College of Plant Health and MedicineKey Laboratory of Integrated Crop Pest Management of Shandong ProvinceShandong Province Key Laboratory of Applied MycologyQingdao Agricultural UniversityQingdaoChina
| | - Liyong Gao
- College of Plant Health and MedicineKey Laboratory of Integrated Crop Pest Management of Shandong ProvinceShandong Province Key Laboratory of Applied MycologyQingdao Agricultural UniversityQingdaoChina
| | - Muhammad Saleem
- Department of Biological SciencesAlabama State UniversityMontgomeryAlabamaUSA
| | - Baohua Li
- College of Plant Health and MedicineKey Laboratory of Integrated Crop Pest Management of Shandong ProvinceShandong Province Key Laboratory of Applied MycologyQingdao Agricultural UniversityQingdaoChina
| | - Caixia Wang
- College of Plant Health and MedicineKey Laboratory of Integrated Crop Pest Management of Shandong ProvinceShandong Province Key Laboratory of Applied MycologyQingdao Agricultural UniversityQingdaoChina
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11
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Martínez-Montero L, Tischler D, Süss P, Schallmey A, Franssen MCR, Hollmann F, Paul CE. Asymmetric azidohydroxylation of styrene derivatives mediated by a biomimetic styrene monooxygenase enzymatic cascade. Catal Sci Technol 2021; 11:5077-5085. [PMID: 34381590 PMCID: PMC8328376 DOI: 10.1039/d1cy00855b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/13/2021] [Indexed: 12/18/2022]
Abstract
Enantioenriched azido alcohols are precursors for valuable chiral aziridines and 1,2-amino alcohols, however their chiral substituted analogues are difficult to access. We established a cascade for the asymmetric azidohydroxylation of styrene derivatives leading to chiral substituted 1,2-azido alcohols via enzymatic asymmetric epoxidation, followed by regioselective azidolysis, affording the azido alcohols with up to two contiguous stereogenic centers. A newly isolated two-component flavoprotein styrene monooxygenase StyA proved to be highly selective for epoxidation with a nicotinamide coenzyme biomimetic as a practical reductant. Coupled with azide as a nucleophile for regioselective ring opening, this chemo-enzymatic cascade produced highly enantioenriched aromatic α-azido alcohols with up to >99% conversion. A bi-enzymatic counterpart with halohydrin dehalogenase-catalyzed azidolysis afforded the alternative β-azido alcohol isomers with up to 94% diastereomeric excess. We anticipate our biocatalytic cascade to be a starting point for more practical production of these chiral compounds with two-component flavoprotein monooxygenases.
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Affiliation(s)
- Lía Martínez-Montero
- Department of Biotechnology, Delft University of Technology Van der Maasweg 9 2629 HZ Delft The Netherlands
| | - Dirk Tischler
- Microbial Biotechnology, Ruhr-Universität Bochum Universitätsstr. 150 44780 Bochum Germany
| | - Philipp Süss
- Enzymicals AG Walther-Rathenau-Straße 49a 17489 Greifswald Germany
| | - Anett Schallmey
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig Spielmannstraße 7 38106 Braunschweig Germany
| | - Maurice C R Franssen
- Laboratory of Organic Chemistry, Wageningen University Stippeneng 4 6708 WE Wageningen The Netherlands
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology Van der Maasweg 9 2629 HZ Delft The Netherlands
| | - Caroline E Paul
- Department of Biotechnology, Delft University of Technology Van der Maasweg 9 2629 HZ Delft The Netherlands
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12
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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: 65] [Impact Index Per Article: 21.7] [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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13
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Winkler C, Schrittwieser JH, Kroutil W. Power of Biocatalysis for Organic Synthesis. ACS CENTRAL SCIENCE 2021; 7:55-71. [PMID: 33532569 PMCID: PMC7844857 DOI: 10.1021/acscentsci.0c01496] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Indexed: 05/05/2023]
Abstract
Biocatalysis, using defined enzymes for organic transformations, has become a common tool in organic synthesis, which is also frequently applied in industry. The generally high activity and outstanding stereo-, regio-, and chemoselectivity observed in many biotransformations are the result of a precise control of the reaction in the active site of the biocatalyst. This control is achieved by exact positioning of the reagents relative to each other in a fine-tuned 3D environment, by specific activating interactions between reagents and the protein, and by subtle movements of the catalyst. Enzyme engineering enables one to adapt the catalyst to the desired reaction and process. A well-filled biocatalytic toolbox is ready to be used for various reactions. Providing nonnatural reagents and conditions and evolving biocatalysts enables one to play with the myriad of options for creating novel transformations and thereby opening new, short pathways to desired target molecules. Combining several biocatalysts in one pot to perform several reactions concurrently increases the efficiency of biocatalysis even further.
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Affiliation(s)
- Christoph
K. Winkler
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße
28, 8010 Graz, Austria
| | - Joerg H. Schrittwieser
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße
28, 8010 Graz, Austria
| | - Wolfgang Kroutil
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße
28, 8010 Graz, Austria
- Field
of Excellence BioHealth − University of Graz, 8010 Graz, Austria
- BioTechMed
Graz, 8010 Graz, Austria
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14
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Toplak M, Matthews A, Teufel R. The devil is in the details: The chemical basis and mechanistic versatility of flavoprotein monooxygenases. Arch Biochem Biophys 2020; 698:108732. [PMID: 33358998 DOI: 10.1016/j.abb.2020.108732] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/15/2020] [Accepted: 12/19/2020] [Indexed: 02/07/2023]
Abstract
The ubiquitous flavoenzymes commonly catalyze redox chemistry such as the monooxygenation of organic substrates and are both widely utilized in nature (e.g., in primary and secondary metabolism) and of significant industrial interest. In this work, we highlight the structural and mechanistic characteristics of the distinct types of flavoprotein monooxygenases (FPMOs). We thereby illustrate the chemical basis of FPMO catalysis, which enables reactions such as (aromatic) hydroxylation, epoxidation, (de)halogenation, heteroatom oxygenation, Baeyer-Villiger oxidation, α-hydroxylation of ketones, or non-oxidative carbon-hetero bond cleavage. This seemingly unmatched versatility in oxygenation chemistry results from extensive fine-tuning and regiospecific functionalization of the flavin cofactor that is tightly controlled by the surrounding protein matrix. Accordingly, FPMOs steer the formation of covalent flavin-oxygen adducts for oxygen transfer in the form of the classical flavin-C4a-(hydro)peroxide or the recently discovered N5-functionalized flavins (i.e. the flavin-N5-oxide and the flavin-N5-peroxide), while in rare cases covalent oxygen adduct formation may be foregone entirely. Finally, we speculate about hitherto undiscovered flavin-mediated oxygenation reactions and compare FPMOs to cytochrome P450 monooxygenases, before addressing open questions and challenges for the future investigation of FPMOs.
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Affiliation(s)
- Marina Toplak
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Arne Matthews
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Robin Teufel
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany.
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15
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Kamathewatta NJB, Deay DO, Karaca BT, Seibold S, Nguyen TM, Tomás B, Richter ML, Berrie CL, Tamerler C. Self-Immobilized Putrescine Oxidase Biocatalyst System Engineered with a Metal Binding Peptide. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:11908-11917. [PMID: 32921059 DOI: 10.1021/acs.langmuir.0c01986] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Flavin oxidases are valuable biocatalysts for the oxidative synthesis of a wide range of compounds, while at the same time reduce oxygen to hydrogen peroxide. Compared to other redox enzymes, their ability to use molecular oxygen as an electron acceptor offers a relatively simple system that does not require a dissociable coenzyme. As such, they are attractive targets for adaptation as cost-effective biosensor elements. Their functional immobilization on surfaces offers unique opportunities to expand their utilization for a wide range of applications. Genetically engineered peptides have been demonstrated as enablers of the functional assembly of biomolecules at solid material interfaces. Once identified as having a high affinity for the material of interest, these peptides can provide a single step bioassembly process with orientation control, a critical parameter for functional immobilization of the enzymes. In this study, for the first time, we explored the bioassembly of a putrescine oxidase enzyme using a gold binding peptide tag. The enzyme was genetically engineered to incorporate a gold binding peptide with an expectation of an effective display of the peptide tag to interact with the gold surface. In this work, the functional activity and expression were investigated, along with the selectivity of the binding of the peptide-tagged enzyme. The fusion enzyme was characterized using multiple techniques, including protein electrophoresis, enzyme activity, and microscopy and spectroscopic methods, to verify the functional expression of the tagged protein with near-native activity. Binding studies using quartz crystal microbalance (QCM), nanoparticle binding studies, and atomic force microscopy studies were used to address the selectivity of the binding through the peptide tag. Surface binding AFM studies show that the binding was selective for gold. Quartz crystal microbalance studies show a strong increase in the affinity of the peptide-tagged protein over the native enzyme, while activity assays of protein bound to nanoparticles provide evidence that the enzyme retained catalytic activity when immobilized. In addition to showing selectivity, AFM images show significant differences in the height of the molecules when immobilized through the peptide tag compared to immobilization of the native enzyme, indicating differences in orientation of the bound enzyme when attached via the affinity tag. Controlling the orientation of surface-immobilized enzymes would further improve their enzymatic activity and impact diverse applications, including oxidative biocatalysis, biosensors, biochips, and biofuel production.
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Affiliation(s)
| | - Dwight O Deay
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Banu Taktak Karaca
- Institute for Bioengineering Research, University of Kansas, Lawrence, Kansas 66045, United States
- Department of Molecular Biology and Genetics, Biruni University, İstanbul 34010, Turkey
| | - Steve Seibold
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Tyler M Nguyen
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Brandon Tomás
- Institute for Bioengineering Research, University of Kansas, Lawrence, Kansas 66045, United States
- Department of Mechanical Engineering, University of Kansas, Lawrence, Kansas 66045, United States
| | - Mark L Richter
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Cindy L Berrie
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
- Institute for Bioengineering Research, University of Kansas, Lawrence, Kansas 66045, United States
| | - Candan Tamerler
- Institute for Bioengineering Research, University of Kansas, Lawrence, Kansas 66045, United States
- Bioengineering Program, University of Kansas, Lawrence, Kansas 66045, United States
- Department of Mechanical Engineering, University of Kansas, Lawrence, Kansas 66045, United States
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16
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Cui C, Lin H, Pu W, Guo C, Liu Y, Pei XQ, Wu ZL. Asymmetric Epoxidation and Sulfoxidation Catalyzed by a New Styrene Monooxygenase from Bradyrhizobium. Appl Biochem Biotechnol 2020; 193:65-78. [PMID: 32808246 DOI: 10.1007/s12010-020-03413-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 08/12/2020] [Indexed: 10/23/2022]
Abstract
Asymmetric epoxidation catalyzed with styrene monooxygenase (SMO) is a powerful enzymatic process producing enantiopure styrene epoxide derivatives. To establish a more diversified reservoir of SMOs, a new SMO from Bradyrhizobium sp. ORS 375, named BrSMO, was mined from the database and characterized. BrSMO was constituted of an epoxygenase component of 415 amino acid residues and an NADH-dependent flavin reductase component of 175 residues. BrSMO catalyzed the epoxidation of styrene and 7 more styrene derivatives, yielding the corresponding (S)-epoxides with excellent enantiomeric excesses (95- > 99% ee), with the highest activity achieved for styrene. BrSMO also catalyzed the asymmetric sulfoxidation of 7 sulfides, producing the corresponding (R)-sulfoxides (20-90% ee) with good yields.
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Affiliation(s)
- Can Cui
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Lin
- College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China.
| | - Wei Pu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Guo
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yan Liu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiao-Qiong Pei
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Zhong-Liu Wu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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17
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Beaupre BA, Reabe KR, Roman JV, Moran GR. Hydrogen movements in the oxidative half-reaction of kynurenine 3-monooxygenase from Pseudomonas fluorescens reveal the mechanism of hydroxylation. Arch Biochem Biophys 2020; 690:108474. [PMID: 32687799 DOI: 10.1016/j.abb.2020.108474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/08/2020] [Accepted: 06/17/2020] [Indexed: 11/30/2022]
Abstract
Kynurenine 3-monoxygenase (KMO) catalyzes the conversion of l-kynurenine (L-Kyn) to 3-hydroxykynurenine (3-OHKyn) in the pathway for tryptophan catabolism. We have investigated the effects of pH and deuterium substitution on the oxidative half-reaction of KMO from P. fluorescens (PfKMO). The three phases observed during the oxidative half reaction are formation of the hydroperoxyflavin, hydroxylation and product release. The measured rate constants for these phases proved largely unchanging with pH, suggesting that the KMO active site is insulated from exchange with solvent during catalysis. A solvent inventory study indicated that a solvent isotope effect of 2-3 is observed for the hydroxylation phase and that two or more protons are in flight during this step. An inverse isotope effect of 0.84 ± 0.01 on the rate constant for the hydroxylation step with ring perdeutero-L-Kyn as a substrate indicates a shift from sp2 to sp3 hybridization in the transition state leading to the formation of a non-aromatic intermediate. The pH dependence of transient state data collected for the substrate analog meta-nitrobenzoylalanine indicate that groups proximal to the hydroperoxyflavin are titrated in the range pH 5-8.5 and can be described by a pKa of 8.8. That higher pH values do not slow the rate of hydroxylation precludes that the pKa measured pertains to the proton of the hydroperoxflavin. Together, these observations indicate that the C4a-hydroperoxyflavin has a pKa ≫ 8.5, that a non-aromatic species is the immediate product of hydroxylation and that at least two solvent derived protons are in-flight during oxygen insertion to the substrate aromatic ring. A unifying mechanistic proposal for these observations is proposed.
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Affiliation(s)
- Brett A Beaupre
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Karen R Reabe
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, WI, 53211-3029, USA
| | - Joseph V Roman
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Graham R Moran
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA.
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18
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Enantioselective Epoxidation by Flavoprotein Monooxygenases Supported by Organic Solvents. Catalysts 2020. [DOI: 10.3390/catal10050568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Styrene and indole monooxygenases (SMO and IMO) are two-component flavoprotein monooxygenases composed of a nicotinamide adenine dinucleotide (NADH)-dependent flavin adenine dinucleotide (FAD)-reductase (StyB or IndB) and a monooxygenase (StyA or IndA). The latter uses reduced FAD to activate oxygen and to oxygenate the substrate while releasing water. We circumvented the need for the reductase by direct FAD reduction in solution using the NAD(P)H-mimic 1-benzyl-1,4-dihydronicotinamide (BNAH) to fuel monooxygenases without NADH requirement. Herein, we report on the hitherto unknown solvent tolerance for the indole monooxygenase from Gemmobacter nectariphilus DSM15620 (GnIndA) and the styrene monooxygenase from Gordonia rubripertincta CWB2 (GrStyA). These enzymes were shown to convert bulky and rather hydrophobic styrene derivatives in the presence of organic cosolvents. Subsequently, BNAH-driven biotransformation was furthermore optimized with regard to the applied cosolvent and its concentration as well as FAD and BNAH concentration. We herein demonstrate that GnIndA and GrStyA enable selective epoxidations of allylic double bonds (up to 217 mU mg−1) in the presence of organic solvents such as tetrahydrofuran, acetonitrile, or several alcohols. Notably, GnIndA was found to resist methanol concentrations up to 25 vol.%. Furthermore, a diverse substrate preference was determined for both enzymes, making their distinct use very interesting. In general, our results seem representative for many IMOs as was corroborated by in silico mutagenetic studies.
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19
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Manenda MS, Picard MÈ, Zhang L, Cyr N, Zhu X, Barma J, Pascal JM, Couture M, Zhang C, Shi R. Structural analyses of the Group A flavin-dependent monooxygenase PieE reveal a sliding FAD cofactor conformation bridging OUT and IN conformations. J Biol Chem 2020; 295:4709-4722. [PMID: 32111738 DOI: 10.1074/jbc.ra119.011212] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/26/2020] [Indexed: 02/02/2023] Open
Abstract
Group A flavin-dependent monooxygenases catalyze the cleavage of the oxygen-oxygen bond of dioxygen, followed by the incorporation of one oxygen atom into the substrate molecule with the aid of NADPH and FAD. These flavoenzymes play an important role in many biological processes, and their most distinct structural feature is the choreographed motions of flavin, which typically adopts two distinct conformations (OUT and IN) to fulfill its function. Notably, these enzymes seem to have evolved a delicate control system to avoid the futile cycle of NADPH oxidation and FAD reduction in the absence of substrate, but the molecular basis of this system remains elusive. Using protein crystallography, size-exclusion chromatography coupled to multi-angle light scattering (SEC-MALS), and small-angle X-ray scattering (SEC-SAXS) and activity assay, we report here a structural and biochemical characterization of PieE, a member of the Group A flavin-dependent monooxygenases involved in the biosynthesis of the antibiotic piericidin A1. This analysis revealed that PieE forms a unique hexamer. Moreover, we found, to the best of our knowledge for the first time, that in addition to the classical OUT and IN conformations, FAD possesses a "sliding" conformation that exists in between the OUT and IN conformations. This observation sheds light on the underlying mechanism of how the signal of substrate binding is transmitted to the FAD-binding site to efficiently initiate NADPH binding and FAD reduction. Our findings bridge a gap currently missing in the orchestrated order of chemical events catalyzed by this important class of enzymes.
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Affiliation(s)
- Mahder S Manenda
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Marie-Ève Picard
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Liping Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Normand Cyr
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Xiaojun Zhu
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Julie Barma
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - John M Pascal
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Manon Couture
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Changsheng Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Rong Shi
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada .,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
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20
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Heine T, Großmann C, Hofmann S, Tischler D. Indigoid dyes by group E monooxygenases: mechanism and biocatalysis. Biol Chem 2020; 400:939-950. [PMID: 30844759 DOI: 10.1515/hsz-2019-0109] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/19/2019] [Indexed: 11/15/2022]
Abstract
Since ancient times, people have been attracted by dyes and they were a symbol of power. Some of the oldest dyes are indigo and its derivative Tyrian purple, which were extracted from plants and snails, respectively. These 'indigoid dyes' were and still are used for coloration of textiles and as a food additive. Traditional Chinese medicine also knows indigoid dyes as pharmacologically active compounds and several studies support their effects. Further, they are interesting for future technologies like organic electronics. In these cases, especially the indigo derivatives are of interest but unfortunately hardly accessible by chemical synthesis. In recent decades, more and more enzymes have been discovered that are able to produce these indigoid dyes and therefore have gained attention from the scientific community. In this study, group E monooxygenases (styrene monooxygenase and indole monooxygenase) were used for the selective oxygenation of indole (derivatives). It was possible for the first time to show that the product of the enzymatic reaction is an epoxide. Further, we synthesized and extracted indigoid dyes and could show that there is only minor by-product formation (e.g. indirubin or isoindigo). Thus, group E monooxygenase can be an alternative biocatalyst for the biosynthesis of indigoid dyes.
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Affiliation(s)
- Thomas Heine
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, D-09599 Freiberg, Germany
| | - Carolin Großmann
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, D-09599 Freiberg, Germany
| | - Sarah Hofmann
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, D-09599 Freiberg, Germany
| | - Dirk Tischler
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, D-09599 Freiberg, Germany.,Microbial Biotechnology, Ruhr University Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
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21
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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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22
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Guarneri A, Westphal AH, Leertouwer J, Lunsonga J, Franssen MCR, Opperman DJ, Hollmann F, Berkel WJH, Paul CE. Flavoenzyme‐mediated Regioselective Aromatic Hydroxylation with Coenzyme Biomimetics. ChemCatChem 2020. [DOI: 10.1002/cctc.201902044] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Alice Guarneri
- Laboratory of Organic ChemistryWageningen University Stippeneng 4 Wageningen 6708 WE The Netherlands
| | - Adrie H. Westphal
- Laboratory of BiochemistryWageningen University Stippeneng 4 Wageningen 6708 WE The Netherlands
| | - Jos Leertouwer
- Department of BiotechnologyDelft University of Technology Van der Maasweg 9 Delft 2629 HZ The Netherlands
| | - Joy Lunsonga
- Laboratory of Organic ChemistryWageningen University Stippeneng 4 Wageningen 6708 WE The Netherlands
| | - Maurice C. R. Franssen
- Laboratory of Organic ChemistryWageningen University Stippeneng 4 Wageningen 6708 WE The Netherlands
| | - Diederik J. Opperman
- Department of BiotechnologyUniversity of the Free State 205 Nelson Mandela Drive Bloemfontein 9300 South Africa
| | - Frank Hollmann
- Department of BiotechnologyDelft University of Technology Van der Maasweg 9 Delft 2629 HZ The Netherlands
| | - Willem J. H. Berkel
- Laboratory of Food ChemistryWageningen University Bornse Weilanden 9 Wageningen 6708 WG The Netherlands
| | - Caroline E. Paul
- Department of BiotechnologyDelft University of Technology Van der Maasweg 9 Delft 2629 HZ The Netherlands
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23
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Willrodt C, Gröning JAD, Nerke P, Koch R, Scholtissek A, Heine T, Schmid A, Bühler B, Tischler D. Highly Efficient Access to (
S
)‐Sulfoxides Utilizing a Promiscuous Flavoprotein Monooxygenase in a Whole‐Cell Biocatalyst Format. ChemCatChem 2020. [DOI: 10.1002/cctc.201901894] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Christian Willrodt
- Department Solar Materials Helmholtz Center for Environmental Research GmbH – UFZ Permoser Str. 15 Leipzig 04138 Germany
- Present address: BASF SE Carl-Bosch-Straße 38 Ludwigshafen am Rhein 67063 Germany
| | - Janosch A. D. Gröning
- Environmental Microbiology Group Institute of Biosciences TU Bergakademie Freiberg Leipziger Str. 29 Freiberg 09599 Germany
- Present address: Institut für Mikrobiologie Universität Stuttgart Allmandring 31 Stuttgart 70569 Germany
| | - Philipp Nerke
- Department Solar Materials Helmholtz Center for Environmental Research GmbH – UFZ Permoser Str. 15 Leipzig 04138 Germany
| | - Rainhard Koch
- Engineering and Technology Bayer AG Kaiser-Wilhelm Allee 3 Leverkusen 51373 Germany
| | - Anika Scholtissek
- Environmental Microbiology Group Institute of Biosciences TU Bergakademie Freiberg Leipziger Str. 29 Freiberg 09599 Germany
| | - Thomas Heine
- Environmental Microbiology Group Institute of Biosciences TU Bergakademie Freiberg Leipziger Str. 29 Freiberg 09599 Germany
| | - Andreas Schmid
- Department Solar Materials Helmholtz Center for Environmental Research GmbH – UFZ Permoser Str. 15 Leipzig 04138 Germany
| | - Bruno Bühler
- Department Solar Materials Helmholtz Center for Environmental Research GmbH – UFZ Permoser Str. 15 Leipzig 04138 Germany
| | - Dirk Tischler
- Environmental Microbiology Group Institute of Biosciences TU Bergakademie Freiberg Leipziger Str. 29 Freiberg 09599 Germany
- Microbial Biotechnology Ruhr University Bochum Universitätsstr. 150 Bochum 44801 Germany
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24
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Tischler D, Kumpf A, Eggerichs D, Heine T. Styrene monooxygenases, indole monooxygenases and related flavoproteins applied in bioremediation and biocatalysis. FLAVIN-DEPENDENT ENZYMES: MECHANISMS, STRUCTURES AND APPLICATIONS 2020; 47:399-425. [DOI: 10.1016/bs.enz.2020.05.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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25
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Directed evolution of carbon–hydrogen bond activating enzymes. Curr Opin Biotechnol 2019; 60:29-38. [DOI: 10.1016/j.copbio.2018.12.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/19/2018] [Accepted: 12/03/2018] [Indexed: 12/26/2022]
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26
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Heine T, Scholtissek A, Hofmann S, Koch R, Tischler D. Accessing Enantiopure Epoxides and Sulfoxides: Related Flavin‐Dependent Monooxygenases Provide Reversed Enantioselectivity. ChemCatChem 2019. [DOI: 10.1002/cctc.201901353] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Thomas Heine
- Institute of BiosciencesTU Bergakademie Freiberg Freiberg 09599 Germany
| | - Anika Scholtissek
- Institute of BiosciencesTU Bergakademie Freiberg Freiberg 09599 Germany
| | - Sarah Hofmann
- Institute of BiosciencesTU Bergakademie Freiberg Freiberg 09599 Germany
| | - Rainhard Koch
- Engineering & TechnologyBayer AG Leverkusen 51368 Germany
| | - Dirk Tischler
- Institute of BiosciencesTU Bergakademie Freiberg Freiberg 09599 Germany
- Microbial BiotechnologyRuhr University Bochum Bochum 44780 Germany
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27
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Pongpamorn P, Watthaisong P, Pimviriyakul P, Jaruwat A, Lawan N, Chitnumsub P, Chaiyen P. Identification of a Hotspot Residue for Improving the Thermostability of a Flavin‐Dependent Monooxygenase. Chembiochem 2019; 20:3020-3031. [DOI: 10.1002/cbic.201900413] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Pornkanok Pongpamorn
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Pratchaya Watthaisong
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Panu Pimviriyakul
- Department of BiotechnologyFaculty of Engineering and Industrial TechnologySilpakorn University 6 Rajamankha Nai Road Nakornpathom 73000 Thailand
| | - Aritsara Jaruwat
- National Center for Genetic Engineering and Biotechnology 113 Thailand Science Park Paholyothin Road Klong 1 Klong Luang Pathumthani 12120 Thailand
| | - Narin Lawan
- Department of ChemistryFaculty of ScienceChiang Mai University Chiang Mai 50200 Thailand
| | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology 113 Thailand Science Park Paholyothin Road Klong 1 Klong Luang Pathumthani 12120 Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
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Özkılıç Y, Tüzün NŞ. Mechanism of Kynurenine 3-Monooxygenase-Catalyzed Hydroxylation Reaction: A Quantum Cluster Approach. J Phys Chem A 2019; 123:3149-3159. [PMID: 30888816 DOI: 10.1021/acs.jpca.8b11831] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The mechanism of the hydroxylation reaction between l-Kyn and model flavin adenine dinucleotide (FAD)-hydroperoxide was investigated via density functional theory (DFT) calculations in the absence and in the presence of the kynurenine 3-monooxygenase (KMO) enzyme by considering possible pathways that can lead to the product 3-hydroxykynurenine (3-HK). Crystal structure (pdb code: 5NAK )-based calculations involved a quantum cluster model in which the active site of the enzyme with the substrate l-Kyn was represented with 348 atoms. According to the deduced mechanism, KMO-catalyzed hydroxylation reaction takes place with four transformations. In the initial transition state, FAD delivers its peroxy hydroxyl to the l-Kyn ring, creating an sp3-hybridized carbon center. Then, the hydrogen on the hydroxyl moiety is immediately transferred back to the proximal oxygen that remained on FAD. These consequent transformations are in line with the somersault rearrangement previously described for similar enzymatic systems. The second step corresponds to a hydride shift from the sp3-hybridized carbon of the substrate ring to its adjacent carbon, producing the keto form of 3-HK. Then, keto-3-HK is transformed into its enol form (3-HK) with a water-assisted tautomerization. Lastly, FAD is oxidized with a water-assisted dehydration, which also involves 3-HK as a catalyst. In the proposed pathway, Asn54, Pro318, and a crystal water molecule were seen to play significant roles in the proton relays. The energies obtained via the cluster approach were calculated at the B3LYP/6-311+G(2d,2p)//B3LYP/6-31G(d,p) level with solvation (polarizable continuum model) and dispersion (DFT-D3(BJ)) corrections.
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Affiliation(s)
- Yılmaz Özkılıç
- Department of Chemistry, Faculty of Science and Letters , Istanbul Technical University , Maslak, Istanbul 34469 , Turkey
| | - Nurcan Ş Tüzün
- Department of Chemistry, Faculty of Science and Letters , Istanbul Technical University , Maslak, Istanbul 34469 , Turkey
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Nakamoto KD, Perkins SW, Campbell RG, Bauerle MR, Gerwig TJ, Gerislioglu S, Wesdemiotis C, Anderson MA, Hicks KA, Snider MJ. Mechanism of 6-Hydroxynicotinate 3-Monooxygenase, a Flavin-Dependent Decarboxylative Hydroxylase Involved in Bacterial Nicotinic Acid Degradation. Biochemistry 2019; 58:1751-1763. [PMID: 30810301 DOI: 10.1021/acs.biochem.8b00969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
6-Hydroxynicotinate 3-monooxygenase (NicC) is a Group A FAD-dependent monooxygenase that catalyzes the decarboxylative hydroxylation of 6-hydroxynicotinic acid (6-HNA) to 2,5-dihydroxypyridine (2,5-DHP) with concomitant oxidation of NADH in nicotinic acid degradation by aerobic bacteria. Two mechanisms for the decarboxylative hydroxylation half-reaction have been proposed [Hicks, K., et al. (2016) Biochemistry 55, 3432-3446]. Results with Bordetella bronchiseptica RB50 NicC here show that a homocyclic analogue of 6-HNA, 4-hydroxybenzoic acid (4-HBA), is decarboxylated and hydroxylated by NicC with a 420-fold lower catalytic efficiency than is 6-HNA. The 13( V/ K), measured with wild-type NicC by isotope ratio mass spectrometry following the natural abundance of 13C in the CO2 product, is inverse for both 6-HNA (0.9989 ± 0.0002) and 4-HBA (0.9942 ± 0.0004) and becomes negligible (0.9999 ± 0.0004) for 5-chloro-6-HNA, an analogue that is 10-fold more catalytically efficient than 6-HNA. Covalently bound 6-HNA complexes of NicC are not observed by mass spectrometry. Comparative steady-state kinetic and Kd6HNA analyses of active site NicC variants (C202A, H211A, H302A, H47E, Y215F, and Y225F) identify Tyr215 and His47 as critical determinants both of 6-HNA binding ( KdY215F/ KdWT > 240; KdH47E/ KdWT > 350) and in coupling rates of 2,5-DHP and NAD+ product formation ([2,5-DHP]/[NAD+] = 1.00 (WT), 0.005 (Y215F), and 0.07 (H47E)]. Results of these functional analyses are in accord with an electrophilic aromatic substitution reaction mechanism in which His47-Tyr215 may serve as the general base to catalyze substrate hydroxylation and refine the structural model for substrate binding by NicC.
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Affiliation(s)
- Kent D Nakamoto
- Department of Chemistry , The College of Wooster , Wooster , Ohio 44691 , United States
| | - Scott W Perkins
- Department of Chemistry , The College of Wooster , Wooster , Ohio 44691 , United States
| | - Ryan G Campbell
- Department of Chemistry , The College of Wooster , Wooster , Ohio 44691 , United States
| | - Matthew R Bauerle
- Department of Chemistry , The College of Wooster , Wooster , Ohio 44691 , United States
| | - Tyler J Gerwig
- Department of Chemistry , The College of Wooster , Wooster , Ohio 44691 , United States
| | - Selim Gerislioglu
- Department of Chemistry , University of Akron , Akron , Ohio 44325 , United States
| | - Chrys Wesdemiotis
- Department of Chemistry , University of Akron , Akron , Ohio 44325 , United States
| | - Mark A Anderson
- Institute for Enzyme Research, Department of Biochemistry , University of Wisconsin , Madison , Wisconsin 53726 , United States
| | - Katherine A Hicks
- Department of Chemistry , The State University of New York College at Cortland , Cortland , New York 13045 , United States
| | - Mark J Snider
- Department of Chemistry , The College of Wooster , Wooster , Ohio 44691 , United States
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Tolmie C, Smit MS, Opperman DJ. Native roles of Baeyer–Villiger monooxygenases in the microbial metabolism of natural compounds. Nat Prod Rep 2019; 36:326-353. [DOI: 10.1039/c8np00054a] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Baeyer–Villiger monooxygenases function in the primary metabolism of atypical carbon sources, as well as the synthesis of complex microbial metabolites.
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Affiliation(s)
- Carmien Tolmie
- Department of Biotechnology
- University of the Free State
- Bloemfontein
- South Africa
| | - Martha S. Smit
- Department of Biotechnology
- University of the Free State
- Bloemfontein
- South Africa
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31
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Westphal AH, Tischler D, Heinke F, Hofmann S, Gröning JAD, Labudde D, van Berkel WJH. Pyridine Nucleotide Coenzyme Specificity of p-Hydroxybenzoate Hydroxylase and Related Flavoprotein Monooxygenases. Front Microbiol 2018; 9:3050. [PMID: 30631308 PMCID: PMC6315137 DOI: 10.3389/fmicb.2018.03050] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/27/2018] [Indexed: 12/03/2022] Open
Abstract
p-Hydroxybenzoate hydroxylase (PHBH; EC 1.14.13.2) is a microbial group A flavoprotein monooxygenase that catalyzes the ortho-hydroxylation of 4-hydroxybenzoate to 3,4-dihydroxybenzoate with the stoichiometric consumption of NAD(P)H and oxygen. PHBH and related enzymes lack a canonical NAD(P)H-binding domain and the way they interact with the pyridine nucleotide coenzyme has remained a conundrum. Previously, we identified a surface exposed protein segment of PHBH from Pseudomonas fluorescens involved in NADPH binding. Here, we report the first amino acid sequences of NADH-preferring PHBHs and a phylogenetic analysis of putative PHBHs identified in currently available bacterial genomes. It was found that PHBHs group into three clades consisting of NADPH-specific, NAD(P)H-dependent and NADH-preferring enzymes. The latter proteins frequently occur in Actinobacteria. To validate the results, we produced several putative PHBHs in Escherichia coli and confirmed their predicted coenzyme preferences. Based on phylogeny, protein energy profiling and lifestyle of PHBH harboring bacteria we propose that the pyridine nucleotide coenzyme specificity of PHBH emerged through adaptive evolution and that the NADH-preferring enzymes are the older versions of PHBH. Structural comparison and distance tree analysis of group A flavoprotein monooxygenases indicated that a similar protein segment as being responsible for the pyridine nucleotide coenzyme specificity of PHBH is involved in determining the pyridine nucleotide coenzyme specificity of the other group A members.
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Affiliation(s)
- Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, Netherlands
| | - Dirk Tischler
- Interdisziplinäres Ökologisches Zentrum, Technische Universität Bergakademie Freiberg, Freiberg, Germany
| | - Florian Heinke
- Bioinformatics Group Mittweida, University of Applied Sciences Mittweida, Mittweida, Germany
| | - Sarah Hofmann
- Interdisziplinäres Ökologisches Zentrum, Technische Universität Bergakademie Freiberg, Freiberg, Germany
| | - Janosch A D Gröning
- Interdisziplinäres Ökologisches Zentrum, Technische Universität Bergakademie Freiberg, Freiberg, Germany
| | - Dirk Labudde
- Bioinformatics Group Mittweida, University of Applied Sciences Mittweida, Mittweida, Germany
| | - Willem J H van Berkel
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, Netherlands
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32
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Heine T, van Berkel WJH, Gassner G, van Pée KH, Tischler D. Two-Component FAD-Dependent Monooxygenases: Current Knowledge and Biotechnological Opportunities. BIOLOGY 2018; 7:biology7030042. [PMID: 30072664 PMCID: PMC6165268 DOI: 10.3390/biology7030042] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 12/11/2022]
Abstract
Flavoprotein monooxygenases create valuable compounds that are of high interest for the chemical, pharmaceutical, and agrochemical industries, among others. Monooxygenases that use flavin as cofactor are either single- or two-component systems. Here we summarize the current knowledge about two-component flavin adenine dinucleotide (FAD)-dependent monooxygenases and describe their biotechnological relevance. Two-component FAD-dependent monooxygenases catalyze hydroxylation, epoxidation, and halogenation reactions and are physiologically involved in amino acid metabolism, mineralization of aromatic compounds, and biosynthesis of secondary metabolites. The monooxygenase component of these enzymes is strictly dependent on reduced FAD, which is supplied by the reductase component. More and more representatives of two-component FAD-dependent monooxygenases have been discovered and characterized in recent years, which has resulted in the identification of novel physiological roles, functional properties, and a variety of biocatalytic opportunities.
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Affiliation(s)
- Thomas Heine
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
| | - Willem J H van Berkel
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - George Gassner
- Department of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA.
| | - Karl-Heinz van Pée
- Allgemeine Biochemie, Technische Universität Dresden, 01062 Dresden, Germany.
| | - Dirk Tischler
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
- Microbial Biotechnology, Ruhr University Bochum, Universitätsstr. 150, 44780 Bochum, Germany.
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Dong J, Fernández‐Fueyo E, Hollmann F, Paul CE, Pesic M, Schmidt S, Wang Y, Younes S, Zhang W. Biocatalytic Oxidation Reactions: A Chemist's Perspective. Angew Chem Int Ed Engl 2018; 57:9238-9261. [PMID: 29573076 PMCID: PMC6099261 DOI: 10.1002/anie.201800343] [Citation(s) in RCA: 267] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Indexed: 01/25/2023]
Abstract
Oxidation chemistry using enzymes is approaching maturity and practical applicability in organic synthesis. Oxidoreductases (enzymes catalysing redox reactions) enable chemists to perform highly selective and efficient transformations ranging from simple alcohol oxidations to stereoselective halogenations of non-activated C-H bonds. For many of these reactions, no "classical" chemical counterpart is known. Hence oxidoreductases open up shorter synthesis routes based on a more direct access to the target products. The generally very mild reaction conditions may also reduce the environmental impact of biocatalytic reactions compared to classical counterparts. In this Review, we critically summarise the most important recent developments in the field of biocatalytic oxidation chemistry and identify the most pressing bottlenecks as well as promising solutions.
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Affiliation(s)
- JiaJia Dong
- Department of BiotechnologyDelft University of Technologyvan der Maasweg 92629HZDelftThe Netherlands
| | - Elena Fernández‐Fueyo
- Department of BiotechnologyDelft University of Technologyvan der Maasweg 92629HZDelftThe Netherlands
| | - Frank Hollmann
- Department of BiotechnologyDelft University of Technologyvan der Maasweg 92629HZDelftThe Netherlands
| | - Caroline E. Paul
- Department of BiotechnologyDelft University of Technologyvan der Maasweg 92629HZDelftThe Netherlands
| | - Milja Pesic
- Department of BiotechnologyDelft University of Technologyvan der Maasweg 92629HZDelftThe Netherlands
| | - Sandy Schmidt
- Department of BiotechnologyDelft University of Technologyvan der Maasweg 92629HZDelftThe Netherlands
| | - Yonghua Wang
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510640P. R. China
| | - Sabry Younes
- Department of BiotechnologyDelft University of Technologyvan der Maasweg 92629HZDelftThe Netherlands
| | - Wuyuan Zhang
- Department of BiotechnologyDelft University of Technologyvan der Maasweg 92629HZDelftThe Netherlands
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Chen X, Tang H, Liu Y, Xu P, Xue Y, Lin K, Cui C. Purification and Initial Characterization of 3-Hydroxybenzoate 6-Hydroxylase From a Halophilic Martelella Strain AD-3. Front Microbiol 2018; 9:1335. [PMID: 30034371 PMCID: PMC6043778 DOI: 10.3389/fmicb.2018.01335] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 05/31/2018] [Indexed: 11/20/2022] Open
Abstract
3-Hydroxybenzoate 6-hydroxylase, an NADH-dependent flavoprotein, can convert 3-hydroxybenzoate which is an important intermediate in the biodegradation of many aromatic hydrocarbons. 3-Hydroxybenzoate is metabolized by entering the TCA cycle through the gentisate pathway. We found a putative 3HB6H gene from a cluster that potentially encodes for gentisic acid degradation from a halophilic Martelella sp. strain AD-3. The corresponding protein was expressed with an N-terminal His-tag and purified by Ni2+-nitrilotriacetic acid affinity chromatography. The protein showed an overexpressed band of about 46 kDa by SDS–PAGE, and it was also proven that the enzyme contains FAD by absorption spectroscopy and HPLC analysis. The optimal activity of 3HB6H from strain AD-3 was observed in phosphate buffer (pH 8.0) at 37°C without salinity (NaCl) and metal salts. The Km values of 3-hydroxybenzoate 6-hydroxylase were determined to be 72.6 ± 10.1 μM and 104.1 ± 18.2 μM for 400 μM NADH and 3-hydroxybenzoate, respectively. Site-directed mutagenesis showed that residues 305, 306 and 308 are important for FAD binding. In addition, we found that Tyr221 and Gln305 of 3HB6H from strain AD-3 are involved in substrate binding.
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Affiliation(s)
- Xin Chen
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yongdi Liu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yong Xue
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Kuangfei Lin
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Changzheng Cui
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
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Dong J, Fernández-Fueyo E, Hollmann F, Paul CE, Pesic M, Schmidt S, Wang Y, Younes S, Zhang W. Biokatalytische Oxidationsreaktionen - aus der Sicht eines Chemikers. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800343] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- JiaJia Dong
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Elena Fernández-Fueyo
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Frank Hollmann
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Caroline E. Paul
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Milja Pesic
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Sandy Schmidt
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Yonghua Wang
- School of Food Science and Engineering; South China University of Technology; Guangzhou 510640 P. R. China
| | - Sabry Younes
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Wuyuan Zhang
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
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36
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Deazaflavins as photocatalysts for the direct reductive regeneration of flavoenzymes. MOLECULAR CATALYSIS 2018. [DOI: 10.1016/j.mcat.2018.04.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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37
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Affiliation(s)
- Yujie Liang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
| | - Jialiang Wei
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
| | - Xu Qiu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
| | - Ning Jiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
- State Key Laboratory of Organometallic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
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38
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Tischler D, Schwabe R, Siegel L, Joffroy K, Kaschabek SR, Scholtissek A, Heine T. VpStyA1/VpStyA2B of Variovorax paradoxus EPS: An Aryl Alkyl Sulfoxidase Rather than a Styrene Epoxidizing Monooxygenase. Molecules 2018; 23:E809. [PMID: 29614810 PMCID: PMC6017014 DOI: 10.3390/molecules23040809] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 03/27/2018] [Accepted: 04/01/2018] [Indexed: 02/08/2023] Open
Abstract
Herein we describe the first representative of an E2-type two-component styrene monooxygenase of proteobacteria. It comprises a single epoxidase protein (VpStyA1) and a two domain protein (VpStyA2B) harboring an epoxidase (A2) and a FAD-reductase (B) domain. It was annotated as VpStyA1/VpStyA2B of Variovorax paradoxus EPS. VpStyA2B serves mainly as NADH:FAD-oxidoreductase. A Km of 33.6 ± 4.0 µM for FAD and a kcat of 22.3 ± 1.1 s-1 were determined and resulted in a catalytic efficiency (kcatKm-1) of 0.64 s-1 μM-1. To investigate its NADH:FAD-oxidoreductase function the linker between A2- and B-domain (AREAV) was mutated. One mutant (AAAAA) showed 18.7-fold higher affinity for FAD (kcatKm-1 of 5.21 s-1 μM-1) while keeping wildtype NADH-affinity and -oxidation activity. Both components, VpStyA2B and VpStyA1, showed monooxygenase activity on styrene of 0.14 U mg-1 and 0.46 U mg-1, as well as on benzyl methyl sulfide of 1.62 U mg-1 and 3.11 U mg-1, respectively. The high sulfoxidase activity was the reason to test several thioanisole-like substrates in biotransformations. VpStyA1 showed high substrate conversions (up to 95% in 2 h) and produced dominantly (S)-enantiomeric sulfoxides of all tested substrates. The AAAAA-mutant showed a 1.6-fold increased monooxygenase activity. In comparison, the GQWCSQY-mutant did neither show monooxygenase nor efficient FAD-reductase activity. Hence, the linker between the two domains of VpStyA2B has effects on the reductase as well as on the monooxygenase performance. Overall, this monooxygenase represents a promising candidate for biocatalyst development and studying natural fusion proteins.
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Affiliation(s)
- Dirk Tischler
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
- Microbial Biotechnology, Ruhr University Bochum, Universitätsstr. 150, 44780 Bochum, Germany.
| | - Ringo Schwabe
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
| | - Lucas Siegel
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
| | - Kristin Joffroy
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
| | - Stefan R Kaschabek
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
| | - Anika Scholtissek
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
| | - Thomas Heine
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
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Oelschlägel M, Zimmerling J, Tischler D. A Review: The Styrene Metabolizing Cascade of Side-Chain Oxygenation as Biotechnological Basis to Gain Various Valuable Compounds. Front Microbiol 2018; 9:490. [PMID: 29623070 PMCID: PMC5874493 DOI: 10.3389/fmicb.2018.00490] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 03/02/2018] [Indexed: 11/16/2022] Open
Abstract
Styrene is one of the most produced and processed chemicals worldwide and is released into the environment during widespread processing. But, it is also produced from plants and microorganisms. The natural occurrence of styrene led to several microbiological strategies to form and also to degrade styrene. One pathway designated as side-chain oxygenation has been reported as a specific route for the styrene degradation among microorganisms. It comprises the following enzymes: styrene monooxygenase (SMO; NADH-consuming and FAD-dependent, two-component system), styrene oxide isomerase (SOI; cofactor independent, membrane-bound protein) and phenylacetaldehyde dehydrogenase (PAD; NAD+-consuming) and allows an intrinsic cofactor regeneration. This specific way harbors a high potential for biotechnological use. Based on the enzymatic steps involved in this degradation route, important reactions can be realized from a large number of substrates which gain access to different interesting precursors for further applications. Furthermore, stereochemical transformations are possible, offering chiral products at high enantiomeric excess. This review provides an actual view on the microbiological styrene degradation followed by a detailed discussion on the enzymes of the side-chain oxygenation. Furthermore, the potential of the single enzyme reactions as well as the respective multi-step syntheses using the complete enzyme cascade are discussed in order to gain styrene oxides, phenylacetaldehydes, or phenylacetic acids (e.g., ibuprofen). Altered routes combining these putative biocatalysts with other enzymes are additionally described. Thus, the substrates spectrum can be enhanced and additional products as phenylethanols or phenylethylamines are reachable. Finally, additional enzymes with similar activities toward styrene and its metabolic intermediates are shown in order to modify the cascade described above or to use these enzyme independently for biotechnological application.
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Affiliation(s)
- Michel Oelschlägel
- Environmental Microbiology Group, Institute of Biosciences, Technische Universität Bergakademie Freiberg, Freiberg, Germany
| | - Juliane Zimmerling
- Environmental Microbiology Group, Institute of Biosciences, Technische Universität Bergakademie Freiberg, Freiberg, Germany
| | - Dirk Tischler
- Environmental Microbiology Group, Institute of Biosciences, Technische Universität Bergakademie Freiberg, Freiberg, Germany
- Microbial Biotechnology, Ruhr University Bochum, Bochum, Germany
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40
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Su T, Su J, Liu S, Zhang C, He J, Huang Y, Xu S, Gu L. Structural and Biochemical Characterization of BdsA from Bacillus subtilis WU-S2B, a Key Enzyme in the "4S" Desulfurization Pathway. Front Microbiol 2018; 9:231. [PMID: 29497411 PMCID: PMC5819316 DOI: 10.3389/fmicb.2018.00231] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/30/2018] [Indexed: 11/13/2022] Open
Abstract
Dibenzothiophene (DBT) and their derivatives, accounting for the major part of the sulfur components in crude oil, make one of the most significant pollution sources. The DBT sulfone monooxygenase BdsA, one of the key enzymes in the “4S” desulfurization pathway, catalyzes the oxidation of DBT sulfone to 2′-hydroxybiphenyl 2-sulfonic acid (HBPSi). Here, we determined the crystal structure of BdsA from Bacillus subtilis WU-S2B, at the resolution of 2.2 Å, and the structure of the BdsA-FMN complex at 2.4 Å. BdsA and the BdsA-FMN complex exist as tetramers. DBT sulfone was placed into the active site by molecular docking. Seven residues (Phe12, His20, Phe56, Phe246, Val248, His316, and Val372) are found to be involved in the binding of DBT sulfone. The importance of these residues is supported by the study of the catalytic activity of the active site variants. Structural analysis and enzyme activity assay confirmed the importance of the right position and orientation of FMN and DBT sulfone, as well as the involvement of Ser139 as a nucleophile in catalysis. This work combined with our previous structure of DszC provides a systematic structural basis for the development of engineered desulfurization enzymes with higher efficiency and stability.
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Affiliation(s)
- Tiantian Su
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China
| | - Jing Su
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China.,Faculty of Light Industry, Province Key Laboratory of Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Shiheng Liu
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China
| | - Conggang Zhang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China
| | - Jing He
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China
| | - Yan Huang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China
| | - Sujuan Xu
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China
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41
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Kim HT, Na BK, Chung J, Kim S, Kwon SK, Cha H, Son J, Cho JM, Hwang KY. Structural Basis for Inhibitor-Induced Hydrogen Peroxide Production by Kynurenine 3-Monooxygenase. Cell Chem Biol 2018; 25:426-438.e4. [PMID: 29429898 DOI: 10.1016/j.chembiol.2018.01.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/17/2017] [Accepted: 01/08/2018] [Indexed: 11/18/2022]
Abstract
Kynurenine 3-monooxygenase (KMO) inhibitors have been developed for the treatment of neurodegenerative disorders. The mechanisms of flavin reduction and hydrogen peroxide production by KMO inhibitors are unknown. Herein, we report the structure of human KMO and crystal structures of Saccharomyces cerevisiae (sc) and Pseudomonas fluorescens (pf) KMO with Ro 61-8048. Proton transfer in the hydrogen bond network triggers flavin reduction in p-hydroxybenzoate hydroxylase, but the mechanism triggering flavin reduction in KMO is different. Conformational changes via π-π interactions between the loop above the flavin and substrate or non-substrate effectors lead to disorder of the C-terminal α helix in scKMO and shifts of domain III in pfKMO, stimulating flavin reduction. Interestingly, Ro 61-8048 has two different binding modes. It acts as a competitive inhibitor in scKMO and as a non-substrate effector in pfKMO. These findings provide understanding of the catalytic cycle of KMO and insight for structure-based drug design of KMO inhibitors.
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Affiliation(s)
- Hyun Tae Kim
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, Korea; Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Byeong Kwan Na
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, Korea
| | - Jiwoung Chung
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, Korea
| | - Sulhee Kim
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Sool Ki Kwon
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, Korea
| | - Hyunju Cha
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, Korea
| | - Jonghyeon Son
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Joong Myung Cho
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, Korea.
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea.
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42
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Heine T, Scholtissek A, Westphal AH, van Berkel WJH, Tischler D. N-terminus determines activity and specificity of styrene monooxygenase reductases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1770-1780. [PMID: 28888693 DOI: 10.1016/j.bbapap.2017.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/10/2017] [Accepted: 09/05/2017] [Indexed: 10/18/2022]
Abstract
Styrene monooxygenases (SMOs) are two-enzyme systems that catalyze the enantioselective epoxidation of styrene to (S)-styrene oxide. The FADH2 co-substrate of the epoxidase component (StyA) is supplied by an NADH-dependent flavin reductase (StyB). The genome of Rhodococcus opacus 1CP encodes two SMO systems. One system, which we define as E1-type, displays homology to the SMO from Pseudomonas taiwanensis VLB120. The other system, originally reported as a fused system (RoStyA2B), is defined as E2-type. Here we found that E1-type RoStyB is inhibited by FMN, while RoStyA2B is known to be active with FMN. To rationalize the observed specificity of RoStyB for FAD, we generated an artificial reductase, designated as RoStyBart, in which the first 22 amino acid residues of RoStyB were joined to the reductase part of RoStyA2B, while the oxygenase part (A2) was removed. RoStyBart mainly purified as apo-protein and mimicked RoStyB in being inhibited by FMN. Pre-incubation with FAD yielded a turnover number at 30°C of 133.9±3.5s-1, one of the highest rates observed for StyB reductases. RoStyBart holo-enzyme switches to a ping-pong mechanism and fluorescence analysis indicated for unproductive binding of FMN to the second (co-substrate) binding site. In summary, it is shown for the first time that optimization of the N-termini of StyB reductases allows the evolution of their activity and specificity.
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Affiliation(s)
- Thomas Heine
- Environmental Microbiology, Interdisciplinary Ecological Center, TU Bergakadmie Freiberg, Leipziger Straße 29, 09599 Freiberg, Germany; Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - Anika Scholtissek
- Environmental Microbiology, Interdisciplinary Ecological Center, TU Bergakadmie Freiberg, Leipziger Straße 29, 09599 Freiberg, Germany; Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Willem J H van Berkel
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dirk Tischler
- Environmental Microbiology, Interdisciplinary Ecological Center, TU Bergakadmie Freiberg, Leipziger Straße 29, 09599 Freiberg, Germany.
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43
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Montersino S, Te Poele E, Orru R, Westphal AH, Barendregt A, Heck AJR, van der Geize R, Dijkhuizen L, Mattevi A, van Berkel WJH. 3-Hydroxybenzoate 6-Hydroxylase from Rhodococcus jostii RHA1 Contains a Phosphatidylinositol Cofactor. Front Microbiol 2017; 8:1110. [PMID: 28670303 PMCID: PMC5472690 DOI: 10.3389/fmicb.2017.01110] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 05/31/2017] [Indexed: 01/05/2023] Open
Abstract
3-Hydroxybenzoate 6-hydroxylase (3HB6H, EC 1.13.14.26) is a FAD-dependent monooxygenase involved in the catabolism of aromatic compounds in soil microorganisms. 3HB6H is unique among flavoprotein hydroxylases in that it harbors a phospholipid ligand. The purified protein obtained from expressing the gene encoding 3HB6H from Rhodococcus jostii RHA1 in the host Escherichia coli contains a mixture of phosphatidylglycerol and phosphatidylethanolamine, which are the major constituents of E. coli's cytoplasmic membrane. Here, we purified 3HB6H (RjHB6H) produced in the host R. jostii RHA#2 by employing a newly developed actinomycete expression system. Biochemical and biophysical analysis revealed that Rj3HB6H possesses similar catalytic and structural features as 3HB6H, but now contains phosphatidylinositol, which is a specific constituent of actinomycete membranes. Native mass spectrometry suggests that the lipid cofactor stabilizes monomer-monomer contact. Lipid analysis of 3HB6H from Pseudomonas alcaligenes NCIMB 9867 (Pa3HB6H) produced in E. coli supports the conclusion that 3HB6H enzymes have an intrinsic ability to bind phospholipids with different specificity, reflecting the membrane composition of their bacterial host.
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Affiliation(s)
- Stefania Montersino
- Laboratory of Biochemistry, Wageningen University and ResearchWageningen, Netherlands
| | - Evelien Te Poele
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningen, Netherlands
| | - Roberto Orru
- Department of Biology and Biotechnology, University of PaviaPavia, Italy
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University and ResearchWageningen, Netherlands
| | - Arjan Barendregt
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Research, Utrecht UniversityUtrecht, Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Research, Utrecht UniversityUtrecht, Netherlands
| | - Robert van der Geize
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningen, Netherlands
| | - Lubbert Dijkhuizen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningen, Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of PaviaPavia, Italy
| | - Willem J H van Berkel
- Laboratory of Biochemistry, Wageningen University and ResearchWageningen, Netherlands
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44
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Chenprakhon P, Dhammaraj T, Chantiwas R, Chaiyen P. Hydroxylation of 4-hydroxyphenylethylamine derivatives by R263 variants of the oxygenase component of p -hydroxyphenylacetate-3-hydroxylase. Arch Biochem Biophys 2017; 620:1-11. [DOI: 10.1016/j.abb.2017.03.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 03/09/2017] [Accepted: 03/10/2017] [Indexed: 11/29/2022]
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45
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Crabo AG, Singh B, Nguyen T, Emami S, Gassner GT, Sazinsky MH. Structure and biochemistry of phenylacetaldehyde dehydrogenase from the Pseudomonas putida S12 styrene catabolic pathway. Arch Biochem Biophys 2017; 616:47-58. [PMID: 28153386 PMCID: PMC5318141 DOI: 10.1016/j.abb.2017.01.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 01/03/2017] [Accepted: 01/23/2017] [Indexed: 01/07/2023]
Abstract
Phenylacetaldehyde dehydrogenase catalyzes the NAD+-dependent oxidation of phenylactealdehyde to phenylacetic acid in the styrene catabolic and detoxification pathway of Pseudomonas putida (S12). Here we report the structure and mechanistic properties of the N-terminally histidine-tagged enzyme, NPADH. The 2.83 Å X-ray crystal structure is similar in fold to sheep liver cytosolic aldehyde dehydrogenase (ALDH1), but has unique set of intersubunit interactions and active site tunnel for substrate entrance. In solution, NPADH occurs as 227 kDa homotetramer. It follows a sequential reaction mechanism in which NAD+ serves as both the leading substrate and homotropic allosteric activator. In the absence of styrene monooxygenase reductase, which regenerates NAD+ from NADH in the first step of styrene catabolism, NPADH is inhibited by a ternary complex involving NADH, product, and phenylacetaldehyde, substrate. Each oligomerization domain of NPADH contains a six-residue insertion that extends this loop over the substrate entrance tunnel of a neighboring subunit, thereby obstructing the active site of the adjacent subunit. This feature could be an important factor in the homotropic activation and product inhibition mechanisms. Compared to ALDH1, the substrate channel of NPADH is narrower and lined with more aromatic residues, suggesting a means for enhancing substrate specificity.
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46
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Heine T, Tucker K, Okonkwo N, Assefa B, Conrad C, Scholtissek A, Schlömann M, Gassner G, Tischler D. Engineering Styrene Monooxygenase for Biocatalysis: Reductase-Epoxidase Fusion Proteins. Appl Biochem Biotechnol 2016; 181:1590-1610. [PMID: 27830466 DOI: 10.1007/s12010-016-2304-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/24/2016] [Indexed: 11/25/2022]
Abstract
The enantioselective epoxidation of styrene and related compounds by two-component styrene monooxygenases (SMOs) has targeted these enzymes for development as biocatalysts. In the present work, we prepare genetically engineered fusion proteins that join the C-terminus of the epoxidase (StyA) to the N-terminus of the reductase (StyB) through a linker peptide and demonstrate their utility as biocatalysts in the synthesis of Tyrain purple and other indigoid dyes. A single-vector expression system offers a simplified platform for transformation and expansion of the catalytic function of styrene monooxygenases, and the resulting fusion proteins are self-regulated and couple efficiently NADH oxidation to styrene epoxidation. We find that the reductase domain proceeds through a sequential ternary-complex mechanism at low FAD concentration and a double-displacement mechanism at higher concentrations of FAD. Single-turnover studies indicate an observed rate constant for FAD-to-FAD hydride transfer of ~8 s-1. This step is rate limiting in the styrene epoxidation reaction and helps to ensure that flavin reduction and styrene epoxidation reactions proceed without wasteful side reactions. Comparison of the reductase activity of the fusion proteins with the naturally occurring reductase, SMOB, and N-terminally histidine-tagged reductase, NSMOB, suggests that the observed changes in catalytic mechanism are due in part to an increase in flavin-binding affinity associated with the N-terminal extension of the reductase.
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Affiliation(s)
| | | | - Nonye Okonkwo
- San Francisco State University, San Francisco, CA, USA
| | | | | | | | | | | | - Dirk Tischler
- TU Bergakademie Freiberg, Freiberg, Germany.
- San Francisco State University, San Francisco, CA, USA.
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47
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Dhammaraj T, Pinthong C, Visitsatthawong S, Tongsook C, Surawatanawong P, Chaiyen P. A Single-Site Mutation at Ser146 Expands the Reactivity of the Oxygenase Component of p-Hydroxyphenylacetate 3-Hydroxylase. ACS Chem Biol 2016; 11:2889-2896. [PMID: 27541707 DOI: 10.1021/acschembio.6b00402] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The oxygenase component (C2) of p-hydroxyphenylacetate (4-HPA) 3-hydroxylase (HPAH) from Acinetobacter baumannii catalyzes the hydroxylation of various phenolic acids. In this report, we found that substitution of a residue close to the phenolic group binding site to yield the S146A variant resulted in an enzyme that is more effective than the wild-type in catalyzing the hydroxylation of 4-aminophenylacetate (4-APA). Product yields for both wild-type and S146A enzymes are better at lower pH values. Multiple turnover reactions of the wild-type and S146A enzymes indicate that both enzymes first hydroxylate 3-APA to give 3-hydroxy-4-aminophenylacetate (3-OH-4-APA), which is further hydroxylated to give 3,5-dihydroxy-4-aminophenylacetate, similar to the reaction of C2 with 4-HPA. Stopped-flow experiments showed that 4-APA can only bind to the wild-type enzyme at pH 6.0 and not at pH 9.0, while it can bind to S146A under both pH conditions. Rapid-quench flow results indicate that the wild-type enzyme has low reactivity toward 4-APA hydroxylation, with a hydroxylation rate constant (kOH) for 4-APA of 0.028 s-1 compared to 17 s-1 for 4-HPA, the native substrate. In contrast, for S146A, the hydroxylation rate constants for both substrates are very similar (2.6 s-1 for 4-HPA versus 2.5 s-1 for 4-APA). These data indicate that Ser146 is a key catalytic residue involved in optimizing C2 reactivity toward a phenolic compound. Removing this hydroxyl group expands C2 activity toward a non-natural aniline substrate. This understanding should be helpful for future rational engineering of other two-component flavin-dependent monooxygenases that have this conserved Ser residue.
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Affiliation(s)
- Taweesak Dhammaraj
- Department
of Biochemistry and Center for Excellence in Protein and Enzyme Technology,
Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400, Thailand
| | - Chatchadaporn Pinthong
- Department
of Biochemistry and Center for Excellence in Protein and Enzyme Technology,
Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400, Thailand
- Institute
for Innovative Learning, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Surawit Visitsatthawong
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry,
Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400, Thailand
| | - Chanakan Tongsook
- Department
of Biochemistry and Center for Excellence in Protein and Enzyme Technology,
Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400, Thailand
| | - Panida Surawatanawong
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry,
Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400, Thailand
| | - Pimchai Chaiyen
- Department
of Biochemistry and Center for Excellence in Protein and Enzyme Technology,
Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400, Thailand
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48
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Holtmann D, Hollmann F. The Oxygen Dilemma: A Severe Challenge for the Application of Monooxygenases? Chembiochem 2016; 17:1391-8. [PMID: 27194219 PMCID: PMC5096067 DOI: 10.1002/cbic.201600176] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Indexed: 12/12/2022]
Abstract
Monooxygenases are promising catalysts because they in principle enable the organic chemist to perform highly selective oxyfunctionalisation reactions that are otherwise difficult to achieve. For this, monooxygenases require reducing equivalents, to allow reductive activation of molecular oxygen at the enzymes' active sites. However, these reducing equivalents are often delivered to O2 either directly or via a reduced intermediate (uncoupling), yielding hazardous reactive oxygen species and wasting valuable reducing equivalents. The oxygen dilemma arises from monooxygenases' dependency on O2 and the undesired uncoupling reaction. With this contribution we hope to generate a general awareness of the oxygen dilemma and to discuss its nature and some promising solutions.
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Affiliation(s)
- Dirk Holtmann
- DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486, Frankfurt am Main, Germany
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Julianalaan 136, 2628BL, Delft, The Netherlands.
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49
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Mascotti ML, Juri Ayub M, Furnham N, Thornton JM, Laskowski RA. Chopping and Changing: the Evolution of the Flavin-dependent Monooxygenases. J Mol Biol 2016; 428:3131-46. [PMID: 27423402 PMCID: PMC4981433 DOI: 10.1016/j.jmb.2016.07.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/24/2016] [Accepted: 07/05/2016] [Indexed: 12/21/2022]
Abstract
Flavin-dependent monooxygenases play a variety of key physiological roles and are also very powerful biotechnological tools. These enzymes have been classified into eight different classes (A–H) based on their sequences and biochemical features. By combining structural and sequence analysis, and phylogenetic inference, we have explored the evolutionary history of classes A, B, E, F, and G and demonstrate that their multidomain architectures reflect their phylogenetic relationships, suggesting that the main evolutionary steps in their divergence are likely to have arisen from the recruitment of different domains. Additionally, the functional divergence within in each class appears to have been the result of other mechanisms such as a complex set of single-point mutations. Our results reinforce the idea that a main constraint on the evolution of cofactor-dependent enzymes is the functional binding of the cofactor. Additionally, a remarkable feature of this family is that the sequence of the key flavin adenine dinucleotide-binding domain is split into at least two parts in all classes studied here. We propose a complex set of evolutionary events that gave rise to the origin of the different classes within this family. Changes in domain architectures reflect the phylogeny of flavin monooxygenases. Recruitment of different domains has been the main force driving its evolution. A notable feature of flavin monooxygenases is that the flavin adenine dinucleotide-binding domain is split. Classes of monooxygenases emerged from an ancestral domain by structural changes.
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Affiliation(s)
- Maria Laura Mascotti
- IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de los Andes 950, San Luis D5700HHW, Argentina.
| | - Maximiliano Juri Ayub
- IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de los Andes 950, San Luis D5700HHW, Argentina
| | - Nicholas Furnham
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Janet M Thornton
- EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Roman A Laskowski
- EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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50
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Kynurenine-3-monooxygenase: a review of structure, mechanism, and inhibitors. Drug Discov Today 2016; 21:315-24. [DOI: 10.1016/j.drudis.2015.11.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/14/2015] [Accepted: 11/05/2015] [Indexed: 01/04/2023]
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