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Hooe S, Thakur M, Lasarte-Aragonés G, Breger JC, Walper SA, Medintz IL, Ellis GA. Exploration of the In Vitro Violacein Synthetic Pathway with Substrate Analogues. ACS OMEGA 2024; 9:3894-3904. [PMID: 38284012 PMCID: PMC10809250 DOI: 10.1021/acsomega.3c08233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/21/2023] [Accepted: 12/26/2023] [Indexed: 01/30/2024]
Abstract
Evolution has gifted enzymes with the ability to synthesize an abundance of small molecules with incredible control over efficiency and selectivity. Central to an enzyme's role is the ability to selectively catalyze reactions in the milieu of chemicals within a cell. However, for chemists it is often desirable to extend the substrate scope of reactions to produce analogue(s) of a desired product and therefore some degree of enzyme promiscuity is often desired. Herein, we examine this dichotomy in the context of the violacein biosynthetic pathway. Importantly, we chose to interrogate this pathway with tryptophan analogues in vitro, to mitigate possible interference from cellular components and endogenous tryptophan. A total of nine tryptophan analogues were screened for by analyzing the substrate promiscuity of the initial enzyme, VioA, and compared to the substrate tryptophan. These results suggested that for VioA, substitutions at either the 2- or 4-position of tryptophan were not viable. The seven analogues that showed successful substrate conversion by VioA were then applied to the five enzyme cascade (VioABEDC) for the production of violacein, where l-tryptophan and 6-fluoro-l-tryptophan were the only substrates which were successfully converted to the corresponding violacein derivative(s). However, many of the other tryptophan analogues did convert to various substituted intermediaries. Overall, our results show substrate promiscuity with the initial enzyme, VioA, but much less for the full pathway. This work demonstrates the complexity involved when attempting to analyze substrate analogues within multienzymatic cascades, where each enzyme involved within the cascade possesses its own inherent promiscuity, which must be compatible with the remaining enzymes in the cascade for successful formation of a desired product.
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Affiliation(s)
- Shelby
L. Hooe
- National
Research Council, Washington, D.C. 20001, United States
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Meghna Thakur
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College
of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Guillermo Lasarte-Aragonés
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College
of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Joyce C. Breger
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Scott A. Walper
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Gregory A. Ellis
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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2
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Lyakhovchenko NS, Travkin VM, Senchenkov VY, Solyanikova IP. Bacterial Violacein: Properties, Biosynthesis and Application Prospects. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822060072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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3
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Sugiura S, Nakano S, Niwa M, Hasebe F, Matsui D, Ito S. Catalytic mechanism of ancestral L-lysine oxidase assigned by sequence data mining. J Biol Chem 2021; 297:101043. [PMID: 34358565 PMCID: PMC8405998 DOI: 10.1016/j.jbc.2021.101043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 07/26/2021] [Accepted: 08/02/2021] [Indexed: 11/23/2022] Open
Abstract
A large number of protein sequences are registered in public databases such as PubMed. Functionally uncharacterized enzymes are included in these databases, some of which likely have potential for industrial applications. However, assignment of the enzymes remained difficult tasks for now. In this study, we assigned a total of 28 original sequences to uncharacterized enzymes in the FAD-dependent oxidase family expressed in some species of bacteria including Chryseobacterium, Flavobacterium, and Pedobactor. Progenitor sequence of the assigned 28 sequences was generated by ancestral sequence reconstruction, and the generated sequence exhibited L-lysine oxidase activity; thus, we named the enzyme AncLLysO. Crystal structures of ligand-free and ligand-bound forms of AncLLysO were determined, indicating that the enzyme recognizes L-Lys by hydrogen bond formation with R76 and E383. The binding of L-Lys to AncLLysO induced dynamic structural change at a plug loop formed by residues 251 to 254. Biochemical assays of AncLLysO variants revealed the functional importance of these substrate recognition residues and the plug loop. R76A and E383D variants were also observed to lose their activity, and the kcat/Km value of G251P and Y253A mutations were approximately 800- to 1800-fold lower than that of AncLLysO, despite the indirect interaction of the substrates with the mutated residues. Taken together, our data demonstrate that combinational approaches to sequence classification from database and ancestral sequence reconstruction may be effective not only to find new enzymes using databases of unknown sequences but also to elucidate their functions.
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Affiliation(s)
- Sayaka Sugiura
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Suruga-ku, Shizuoka, Japan
| | - Shogo Nakano
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Suruga-ku, Shizuoka, Japan; PREST, Japan Science and Technology Agency, Kawaguchi, Japan.
| | - Masazumi Niwa
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Suruga-ku, Shizuoka, Japan
| | - Fumihito Hasebe
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Suruga-ku, Shizuoka, Japan
| | - Daisuke Matsui
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Sohei Ito
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Suruga-ku, Shizuoka, Japan
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4
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Ritota M, Manzi P. Rapid Determination of Total Tryptophan in Yoghurt by Ultra High Performance Liquid Chromatography with Fluorescence Detection. Molecules 2020; 25:molecules25215025. [PMID: 33138259 PMCID: PMC7662364 DOI: 10.3390/molecules25215025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/27/2020] [Accepted: 10/27/2020] [Indexed: 12/04/2022] Open
Abstract
Tryptophan (TRP) is an essential amino acid which cannot be synthesized by humans and animals, but has to be supplied by exogenous sources, notably through the diet. The bulk of dietary TRP flows into the synthesis of body’s proteins, but the TRP metabolism also involves several biochemical reactions (i.e., serotonin and kynurenine pathways). Defects in the TRP transport mechanism or catabolism are related to a large number of clinical abnormalities. Therefore, dietary TRP intake is necessary not only for the body’s growth but also for most of the body’s metabolic functions. Among protein-based foods, milk proteins provide a relatively high amount of TRP. In this paper, a rapid chromatographic method for TRP determination in yoghurt, by ultra high performance liquid chromatography on a reversed-phase column with fluorescence detection (280 nm Ex; 360 nm Em), is provided. A linear gradient elution of acetonitrile in water allowed TRP analysis in 8.0 min. The limit of detection and limit of quantification of the method were 0.011 ng/µL and 0.029 ng/µL, respectively, using 5-methyl-l-tryptophan as the internal standard. The analytical method was successfully applied to commercial yoghurts from different animal species, and the TRP values ranged between 35.19 and 121.97 mg/100 g (goat and cow Greek type yoghurt, respectively).
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5
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Kumar R. NiCo 2O 4 Nano-/Microstructures as High-Performance Biosensors: A Review. NANO-MICRO LETTERS 2020; 12:122. [PMID: 34138118 PMCID: PMC7770908 DOI: 10.1007/s40820-020-00462-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/28/2020] [Indexed: 05/13/2023]
Abstract
Non-enzymatic biosensors based on mixed transition metal oxides are deemed as the most promising devices due to their high sensitivity, selectivity, wide concentration range, low detection limits, and excellent recyclability. Spinel NiCo2O4 mixed oxides have drawn considerable attention recently due to their outstanding advantages including large specific surface area, high permeability, short electron, and ion diffusion pathways. Because of the rapid development of non-enzyme biosensors, the current state of methods for synthesis of pure and composite/hybrid NiCo2O4 materials and their subsequent electrochemical biosensing applications are systematically and comprehensively reviewed herein. Comparative analysis reveals better electrochemical sensing of bioanalytes by one-dimensional and two-dimensional NiCo2O4 nano-/microstructures than other morphologies. Better biosensing efficiency of NiCo2O4 as compared to corresponding individual metal oxides, viz. NiO and Co3O4, is attributed to the close intrinsic-state redox couples of Ni3+/Ni2+ (0.58 V/0.49 V) and Co3+/Co2+ (0.53 V/0.51 V). Biosensing performance of NiCo2O4 is also significantly improved by making the composites of NiCo2O4 with conducting carbonaceous materials like graphene, reduced graphene oxide, carbon nanotubes (single and multi-walled), carbon nanofibers; conducting polymers like polypyrrole (PPy), polyaniline (PANI); metal oxides NiO, Co3O4, SnO2, MnO2; and metals like Au, Pd, etc. Various factors affecting the morphologies and biosensing parameters of the nano-/micro-structured NiCo2O4 are also highlighted. Finally, some drawbacks and future perspectives related to this promising field are outlined.
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Affiliation(s)
- Rajesh Kumar
- Department of Chemistry, Jagdish Chandra DAV College, Dasuya, Distt. Hoshiarpur, 144205, Punjab, India.
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6
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Kneuttinger AC, Zwisele S, Straub K, Bruckmann A, Busch F, Kinateder T, Gaim B, Wysocki VH, Merkl R, Sterner R. Light-Regulation of Tryptophan Synthase by Combining Protein Design and Enzymology. Int J Mol Sci 2019; 20:E5106. [PMID: 31618845 PMCID: PMC6829457 DOI: 10.3390/ijms20205106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/11/2019] [Accepted: 10/12/2019] [Indexed: 01/24/2023] Open
Abstract
The spatiotemporal control of enzymes by light is of growing importance for industrial biocatalysis. Within this context, the photo-control of allosteric interactions in enzyme complexes, common to practically all metabolic pathways, is particularly relevant. A prominent example of a metabolic complex with a high application potential is tryptophan synthase from Salmonella typhimurium (TS), in which the constituting TrpA and TrpB subunits mutually stimulate each other via a sophisticated allosteric network. To control TS allostery with light, we incorporated the unnatural amino acid o-nitrobenzyl-O-tyrosine (ONBY) at seven strategic positions of TrpA and TrpB. Initial screening experiments showed that ONBY in position 58 of TrpA (aL58ONBY) inhibits TS activity most effectively. Upon UV irradiation, ONBY decages to tyrosine, largely restoring the capacity of TS. Biochemical characterization, extensive steady-state enzyme kinetics, and titration studies uncovered the impact of aL58ONBY on the activities of TrpA and TrpB and identified reaction conditions under which the influence of ONBY decaging on allostery reaches its full potential. By applying those optimal conditions, we succeeded to directly light-activate TS(aL58ONBY) by a factor of ~100. Our findings show that rational protein design with a photo-sensitive unnatural amino acid combined with extensive enzymology is a powerful tool to fine-tune allosteric light-activation of a central metabolic enzyme complex.
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Affiliation(s)
- Andrea C Kneuttinger
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.
| | - Stefanie Zwisele
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.
| | - Kristina Straub
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.
| | - Astrid Bruckmann
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.
| | - Florian Busch
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA.
| | - Thomas Kinateder
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.
| | - Barbara Gaim
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA.
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.
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7
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Matsui D, Asano Y. Creation of thermostable l-tryptophan dehydrogenase by protein engineering and its application for l-tryptophan quantification. Anal Biochem 2019; 579:57-63. [DOI: 10.1016/j.ab.2019.05.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/11/2019] [Accepted: 05/13/2019] [Indexed: 02/08/2023]
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8
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Asano Y, Yasukawa K. Identification and development of amino acid oxidases. Curr Opin Chem Biol 2019; 49:76-83. [DOI: 10.1016/j.cbpa.2018.10.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/16/2018] [Accepted: 10/22/2018] [Indexed: 12/23/2022]
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9
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Asano Y. Screening and development of enzymes for determination and transformation of amino acids. Biosci Biotechnol Biochem 2019; 83:1402-1416. [PMID: 30621552 DOI: 10.1080/09168451.2018.1559027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The high stereo- and substrate specificities of enzymes have been utilized for micro-determination of amino acids. Here, I review the discovery of l-Phe dehydrogenase and its practical use in the diagnosis of phenylketonuria in more than 5,400,000 neonates over two decades in Japan. Screening and uses of other selective enzymes for micro-determination of amino acids have also been discussed. In addition, novel enzymatic assays with the systematic use of known enzymes, including assays based on a pyrophosphate detection system using pyrophosphate dikinase for a variety of l-amino acids with amino-acyl-tRNA synthetase have been reviewed. Finally, I review the substrate specificities of a few amino acid-metabolizing enzymes that have been altered, using protein engineering techniques, mainly for production of useful chemicals, thus enabling the wider use of natural enzymes.
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Affiliation(s)
- Yasuhisa Asano
- a Biotechnology Research Center and Department of Biotechnology , Toyama Prefectural University , Imizu , Toyama , Japan
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10
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Yamaguchi H, Tatsumi M, Takahashi K, Tagami U, Sugiki M, Kashiwagi T, Kameya M, Okazaki S, Mizukoshi T, Asano Y. Protein engineering for improving the thermostability of tryptophan oxidase and insights from structural analysis. J Biochem 2018; 164:359-367. [DOI: 10.1093/jb/mvy065] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/23/2018] [Indexed: 11/15/2022] Open
Affiliation(s)
- Hiroki Yamaguchi
- Fundamental Technology Labs., Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Moemi Tatsumi
- Fundamental Technology Labs., Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Kazutoshi Takahashi
- Fundamental Technology Labs., Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Uno Tagami
- Fundamental Technology Labs., Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Masayuki Sugiki
- Fundamental Technology Labs., Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Tatsuki Kashiwagi
- Fundamental Technology Labs., Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Masafumi Kameya
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama, Japan
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, Japan
| | - Seiji Okazaki
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama, Japan
| | - Toshimi Mizukoshi
- Fundamental Technology Labs., Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama, Japan
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11
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Asamizu S. Biosynthesis of nitrogen-containing natural products, C7N aminocyclitols and bis-indoles, from actinomycetes. Biosci Biotechnol Biochem 2017; 81:871-881. [DOI: 10.1080/09168451.2017.1281726] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Abstract
Actinomycetes are a major source of bioactive natural products with important pharmaceutical properties. Understanding the natural enzymatic assembly of complex small molecules is important for rational metabolic pathway design to produce “artificial” natural products in bacterial cells. This review will highlight current research on the biosynthetic mechanisms of two classes of nitrogen-containing natural products, C7N aminocyclitols and bis-indoles. Validamycin A is a member of C7N aminocyclitol natural products from Streptomyces hygroscopicus. Here, two important biosynthetic steps, pseudoglycosyltranferase-catalyzed C–N bond formation, and C7-sugar phosphate cyclase-catalyzed divergent carbasugar formation, will be reviewed. In addition, the bis-indolic natural products indolocarbazole, staurosporine from Streptomyces sp. TP-A0274, and rearranged bis-indole violacein from Chromobacterium violaceum are reviewed including the oxidative course of the assembly pathway for the bis-indolic scaffold. The identified biosynthesis mechanisms will be useful to generating new biocatalytic tools and bioactive compounds.
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Affiliation(s)
- Shumpei Asamizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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12
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Translation-dependent bioassay for amino acid quantification using auxotrophic microbes as biocatalysts of protein synthesis. Appl Microbiol Biotechnol 2016; 101:2523-2531. [DOI: 10.1007/s00253-016-8027-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/20/2016] [Accepted: 11/23/2016] [Indexed: 10/20/2022]
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13
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Tirado-Guizar A, Paraguay-Delgado F, Pina-Luis GE. A molecularly imprinted polymer-coated CdTe quantum dot nanocomposite for tryptophan recognition based on the Förster resonance energy transfer process. Methods Appl Fluoresc 2016; 4:045003. [DOI: 10.1088/2050-6120/4/4/045003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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14
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Characterization of the Aminotransferase ThdN from Thienodolin Biosynthesis inStreptomyces albogriseolus. Chembiochem 2016; 17:1859-1864. [DOI: 10.1002/cbic.201600304] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Indexed: 11/07/2022]
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15
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Füller JJ, Röpke R, Krausze J, Rennhack KE, Daniel NP, Blankenfeldt W, Schulz S, Jahn D, Moser J. Biosynthesis of Violacein, Structure and Function of l-Tryptophan Oxidase VioA from Chromobacterium violaceum. J Biol Chem 2016; 291:20068-84. [PMID: 27466367 DOI: 10.1074/jbc.m116.741561] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Indexed: 11/06/2022] Open
Abstract
Violacein is a natural purple pigment of Chromobacterium violaceum with potential medical applications as antimicrobial, antiviral, and anticancer drugs. The initial step of violacein biosynthesis is the oxidative conversion of l-tryptophan into the corresponding α-imine catalyzed by the flavoenzyme l-tryptophan oxidase (VioA). A substrate-related (3-(1H-indol-3-yl)-2-methylpropanoic acid) and a product-related (2-(1H-indol-3-ylmethyl)prop-2-enoic acid) competitive VioA inhibitor was synthesized for subsequent kinetic and x-ray crystallographic investigations. Structures of the binary VioA·FADH2 and of the ternary VioA·FADH2·2-(1H-indol-3-ylmethyl)prop-2-enoic acid complex were resolved. VioA forms a "loosely associated" homodimer as indicated by small-angle x-ray scattering experiments. VioA belongs to the glutathione reductase family 2 of FAD-dependent oxidoreductases according to the structurally conserved cofactor binding domain. The substrate-binding domain of VioA is mainly responsible for the specific recognition of l-tryptophan. Other canonical amino acids were efficiently discriminated with a minor conversion of l-phenylalanine. Furthermore, 7-aza-tryptophan, 1-methyl-tryptophan, 5-methyl-tryptophan, and 5-fluoro-tryptophan were efficient substrates of VioA. The ternary product-related VioA structure indicated involvement of protein domain movement during enzyme catalysis. Extensive structure-based mutagenesis in combination with enzyme kinetics (using l-tryptophan and substrate analogs) identified Arg(64), Lys(269), and Tyr(309) as key catalytic residues of VioA. An increased enzyme activity of protein variant H163A in the presence of l-phenylalanine indicated a functional role of His(163) in substrate binding. The combined structural and mutational analyses lead to the detailed understanding of VioA substrate recognition. Related strategies for the in vivo synthesis of novel violacein derivatives are discussed.
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Affiliation(s)
| | - René Röpke
- the Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, D-38106 Braunschweig, and
| | - Joern Krausze
- the Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | | | | | - Wulf Blankenfeldt
- the Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig
| | - Stefan Schulz
- the Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, D-38106 Braunschweig, and
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16
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Campillo-Brocal JC, Lucas-Elío P, Sanchez-Amat A. Distribution in Different Organisms of Amino Acid Oxidases with FAD or a Quinone As Cofactor and Their Role as Antimicrobial Proteins in Marine Bacteria. Mar Drugs 2015; 13:7403-18. [PMID: 26694422 PMCID: PMC4699246 DOI: 10.3390/md13127073] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 11/27/2015] [Accepted: 12/08/2015] [Indexed: 12/27/2022] Open
Abstract
Amino acid oxidases (AAOs) catalyze the oxidative deamination of amino acids releasing ammonium and hydrogen peroxide. Several kinds of these enzymes have been reported. Depending on the amino acid isomer used as a substrate, it is possible to differentiate between l-amino acid oxidases and d-amino acid oxidases. Both use FAD as cofactor and oxidize the amino acid in the alpha position releasing the corresponding keto acid. Recently, a novel class of AAOs has been described that does not contain FAD as cofactor, but a quinone generated by post-translational modification of residues in the same protein. These proteins are named as LodA-like proteins, after the first member of this group described, LodA, a lysine epsilon oxidase synthesized by the marine bacterium Marinomonas mediterranea. In this review, a phylogenetic analysis of all the enzymes described with AAO activity has been performed. It is shown that it is possible to recognize different groups of these enzymes and those containing the quinone cofactor are clearly differentiated. In marine bacteria, particularly in the genus Pseudoalteromonas, most of the proteins described as antimicrobial because of their capacity to generate hydrogen peroxide belong to the group of LodA-like proteins.
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Affiliation(s)
- Jonatan C Campillo-Brocal
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Murcia 30100, Spain.
| | - Patricia Lucas-Elío
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Murcia 30100, Spain.
| | - Antonio Sanchez-Amat
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Murcia 30100, Spain.
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17
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Matsui D, Terai A, Asano Y. L-Arginine oxidase from Pseudomonas sp. TPU 7192: Characterization, gene cloning, heterologous expression, and application to L-arginine determination. Enzyme Microb Technol 2015; 82:151-157. [PMID: 26672462 DOI: 10.1016/j.enzmictec.2015.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 10/01/2015] [Accepted: 10/03/2015] [Indexed: 10/22/2022]
Abstract
L-Arginine oxidase (AROD, EC 1.4.3.-) was discovered in newly discovered Pseudomonas sp. TPU 7192 and its characteristics were described. The molecular mass (MS) of the enzyme was estimated to be 528 kDa, which was accounted for by eight identical subunits with MS of 66 kDa each. AROD was identified as a flavin adenine dinucleotide (FAD)-dependent enzyme with 1 mol of FAD being contained in each subunit. It catalyzed the oxidative deamination of L-arginine and converted L-arginine to 2-ketoarginine, which was non-enzymatically converted into 4-guanidinobutyric acid when the hydrogen peroxide (H2O2) formed by L-arginine oxidation was not removed. In contrast, 2-ketoarginine was present when H2O2was decomposed. AROD was specific to L-arginine with a Km value of 149 μM. It exhibited maximal activity at 55 °C and pH 5.5. AROD was stable in the pH range 5.5-7.5 and >95% of its original activity was below 60 °C at pH 7.0. Since these enzymatic properties are considered suitable for the determination of L-arginine, the gene was cloned and expressed in a heterologous expression system. We herein successfully developed a new simple enzymatic method for the determination of L-arginine using Pseudomonas AROD.
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Affiliation(s)
- Daisuke Matsui
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan; Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Anna Terai
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan; Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.
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Enhancement of stability of l-tryptophan dehydrogenase from Nostoc punctiforme ATCC29133 and its application to l-tryptophan assay. J Biotechnol 2015; 196-197:27-32. [DOI: 10.1016/j.jbiotec.2015.01.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 01/04/2015] [Accepted: 01/12/2015] [Indexed: 11/20/2022]
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Tadayon F, Sepehri Z. A new electrochemical sensor based on a nitrogen-doped graphene/CuCo2O4 nanocomposite for simultaneous determination of dopamine, melatonin and tryptophan. RSC Adv 2015. [DOI: 10.1039/c5ra12020a] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An electrochemical sensor was fabricated for the simultaneous determination of dopamine, melatonin and tryptophan in biological and pharmaceutical samples.
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Affiliation(s)
- F. Tadayon
- Department of Chemistry
- Islamic Azad University
- Tehran
- Iran
| | - Z. Sepehri
- Department of Internal Medicine
- Zabol University of Medical Sciences
- Zabol
- Iran
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Kameya M, Asano Y. Rapid enzymatic assays for l-citrulline and l-arginine based on the platform of pyrophosphate detection. Enzyme Microb Technol 2014; 57:36-41. [DOI: 10.1016/j.enzmictec.2014.01.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 01/13/2014] [Accepted: 01/16/2014] [Indexed: 12/13/2022]
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Kameya M, Himi M, Asano Y. Rapid and selective enzymatic assay for L-methionine based on a pyrophosphate detection system. Anal Biochem 2013; 447:33-8. [PMID: 24239571 DOI: 10.1016/j.ab.2013.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Revised: 10/31/2013] [Accepted: 11/01/2013] [Indexed: 12/14/2022]
Abstract
An enzymatic assay for L-methionine was developed by coupling adenosylmethionine synthetase (AdoMetS) to a pyrophosphate (PP(i)) detection system, which was constructed using pyruvate, phosphate dikinase. To expand the use of this assay, the PP(i) detection system was embodied as three different forms, which allowed PP(i) to be measured by UV, visible, and fluorescent light detectors. The assay system was robust and could tolerate the addition of inorganic phosphate and ATP to the assay mixtures. L-Methionine could be accurately determined by coupling the PP(i) detection system and AdoMetS. This AdoMetS coupling assay was highly selective to L-methionine and exhibited no significant activity to other proteinaceous amino acids, ammonia, or urea, unlike conventional enzymatic assays for L-methionine. Spike and recovery tests showed that the AdoMetS assay could accurately and reproducibly determine increases in L-methionine in human plasma samples without any pretreatment to remove proteins and potentially interfering low-molecular-weight molecules. The high selectivity and robustness of the AdoMetS assay provide rapid and high-throughput analysis of L-methionine in various kinds of analytes.
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Affiliation(s)
- Masafumi Kameya
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan; Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Mariko Himi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan; Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.
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