1
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Banach M. Structural Outlier Detection and Zernike-Canterakis Moments for Molecular Surface Meshes-Fast Implementation in Python. Molecules 2023; 29:52. [PMID: 38202635 PMCID: PMC10779519 DOI: 10.3390/molecules29010052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024] Open
Abstract
Object retrieval systems measure the degree of similarity of the shape of 3D models. They search for the elements of the 3D model databases that resemble the query model. In structural bioinformatics, the query model is a protein tertiary/quaternary structure and the objective is to find similarly shaped molecules in the Protein Data Bank. With the ever-growing size of the PDB, a direct atomic coordinate comparison with all its members is impractical. To overcome this problem, the shape of the molecules can be encoded by fixed-length feature vectors. The distance of a protein to the entire PDB can be measured in this low-dimensional domain in linear time. The state-of-the-art approaches utilize Zernike-Canterakis moments for the shape encoding and supply the retrieval process with geometric data of the input structures. The BioZernike descriptors are a standard utility of the PDB since 2020. However, when trying to calculate the ZC moments locally, the issue of the deficiency of libraries readily available for use in custom programs (i.e., without relying on external binaries) is encountered, in particular programs written in Python. Here, a fast and well-documented Python implementation of the Pozo-Koehl algorithm is presented. In contrast to the more popular algorithm by Novotni and Klein, which is based on the voxelized volume, the PK algorithm produces ZC moments directly from the triangular surface meshes of 3D models. In particular, it can accept the molecular surfaces of proteins as its input. In the presented PK-Zernike library, owing to Numba's just-in-time compilation, a mesh with 50,000 facets is processed by a single thread in a second at the moment order 20. Since this is the first time the PK algorithm is used in structural bioinformatics, it is employed in a novel, simple, but efficient protein structure retrieval pipeline. The elimination of the outlying chain fragments via a fast PCA-based subroutine improves the discrimination ability, allowing for this pipeline to achieve an 0.961 area under the ROC curve in the BioZernike validation suite (0.997 for the assemblies). The correlation between the results of the proposed approach and of the 3D Surfer program attains values up to 0.99.
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Affiliation(s)
- Mateusz Banach
- Department of Bioinformatics and Telemedicine, Faculty of Medicine, Jagiellonian University Medical College, Medyczna 7, 30-688 Kraków, Poland
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2
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Synthesis of (S)- and (R)-β-Tyrosine by Redesigned Phenylalanine Aminomutase. Catalysts 2022. [DOI: 10.3390/catal12040397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Phenylalanine aminomutase from Taxus chinensis (TchPAM) is employed in the biosynthesis of the widely used antitumor drug paclitaxel. TchPAM has received substantial attention due to its strict enantioselectivity towards (R)-β-phenylalanine, in contrast to the bacterial enzymes classified as EC 5.4.3.11 which are (S)-selective for this substrate. However, the understanding of the isomerization mechanism of the reorientation and rearrangement reactions in TchPAM might support and promote further research on expanding the scope of the substrate and thus the establishment of large-scale production of potential synthesis for drug development. Upon conservation analysis, computational simulation, and mutagenesis experiments, we report a mutant from TchPAM, which can catalyze the amination reaction of trans-p-hydroxycinnamic acid to (R)- and (S)-β-tyrosine. We propose a mechanism for the function of the highly conserved residues L179, N458, and Q459 in the active site of TchPAM. This work highlights the importance of the hydrophobic residues in the active site, including the residues L104, L108, and I431, for maintaining the strict enantioselectivity of TchPAM, and the importance of these residues for substrate specificity and activation by altering the substrate binding position or varying the location of neighboring residues. Furthermore, an explanation of (R)-selectivity in TchPAM is proposed based on the mutagenesis study of these hydrophobic residues. In summary, these studies support the future exploitation of the rational engineering of corresponding enzymes with MIO moiety (3,5-dihydro-5-methylidene-4H-imidazole-4-one) such as ammonia lyases and aminomutases of aromatic amino acids.
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3
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Trivedi VD, Chappell TC, Krishna NB, Shetty A, Sigamani GG, Mohan K, Ramesh A, R PK, Nair NU. In-Depth Sequence–Function Characterization Reveals Multiple Pathways to Enhance Enzymatic Activity. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05508] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Vikas D. Trivedi
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Todd C. Chappell
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | | | - Anuj Shetty
- Kcat Enzymatic Private Limited, Bengaluru, Karnataka, India 560005
| | | | - Karishma Mohan
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Athreya Ramesh
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Pravin Kumar R
- Kcat Enzymatic Private Limited, Bengaluru, Karnataka, India 560005
| | - Nikhil U. Nair
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, United States
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4
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Abstract
Lignin is an underutilized sustainable source of aromatic compounds. To valorize the low-value lignin monomers, we proposed an efficient strategy, involving enzymatic conversion from trans-p-hydroxycinnamic acids to generate valued-added canonical and non-canonical aromatic amino acids. Among them, β-amino acids are recognized as building blocks for bioactive natural products and pharmaceutical ingredients due to their attractive antitumor properties. Using computational enzyme design, the (R)-β-selective phenylalanine aminomutase from Taxus chinensis (TchPAM) was successfully mutated to accept β-tyrosine as the substrate, as well as to generate the (R)-β-tyrosine with excellent enantiopurity (ee > 99%) as the unique product from trans-p-hydroxycinnamic acid. Moreover, the kinetic parameters were determined for the reaction of four Y424 enzyme variants with the synthesis of different phenylalanine and tyrosine enantiomers. In the ammonia elimination reaction of (R)-β-tyrosine, the variants Y424N and Y424C displayed a two-fold increased catalytic efficiency of the wild type. In this work, a binding pocket in the active site, including Y424, K427, I431, and E455, was examined for its influence on the β-enantioselectivity of this enzyme family. Combining the upstream lignin depolymerization and downstream production, a sustainable value chain based on lignin is enabled. In summary, we report a β-tyrosine synthesis process from a monolignol component, offering a new way for lignin valorization by biocatalyst modification.
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5
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Xu S, Ding Y, Sun J, Zhang Z, Wu Z, Yang T, Shen F, Xue G. A high-quality genome assembly of Jasminum sambac provides insight into floral trait formation and Oleaceae genome evolution. Mol Ecol Resour 2021; 22:724-739. [PMID: 34460989 DOI: 10.1111/1755-0998.13497] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 11/29/2022]
Abstract
As one of the most economically significant Oleaceae family members, Jasminum sambac is renowned for its distinct sweet, heady fragrance. Using Illumina reads, Nanopore long reads, and HiC-sequencing, we efficiently assembled and annotated the J. sambac genome. The high-quality genome assembly consisted of a total of 507 Mb sequence (contig N50 = 17.6 Mb) with 13 pseudomolecules. A total of 21,143 protein-coding genes and 303 Mb repeat sequences were predicted. An ancient whole-genome triplication event at the base of Oleaceae (~66 million years ago [Ma], Late Cretaceous) was identified and this may have contributed to the diversification of the Oleaceae ancestor and its divergence from the Lamiales. Stress-related (e.g., WRKY) and flowering-related (e.g., MADS-box) genes were located in the triplicated regions, suggesting that the polyploidy event might have contributed adaptive potential. Genes related to terpenoid biosynthesis, for example, FTA and TPS, were observed to be duplicated to a great extent in the J. sambac genome, perhaps explaining the strong fragrance of the flowers. Copy number changes in distinct phylogenetic clades of the MADS-box family were observed in J. sambac genome, for example, AGL6- and Mα- were lost and SOC- expanded, features that might underlie the long flowering period of J. sambac. The structural genes implicated in anthocyanin biosynthesis were depleted and this may explain the absence of vivid colours in jasmine. Collectively, assembling the J. sambac genome provides new insights into the genome evolution of the Oleaceae family and provides mechanistic insights into floral properties.
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Affiliation(s)
- Shixiao Xu
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China.,Scientific Observation and Experiment Station of Tobacco Biology & Processing, Ministry of Agriculture, Zhengzhou City, Henan Province, China.,National Tobacco Cultivation & Physiology & Biochemisty Research Centre, Zhengzhou City, Henan Province, China
| | - Yongle Ding
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China.,Scientific Observation and Experiment Station of Tobacco Biology & Processing, Ministry of Agriculture, Zhengzhou City, Henan Province, China.,National Tobacco Cultivation & Physiology & Biochemisty Research Centre, Zhengzhou City, Henan Province, China
| | - Juntao Sun
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China.,Scientific Observation and Experiment Station of Tobacco Biology & Processing, Ministry of Agriculture, Zhengzhou City, Henan Province, China.,National Tobacco Cultivation & Physiology & Biochemisty Research Centre, Zhengzhou City, Henan Province, China
| | - Zhiqiang Zhang
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China.,Scientific Observation and Experiment Station of Tobacco Biology & Processing, Ministry of Agriculture, Zhengzhou City, Henan Province, China.,National Tobacco Cultivation & Physiology & Biochemisty Research Centre, Zhengzhou City, Henan Province, China
| | - Zhaoyun Wu
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China.,Scientific Observation and Experiment Station of Tobacco Biology & Processing, Ministry of Agriculture, Zhengzhou City, Henan Province, China.,National Tobacco Cultivation & Physiology & Biochemisty Research Centre, Zhengzhou City, Henan Province, China
| | - Tiezhao Yang
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China
| | - Fei Shen
- Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Gang Xue
- Tobacco College, Henan Agricultural University, Zhengzhou City, Henan Province, China.,Scientific Observation and Experiment Station of Tobacco Biology & Processing, Ministry of Agriculture, Zhengzhou City, Henan Province, China.,National Tobacco Cultivation & Physiology & Biochemisty Research Centre, Zhengzhou City, Henan Province, China
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6
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Kempa EE, Galman JL, Parmeggiani F, Marshall JR, Malassis J, Fontenelle CQ, Vendeville JB, Linclau B, Charnock SJ, Flitsch SL, Turner NJ, Barran PE. Rapid Screening of Diverse Biotransformations for Enzyme Evolution. JACS AU 2021; 1:508-516. [PMID: 34056634 PMCID: PMC8154213 DOI: 10.1021/jacsau.1c00027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Indexed: 06/12/2023]
Abstract
The lack of label-free high-throughput screening technologies presents a major bottleneck in the identification of active and selective biocatalysts, with the number of variants often exceeding the capacity of traditional analytical platforms to assess their activity in a practical time scale. Here, we show the application of direct infusion of biotransformations to the mass spectrometer (DiBT-MS) screening to a variety of enzymes, in different formats, achieving sample throughputs equivalent to ∼40 s per sample. The heat map output allows rapid selection of active enzymes within 96-well plates facilitating identification of industrially relevant biocatalysts. This DiBT-MS screening workflow has been applied to the directed evolution of a phenylalanine ammonia lyase (PAL) as a case study, enhancing its activity toward electron-rich cinnamic acid derivatives which are relevant to lignocellulosic biomass degradation. Additional benefits of the screening platform include the discovery of biocatalysts (kinases, imine reductases) with novel activities and the incorporation of ion mobility technology for the identification of product hits with increased confidence.
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Affiliation(s)
- Emily E Kempa
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - James L Galman
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Fabio Parmeggiani
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, Via Mancinelli 7, 20131 Milano, Italy
| | - James R Marshall
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Julien Malassis
- School of Chemistry, University of Southampton, Highfield, SO17 1BJ Southampton, United Kingdom
| | - Clement Q Fontenelle
- School of Chemistry, University of Southampton, Highfield, SO17 1BJ Southampton, United Kingdom
| | | | - Bruno Linclau
- School of Chemistry, University of Southampton, Highfield, SO17 1BJ Southampton, United Kingdom
| | - Simon J Charnock
- Prozomix Ltd., Building 4, West End Ind. Estate, Haltwhistle, Northumberland NE49 9HA, United Kingdom
| | - Sabine L Flitsch
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Nicholas J Turner
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita E Barran
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
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7
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Bata Z, Molnár Z, Madaras E, Molnár B, Sánta-Bell E, Varga A, Leveles I, Qian R, Hammerschmidt F, Paizs C, Vértessy BG, Poppe L. Substrate Tunnel Engineering Aided by X-ray Crystallography and Functional Dynamics Swaps the Function of MIO-Enzymes. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00266] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Zsófia Bata
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- Institute of Enzymology, ELKH Research Center of Natural Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| | - Zsófia Molnár
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- Institute of Enzymology, ELKH Research Center of Natural Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| | - Erzsébet Madaras
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- Institute of Enzymology, ELKH Research Center of Natural Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| | - Bence Molnár
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- Institute of Enzymology, ELKH Research Center of Natural Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| | - Evelin Sánta-Bell
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Andrea Varga
- Biocatalysis and Biotransformation Research Centre, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Str. 11, RO-400028 Cluj-Napoca, Romania
| | - Ibolya Leveles
- Institute of Enzymology, ELKH Research Center of Natural Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Renzhe Qian
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, A-1090 Vienna, Austria
| | - Friedrich Hammerschmidt
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, A-1090 Vienna, Austria
| | - Csaba Paizs
- Biocatalysis and Biotransformation Research Centre, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Str. 11, RO-400028 Cluj-Napoca, Romania
| | - Beáta G. Vértessy
- Institute of Enzymology, ELKH Research Center of Natural Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - László Poppe
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- Biocatalysis and Biotransformation Research Centre, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Str. 11, RO-400028 Cluj-Napoca, Romania
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8
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Shee PK, Yan H, Walker KD. Intermolecular Amine Transfer to Enantioenriched trans-3-Phenylglycidates by an α/β-Aminomutase to Access Both anti-Phenylserine Isomers. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Prakash K. Shee
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Honggao Yan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Kevin D. Walker
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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9
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Moisă ME, Amariei DA, Nagy EZA, Szarvas N, Toșa MI, Paizs C, Bencze LC. Fluorescent enzyme-coupled activity assay for phenylalanine ammonia-lyases. Sci Rep 2020; 10:18418. [PMID: 33116226 PMCID: PMC7595223 DOI: 10.1038/s41598-020-75474-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/07/2020] [Indexed: 11/30/2022] Open
Abstract
Phenylalanine ammonia-lyases (PALs) catalyse the non-oxidative deamination of l-phenylalanine to trans-cinnamic acid, while in the presence of high ammonia concentration the reverse reaction occurs. PALs have been intensively studied, however, their industrial applications for amino acids synthesis remained limited, mainly due to their decreased operational stability or limited substrate specificity. The application of extensive directed evolution procedures to improve their stability, activity or selectivity, is hindered by the lack of reliable activity assays allowing facile screening of PAL-activity within large-sized mutant libraries. Herein, we describe the development of an enzyme-coupled fluorescent assay applicable for PAL-activity screens at whole cell level, involving decarboxylation of trans-cinnamic acid (the product of the PAL reaction) by ferulic acid decarboxylase (FDC1) and a photochemical reaction of the produced styrene with a diaryltetrazole, that generates a detectable, fluorescent pyrazoline product. The general applicability of the fluorescent assay for PALs of different origin, as well as its versatility for the detection of tyrosine ammonia-lyase (TAL) activity have been also demonstrated. Accordingly, the developed procedure provides a facile tool for the efficient activity screens of large mutant libraries of PALs in presence of non-natural substrates of interest, being essential for the substrate-specificity modifications/tailoring of PALs through directed evolution-based protein engineering.
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Affiliation(s)
- Mădălina E Moisă
- Biocatalysis and Biotransformations Research Center, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Arany János Str. 11, 400028, Cluj-Napoca, Romania
| | - Diana A Amariei
- Biocatalysis and Biotransformations Research Center, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Arany János Str. 11, 400028, Cluj-Napoca, Romania
| | - Emma Z A Nagy
- Biocatalysis and Biotransformations Research Center, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Arany János Str. 11, 400028, Cluj-Napoca, Romania
| | - Nóra Szarvas
- Biocatalysis and Biotransformations Research Center, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Arany János Str. 11, 400028, Cluj-Napoca, Romania
| | - Monica I Toșa
- Biocatalysis and Biotransformations Research Center, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Arany János Str. 11, 400028, Cluj-Napoca, Romania
| | - Csaba Paizs
- Biocatalysis and Biotransformations Research Center, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Arany János Str. 11, 400028, Cluj-Napoca, Romania
| | - László C Bencze
- Biocatalysis and Biotransformations Research Center, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Arany János Str. 11, 400028, Cluj-Napoca, Romania.
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10
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Miranda RR, Silva M, Barisón MJ, Silber AM, Iulek J. Crystal structure of histidine ammonia-lyase from Trypanosoma cruzi. Biochimie 2020; 175:181-188. [PMID: 32464165 DOI: 10.1016/j.biochi.2020.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/10/2020] [Accepted: 05/17/2020] [Indexed: 10/24/2022]
Abstract
Chagas disease is one of seventeen neglected tropical diseases according to the World Health Organization (WHO). The histidine-glutamate metabolic pathway is an oxidative route that has shown to be relevant for the bioenergetics in Trypanosoma cruzi, the etiological agent for Chagas disease. Histidine ammonia-lyase participates in the first stage of the histidine catabolism, catalyzing the conversion of l-histidine into urocanate. This work presents the three-dimensional (3D) structure of Trypanosoma cruzi histidine ammonia-lyase enzyme (TcHAL) and some comparisons of it to homologous structures. The enzyme was expressed, purified and assayed for crystallization, what allowed the obtainment of crystals of sufficient quality to collect X-ray diffraction data up to 2.55 Å resolution. After refinement, some structural analyses indicated that the structure does not contain the active site protection domain, in opposition to previously known 3D structures from plants and fungi phenylalanine ammonia-lyase, therefore, it is the first structure of eukaryotic ammonia-lyases that lacks this domain.
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Affiliation(s)
- Robson R Miranda
- Department of Chemistry, State University of Ponta Grossa, Brazil
| | - Marcio Silva
- Department of Education, Federal Technological University of Paraná, Brazil
| | - Maria J Barisón
- Department of Parasitology, Institute of Biomedical Sciences, University of São, Paulo, Brazil
| | - Ariel M Silber
- Department of Parasitology, Institute of Biomedical Sciences, University of São, Paulo, Brazil
| | - Jorge Iulek
- Department of Chemistry, State University of Ponta Grossa, Brazil.
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11
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Viola RE. The ammonia-lyases: enzymes that use a wide range of approaches to catalyze the same type of reaction. Crit Rev Biochem Mol Biol 2020; 54:467-483. [PMID: 31906712 DOI: 10.1080/10409238.2019.1708261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The paradigm that protein structure determines protein function has been clearly established. What is less clear is whether a specific protein structure is always required to carry out a specific function. Numerous cases are now known where there is no apparent connection between the biological function of a protein and the other members of its structural class, and where functionally related proteins can have quite diverse structures. A set of enzymes with these diverse properties, the ammonia-lyases, will be examined in this review. These are a class of enzymes that catalyze a relatively straightforward deamination reaction. However, the individual enzymes of this class possess a wide variety of different structures, utilize a diverse set of cofactors, and appear to catalyze this related reaction through a range of different mechanisms. This review aims to address a basic question: if there is not a specific protein structure and active site architecture that is both required and sufficient to define a catalyst for a given chemical reaction, then what factor(s) determine the structure and the mechanism that is selected to catalyze a particular reaction?
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Affiliation(s)
- Ronald E Viola
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH, USA
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12
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Investigation into isomerization reaction of phenylalanine aminomutase from Pantoea agglomerans. Enzyme Microb Technol 2019; 132:109428. [PMID: 31731949 DOI: 10.1016/j.enzmictec.2019.109428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 08/30/2019] [Accepted: 09/10/2019] [Indexed: 11/23/2022]
Abstract
Phenylalanine aminomutase (PaPAM) from Pantoea agglomerans is a member of the MIO (4-methylene-imidazol-5-one) family of enzymes, which isomerizes α-phenylalanine to β-phenylalanine, and could be used to synthesize unnatural β-arylalanine. However, the mechanism of isomerization reaction is not clear. To investigate the mechanism, the gene (pam), which encodes PaPAM, was first expressed in E.coli, and recombinant PaPAM was prepared using affinity chromatography. Then, 15N-(2S)-α-phenylalanine, (2S)-(3-2H2)-α-phenylalanine and (2S,3S)-[2,3-2H2]-α-phenylalanine were used as substrates to analyze the mechanism of isomerization reaction. The results of MS and NMR showed that the isomerization reaction was performed through the intramolecular exchange of NH2 with pro-3R hydrogen of α-phenylalanine. The PaPAM shuttles the α-NH2 of α-phenylalanine to β site to replace the pro-3R hydrogen. Simultaneously, the pro-3R hydrogen is shifted to α site to produce β-phenylalanine. Furthermore, a key residue, Phe at position 455 in the active site, was determined to control the exchange way using molecular docking and sequence alignment of MIO family enzymes. The results indicated that the key 455 Phe residue is involved in changing the binding orientation of the carboxyl group of the intermediate trans-cinnamic acid to control the NH2-H pair exchange.
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13
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Nagy EZA, Tork SD, Lang PA, Filip A, Irimie FD, Poppe L, Toşa MI, Schofield CJ, Brem J, Paizs C, Bencze LC. Mapping the Hydrophobic Substrate Binding Site of Phenylalanine Ammonia-Lyase from Petroselinum crispum. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02108] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Emma Z. A. Nagy
- Biocatalysis and Biotransformation Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Street 11, RO-400028 Cluj-Napoca, Romania
| | - Souad D. Tork
- Biocatalysis and Biotransformation Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Street 11, RO-400028 Cluj-Napoca, Romania
| | - Pauline A. Lang
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Alina Filip
- Biocatalysis and Biotransformation Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Street 11, RO-400028 Cluj-Napoca, Romania
| | - Florin D. Irimie
- Biocatalysis and Biotransformation Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Street 11, RO-400028 Cluj-Napoca, Romania
| | - László Poppe
- Biocatalysis and Biotransformation Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Street 11, RO-400028 Cluj-Napoca, Romania
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Monica I. Toşa
- Biocatalysis and Biotransformation Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Street 11, RO-400028 Cluj-Napoca, Romania
| | - Christopher J. Schofield
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Jürgen Brem
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Csaba Paizs
- Biocatalysis and Biotransformation Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Street 11, RO-400028 Cluj-Napoca, Romania
| | - László C. Bencze
- Biocatalysis and Biotransformation Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Street 11, RO-400028 Cluj-Napoca, Romania
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14
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Shee PK, Ratnayake ND, Walter T, Goethe O, Onyeozili EN, Walker KD. Exploring the Scope of an α/β-Aminomutase for the Amination of Cinnamate Epoxides to Arylserines and Arylisoserines. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01557] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
| | | | | | | | - Edith Ndubuaku Onyeozili
- Department of Chemistry, Florida Agricultural & Mechanical University, Tallahassee, Florida 32307, United States
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15
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Zhu L, Feng G, Ge F, Song P, Wang T, Liu Y, Tao Y, Zhou Z. One-Pot Enzymatic Synthesis of D-Arylalanines Using Phenylalanine Ammonia Lyase and L-Amino Acid Deaminase. Appl Biochem Biotechnol 2018; 187:75-89. [PMID: 29882193 DOI: 10.1007/s12010-018-2794-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/23/2018] [Indexed: 11/27/2022]
Abstract
The phenylalanine ammonia-lyase (AvPAL) from Anabaena variabilis catalyzes the amination of substituent trans-cinnamic acid (t-CA) to produce racemic D,L-enantiomer arylalanine mixture owing to its low stereoselectivity. To produce high optically pure D-arylalanine, a modified AvPAL with high D-selectivity is expected. Based on the analyses of catalytic mechanism and structure, the Asn347 residue in the active site was proposed to control stereoselectivity. Therefore, Asn347 was mutated to construct mutant AvPAL-N347A, the stereoselectivity of AvPAL-N347A for D-enantiomer arylalanine was 2.3-fold higher than that of wild-type AvPAL (WtPAL). Furthermore, the residual L-enantiomer product in reaction solution could be converted into the D-enantiomer product through stereoselective oxidation by PmLAAD and nonselective reduction by reducing agent NH3BH3. At optimal conditions, the conversion rate of t-CA and optical purity (enantiomeric excess (eeD)) of D-phenylalanine reached 82% and exceeded 99%, respectively. The two enzymes displayed activity toward a broad range of substrate and could be used to efficiently synthesize D-arylalanine with different groups on the phenyl ring. Among these D-arylalanines, the yield of m-nitro-D-phenylalanine was highest and reached 96%, and the eeD exceeded 99%. This one-pot synthesis using AvPAL and PmLAAD has prospects for industrial application.
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Affiliation(s)
- Longbao Zhu
- School of Biochemical Engineering, Anhui Polytechnic University, 8 Zheshan Road, Wuhu, Anhui, 241000, People's Republic of China
| | - Guoqiang Feng
- School of Biochemical Engineering, Anhui Polytechnic University, 8 Zheshan Road, Wuhu, Anhui, 241000, People's Republic of China
| | - Fei Ge
- School of Biochemical Engineering, Anhui Polytechnic University, 8 Zheshan Road, Wuhu, Anhui, 241000, People's Republic of China
| | - Ping Song
- School of Biochemical Engineering, Anhui Polytechnic University, 8 Zheshan Road, Wuhu, Anhui, 241000, People's Republic of China
| | - Taotao Wang
- School of Biochemical Engineering, Anhui Polytechnic University, 8 Zheshan Road, Wuhu, Anhui, 241000, People's Republic of China
| | - Yi Liu
- Key Laboratory of Food and Biotechnology, School of Food and Biotechnology, Xihua University, Chengdu, 610039, China.
| | - Yugui Tao
- School of Biochemical Engineering, Anhui Polytechnic University, 8 Zheshan Road, Wuhu, Anhui, 241000, People's Republic of China
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
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16
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Attanayake G, Walter T, Walker KD. Understanding Which Residues of the Active Site and Loop Structure of a Tyrosine Aminomutase Define Its Mutase and Lyase Activities. Biochemistry 2018; 57:3503-3514. [PMID: 29757631 DOI: 10.1021/acs.biochem.8b00269] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Site-directed mutations and substrate analogues were used to gain insights into the branch-point reaction of the 3,5-dihydro-5-methylidene-4 H-imidazol-4-one (MIO)-tyrosine aminomutase from Oryza sativa ( OsTAM). Exchanging the active residues of OsTAM (Y125C/N446K) for those in a phenylalanine aminomutase TcPAM altered its substrate specificity from tyrosine to phenylalanine. The aminomutase mechanism of OsTAM surprisingly changed almost exclusively to that of an ammonia lyase making cinnamic acid (>95%) over β-phenylalanine [Walter, T., et al. (2016) Biochemistry 55, 3497-3503]. We hypothesized that the missing electronics or sterics on the aryl ring of the phenylalanine substrate, compared with the sizable electron-donating hydroxyl of the natural tyrosine substrate, influenced the unexpected lyase reactivity of the OsTAM mutant. The double mutant was incubated with 16 α-phenylalanine substituent analogues of varying electronic strengths and sterics. The mutant converted each analogue principally to its acrylate with ∼50% conversion of the p-Br substrate, making only a small amount of the β-amino acid. The inner loop structure over the entrance to the active site was also mutated to assess how the lyase and mutase activities are affected. An OsTAM loop mutant, matching the loop residues of TcPAM, still chiefly made >95% of the acrylate from each substrate. A combined active site:loop mutant was most reactive but remained a lyase, making 10-fold more acrylates than other mutants did. While mutations within the active site changed the substrate specificity of OsTAM, continued exploration is needed to fully understand the interplay among the inner loop, the substrate, and the active site in defining the mutase and lyase activities.
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Affiliation(s)
- Gayanthi Attanayake
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Tyler Walter
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Kevin D Walker
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States.,Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States
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17
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Zhu L, Ge F, Li W, Song P, Tang H, Tao Y, Liu Y, Du G. One step synthesis of unnatural β-arylalanines using mutant phenylalanine aminomutase from Taxus chinensis with high β-regioselectivity. Enzyme Microb Technol 2018; 114:22-28. [PMID: 29685349 DOI: 10.1016/j.enzmictec.2018.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 03/18/2018] [Accepted: 03/20/2018] [Indexed: 11/30/2022]
Abstract
Phenylalanine aminomutase (TcPAM) from Taxus chinensis catalyzes the regioselective hydroamination of trans-cinnamic acid (t-CA) to yield β-phe. However, the final product mixture consists of both α- and β-phe owing to low regioselectivity, which is still a challenge to synthesize highly pure β-phe. Therefore, a modified TcPAM with high β-selectivity is expected. Based on the catalytic mechanism and structure, two amino acid residues (Asn458 and Leu108) in active sites were identified as the key residues for controlling the regioselective hydroamination of t-CA and as promising candidates for mutagenesis to enhance β-selectivity and decrease α-selectivity. The Asn458 and Leu108 residues were mutated to yield variant TcPAM-Asn458Phe/Leu108Glu, and the β-selectivity was approximately 5.2-fold higher than that of wild-type TcPAM, while α-selectivity decreased to 68%, and the percentage of β-phe in the product mixture increased from 42% to 83%. In addition, the mutant was applied to synthesize β-arylalanines using substituent t-CA as a substrate. The regioselectivity was also affected by the substituent groups at the phenyl ring of t-CA with respect to their electronic properties and position, and the 4-methoxy and methyl substituent t-CA were transferred into β-arylalanines. The conversion rate also exceeded 90%. In summary, the engineered TcPAM proved to be useful for one-step asymmetric amination of t-CA and its derivatives to synthesize highly pure β-arylalanines.
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Affiliation(s)
- Longbao Zhu
- School of Biochemical Engineering, Anhui Polytechnic University, 8 Zheshan Road, Wuhu, Anhui, 241000, People's Republic of China
| | - Fei Ge
- School of Biochemical Engineering, Anhui Polytechnic University, 8 Zheshan Road, Wuhu, Anhui, 241000, People's Republic of China
| | - Wanzhen Li
- School of Biochemical Engineering, Anhui Polytechnic University, 8 Zheshan Road, Wuhu, Anhui, 241000, People's Republic of China
| | - Ping Song
- School of Biochemical Engineering, Anhui Polytechnic University, 8 Zheshan Road, Wuhu, Anhui, 241000, People's Republic of China
| | - Hongjin Tang
- School of Biochemical Engineering, Anhui Polytechnic University, 8 Zheshan Road, Wuhu, Anhui, 241000, People's Republic of China
| | - Yugui Tao
- School of Biochemical Engineering, Anhui Polytechnic University, 8 Zheshan Road, Wuhu, Anhui, 241000, People's Republic of China.
| | - Yi Liu
- Key Laboratory of Food and Biotechnology, School of Food and Biotechnology, Xihua University, Chengdu, 610039, People's Republic of China
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
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18
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Weise NJ, Parmeggiani F, Ahmed ST, Turner NJ. Discovery and Investigation of Mutase-like Activity in a Phenylalanine Ammonia Lyase from Anabaena variabilis. Top Catal 2018; 61:288-295. [PMID: 30956511 PMCID: PMC6413883 DOI: 10.1007/s11244-018-0898-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effect of extended reaction times on the regio- and enantioselectivity of the phenylalanine ammonia lyase (PAL)-catalysed amination of a subset of cinnamate derivatives was investigated. This was done using a PAL from the cyanobacterium Anabaena variabilis and incubation in a concentrated ammonia buffer. Whilst early time point analyses revealed excellent selectivities to give mostly the well-documented (S)-α-amino acid products, subsequent accumulation of other regio-/stereo- isomers was seen. For many para-substituted substrates, the β-regioisomer, a previously-unreported product with this enzyme class, was found to become more abundant than the α-, after sufficient incubation, with slight preference for the (R)-enantiomer. Although attempts to tune the selectivity of the PAL toward any of the three side products were largely unsuccessful, the results provide insight into the evolutionary history of this class of enzymes and reinforce the prominence of the toolbox of specific and selective cinnamate-aminating enzymes.
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Affiliation(s)
- Nicholas J. Weise
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
| | - Fabio Parmeggiani
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
| | - Syed T. Ahmed
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
| | - Nicholas J. Turner
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
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19
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Csuka P, Juhász V, Kohári S, Filip A, Varga A, Sátorhelyi P, Bencze LC, Barton H, Paizs C, Poppe L. Pseudomonas fluorescensStrain R124 Encodes Three Different MIO Enzymes. Chembiochem 2018; 19:411-418. [DOI: 10.1002/cbic.201700530] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Pál Csuka
- Department of Organic Chemistry and Technology; Budapest University of Technology and Economics; Műegyetem rkp. 3 1111 Budapest Hungary
| | - Vivien Juhász
- Department of Organic Chemistry and Technology; Budapest University of Technology and Economics; Műegyetem rkp. 3 1111 Budapest Hungary
| | - Szabolcs Kohári
- Fermentia Microbiological Ltd; Berlini út 47-49 1049 Budapest Hungary
| | - Alina Filip
- Biocatalysis and Biotransformation Research Center; Faculty of Chemistry and Chemical Engineering; Babeş-Bolyai University of Cluj-Napoca; Arany János str. 11 400028 Cluj-Napoca Romania
| | - Andrea Varga
- Biocatalysis and Biotransformation Research Center; Faculty of Chemistry and Chemical Engineering; Babeş-Bolyai University of Cluj-Napoca; Arany János str. 11 400028 Cluj-Napoca Romania
| | - Péter Sátorhelyi
- Fermentia Microbiological Ltd; Berlini út 47-49 1049 Budapest Hungary
| | - László Csaba Bencze
- Biocatalysis and Biotransformation Research Center; Faculty of Chemistry and Chemical Engineering; Babeş-Bolyai University of Cluj-Napoca; Arany János str. 11 400028 Cluj-Napoca Romania
| | - Hazel Barton
- Department of Biology; The University of Akron; ASEC West Tower 178 Akron OH 44325 USA
| | - Csaba Paizs
- Biocatalysis and Biotransformation Research Center; Faculty of Chemistry and Chemical Engineering; Babeş-Bolyai University of Cluj-Napoca; Arany János str. 11 400028 Cluj-Napoca Romania
| | - László Poppe
- Department of Organic Chemistry and Technology; Budapest University of Technology and Economics; Műegyetem rkp. 3 1111 Budapest Hungary
- Biocatalysis and Biotransformation Research Center; Faculty of Chemistry and Chemical Engineering; Babeş-Bolyai University of Cluj-Napoca; Arany János str. 11 400028 Cluj-Napoca Romania
- SynBiocat Ltd; Szilasliget u. 3 1172 Budapest Hungary
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20
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Xue YP, Cao CH, Zheng YG. Enzymatic asymmetric synthesis of chiral amino acids. Chem Soc Rev 2018; 47:1516-1561. [DOI: 10.1039/c7cs00253j] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
This review summarizes the progress achieved in the enzymatic asymmetric synthesis of chiral amino acids from prochiral substrates.
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Affiliation(s)
- Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Cheng-Hao Cao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
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21
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Bata Z, Qian R, Roller A, Horak J, Bencze LC, Paizs C, Hammerschmidt F, Vértessy BG, Poppe L. A Methylidene Group in the Phosphonic Acid Analogue of Phenylalanine Reverses the Enantiopreference of Binding to Phenylalanine Ammonia-Lyases. Adv Synth Catal 2017; 359:2109-2120. [PMID: 28919846 PMCID: PMC5573973 DOI: 10.1002/adsc.201700428] [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: 04/05/2017] [Revised: 05/02/2017] [Indexed: 12/19/2022]
Abstract
Aromatic amino acid ammonia‐lyases and aromatic amino acid 2,3‐aminomutases contain the post‐translationally formed prosthetic 3,5‐dihydro‐4‐methylidene‐5H‐imidazol‐5‐one (MIO) group. MIO enzymes catalyze the stereoselective synthesis of α‐ or β‐amino acid enantiomers, making these chemical processes environmentally friendly and affordable. Characterization of novel inhibitors enables structural understanding of enzyme mechanism and recognizes promising herbicide candidates as well. The present study found that both enantiomers of the aminophosphonic acid analogue of the natural substrate phenylalanine and a novel derivative bearing a methylidene at the β‐position inhibited phenylalanine ammonia‐lyases (PAL), representing MIO enzymes. X‐ray methods unambiguously determined the absolute configuration of all tested enantiomers during their synthesis. Enzyme kinetic measurements revealed the enantiomer of the methylidene‐substituted substrate analogue as being a mirror image relation to the natural l‐phenylalanine as the strongest inhibitor. Isothermal titration calorimetry (ITC) confirmed the binding constants and provided a detailed analysis of the thermodynamic driving forces of ligand binding. Molecular docking suggested that binding of the (R)‐ and (S)‐enantiomers is possible by a mirror image packing. ![]()
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Affiliation(s)
- Zsófia Bata
- Department of Organic Chemistry and Technology Budapest University of Technology and Economics Műegyetem rkp. 3. H-1111 Budapest Hungary.,Institute of Enzymology HAS-Research Center of Natural Sciences, Budapest, H-1117 Magyar tudósok krt. 2. Budapest Hungary
| | - Renzhe Qian
- Institute of Organic Chemistry University of Vienna Währinger Str. 38 1090 Vienna Austria
| | - Alexander Roller
- Institute of Inorganic Chemistry University of Vienna Währinger Str. 42. A-1090 Vienna Austria
| | - Jeannie Horak
- Institute of Pharmaceutical Sciences Pharmaceutical (Bio-)Analysis Eberhard-Karls-University Tübingen Auf der Morgensstelle 872076 Tübingen Germany
| | - László Csaba Bencze
- Biocatalysis and Biotransformation Research Centre Faculty of Chemistry and Chemical Engineering Babeş-Bolyai University of Cluj-Napoca Arany János Str. 11400028 Cluj-Napoca Romania
| | - Csaba Paizs
- Biocatalysis and Biotransformation Research Centre Faculty of Chemistry and Chemical Engineering Babeş-Bolyai University of Cluj-Napoca Arany János Str. 11400028 Cluj-Napoca Romania
| | | | - Beáta G Vértessy
- Institute of Enzymology HAS-Research Center of Natural Sciences, Budapest, H-1117 Magyar tudósok krt. 2. Budapest Hungary.,Department of Applied Biotechnology and Food Science Budapest University of Technology and Economics Műegyetem rkp. 3. H-1111 Budapest Hungary
| | - László Poppe
- Department of Organic Chemistry and Technology Budapest University of Technology and Economics Műegyetem rkp. 3. H-1111 Budapest Hungary.,Biocatalysis and Biotransformation Research Centre Faculty of Chemistry and Chemical Engineering Babeş-Bolyai University of Cluj-Napoca Arany János Str. 11400028 Cluj-Napoca Romania
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22
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Parmeggiani F, Weise NJ, Ahmed ST, Turner NJ. Synthetic and Therapeutic Applications of Ammonia-lyases and Aminomutases. Chem Rev 2017; 118:73-118. [DOI: 10.1021/acs.chemrev.6b00824] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Fabio Parmeggiani
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
| | - Nicholas J. Weise
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
| | - Syed T. Ahmed
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
| | - Nicholas J. Turner
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
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23
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Weise NJ, Ahmed ST, Parmeggiani F, Turner NJ. Kinetic Resolution of Aromatic β-Amino Acids Using a Combination of Phenylalanine Ammonia Lyase and Aminomutase Biocatalysts. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201600894] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Nicholas J. Weise
- Manchester Institute of Biotechnology & School of Chemistry; Faculty of Science & Engineering; University of Manchester; 131 Princess Street M1 7DN Manchester United Kingdom
| | - Syed T. Ahmed
- Manchester Institute of Biotechnology & School of Chemistry; Faculty of Science & Engineering; University of Manchester; 131 Princess Street M1 7DN Manchester United Kingdom
| | - Fabio Parmeggiani
- Manchester Institute of Biotechnology & School of Chemistry; Faculty of Science & Engineering; University of Manchester; 131 Princess Street M1 7DN Manchester United Kingdom
| | - Nicholas J. Turner
- Manchester Institute of Biotechnology & School of Chemistry; Faculty of Science & Engineering; University of Manchester; 131 Princess Street M1 7DN Manchester United Kingdom
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24
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Walter T, Wijewardena D, Walker KD. Mutation of Aryl Binding Pocket Residues Results in an Unexpected Activity Switch in an Oryza sativa Tyrosine Aminomutase. Biochemistry 2016; 55:3497-503. [DOI: 10.1021/acs.biochem.6b00331] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tyler Walter
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Devinda Wijewardena
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Kevin D. Walker
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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25
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Varga A, Bánóczi G, Nagy B, Bencze LC, Toşa MI, Gellért Á, Irimie FD, Rétey J, Poppe L, Paizs C. Influence of the aromatic moiety in α- and β-arylalanines on their biotransformation with phenylalanine 2,3-aminomutase from Pantoea agglomerans. RSC Adv 2016. [DOI: 10.1039/c6ra02964g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In this study enantiomer selective isomerization of various racemic α- and β-arylalanines catalysed by phenylalanine 2,3-aminomutase from Pantoea agglomerans (PaPAM) was investigated.
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Affiliation(s)
- Andrea Varga
- Biocatalysis and Biotransformation Research Group
- Babeş-Bolyai University of Cluj-Napoca
- RO-400028 Cluj-Napoca
- Romania
| | - Gergely Bánóczi
- Department of Organic Chemistry and Technology
- Budapest University of Technology and Economics
- H-1111 Budapest
- Hungary
| | - Botond Nagy
- Biocatalysis and Biotransformation Research Group
- Babeş-Bolyai University of Cluj-Napoca
- RO-400028 Cluj-Napoca
- Romania
| | - László Csaba Bencze
- Biocatalysis and Biotransformation Research Group
- Babeş-Bolyai University of Cluj-Napoca
- RO-400028 Cluj-Napoca
- Romania
| | - Monica Ioana Toşa
- Biocatalysis and Biotransformation Research Group
- Babeş-Bolyai University of Cluj-Napoca
- RO-400028 Cluj-Napoca
- Romania
| | - Ákos Gellért
- Agricultural Institute
- Centre of Agricultural Research
- Hungarian Academy of Sciences
- H-2462 Martonvásár
- Hungary
| | - Florin Dan Irimie
- Biocatalysis and Biotransformation Research Group
- Babeş-Bolyai University of Cluj-Napoca
- RO-400028 Cluj-Napoca
- Romania
| | - János Rétey
- Institute of Organic Chemistry
- Karlsruhe Institute of Technology
- D-76128 Karlsruhe
- Germany
| | - László Poppe
- Department of Organic Chemistry and Technology
- Budapest University of Technology and Economics
- H-1111 Budapest
- Hungary
- SynBiocat Ltd
| | - Csaba Paizs
- Biocatalysis and Biotransformation Research Group
- Babeş-Bolyai University of Cluj-Napoca
- RO-400028 Cluj-Napoca
- Romania
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26
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Walter T, King Z, Walker KD. A Tyrosine Aminomutase from Rice (Oryza sativa) Isomerizes (S)-α- to (R)-β-Tyrosine with Unique High Enantioselectivity and Retention of Configuration. Biochemistry 2015; 55:1-4. [DOI: 10.1021/acs.biochem.5b01331] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Zayna King
- Medgar Evers College, Brooklyn, New York 11225, United States
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27
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Weiser D, Bencze LC, Bánóczi G, Ender F, Kiss R, Kókai E, Szilágyi A, Vértessy BG, Farkas Ö, Paizs C, Poppe L. Phenylalanine Ammonia-Lyase-Catalyzed Deamination of an Acyclic Amino Acid: Enzyme Mechanistic Studies Aided by a Novel Microreactor Filled with Magnetic Nanoparticles. Chembiochem 2015; 16:2283-8. [DOI: 10.1002/cbic.201500444] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Indexed: 01/09/2023]
Affiliation(s)
- Diána Weiser
- Department of Organic Chemistry and Technology; Budapest University of Technology and Economics; Műegyetem rkp. 3 1111 Budapest Hungary
| | - László Csaba Bencze
- Babeş-Bolyai University of Cluj-Napoca; Arany János str. 11 400028 Cluj-Napoca Romania
| | - Gergely Bánóczi
- Department of Organic Chemistry and Technology; Budapest University of Technology and Economics; Műegyetem rkp. 3 1111 Budapest Hungary
| | - Ferenc Ender
- Department of Electron Devices; Budapest University of Technology and Economics; Magyar tudósok körútja 2 1117 Budapest Hungary
| | - Róbert Kiss
- Gedeon Richter Plc. Gyömrői út 19-21; 1103 Budapest Hungary
| | - Eszter Kókai
- Department of Organic Chemistry and Technology; Budapest University of Technology and Economics; Műegyetem rkp. 3 1111 Budapest Hungary
| | - András Szilágyi
- Department of Physical Chemistry and Materials Science; Budapest University of Technology and Economics; Budafoki út 8 1111 Budapest Hungary
| | - Beáta G. Vértessy
- Institute of Enzymology; Research Centre for Natural Sciences of Hungarian Academy of Sciences; Magyar tudósok körútja 2 1117 Budapest Hungary
- Department of Biotechnology and Food Sciences; Budapest University of Technology and Economics; Szt. Gellért tér 4 1111 Budapest Hungary
| | - Ödön Farkas
- Department of Organic Chemistry; Eötvös Lóránd University; Pázmány Péter sétány 1A 1117 Budapest Hungary
| | - Csaba Paizs
- Babeş-Bolyai University of Cluj-Napoca; Arany János str. 11 400028 Cluj-Napoca Romania
| | - László Poppe
- Department of Organic Chemistry and Technology; Budapest University of Technology and Economics; Műegyetem rkp. 3 1111 Budapest Hungary
- SynBiocat Ltd.; Lázár deák u 4/1 1173 Budapest Hungary
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28
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Heberling MM, Masman MF, Bartsch S, Wybenga GG, Dijkstra BW, Marrink SJ, Janssen DB. Ironing out their differences: dissecting the structural determinants of a phenylalanine aminomutase and ammonia lyase. ACS Chem Biol 2015; 10:989-97. [PMID: 25494407 DOI: 10.1021/cb500794h] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Deciphering the structural features that functionally separate ammonia lyases from aminomutases is of interest because it may allow for the engineering of more efficient aminomutases for the synthesis of unnatural amino acids (e.g., β-amino acids). However, this has proved to be a major challenge that involves understanding the factors that influence their activity and regioselectivity differences. Herein, we report evidence of a structural determinant that dictates the activity differences between a phenylalanine ammonia lyase (PAL) and aminomutase (PAM). An inner loop region that closes the active sites of both PAM and PAL was mutated within PAM (PAM residues 77-97) in a stepwise approach to study the effects when the equivalent residue(s) found in the PAL loop were introduced into the PAM loop. Almost all of the single loop mutations triggered a lyase phenotype in PAM. Experimental and computational evidence suggest that the induced lyase features result from inner loop mobility enhancements, which are possibly caused by a 310-helix cluster, flanking α-helices, and hydrophobic interactions. These findings pinpoint the inner loop as a structural determinant of the lyase and mutase activities of PAM.
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Affiliation(s)
- Matthew M. Heberling
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Marcelo F. Masman
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Sebastian Bartsch
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | | | | | | | - Dick B. Janssen
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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29
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Ratnayake ND, Liu N, Kuhn LA, Walker KD. Ring-Substituted α-Arylalanines for Probing Substituent Effects on the Isomerization Reaction Catalyzed by an Aminomutase. ACS Catal 2014. [DOI: 10.1021/cs500474s] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Nishanka Dilini Ratnayake
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §Computer Science & Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - Nan Liu
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §Computer Science & Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - Leslie A. Kuhn
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §Computer Science & Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - Kevin D. Walker
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §Computer Science & Engineering, Michigan State University, East Lansing, Michigan 48824, United States
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30
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Wybenga GG, Szymanski W, Wu B, Feringa BL, Janssen DB, Dijkstra BW. Structural Investigations into the Stereochemistry and Activity of a Phenylalanine-2,3-aminomutase from Taxus chinensis. Biochemistry 2014; 53:3187-98. [DOI: 10.1021/bi500187a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gjalt G. Wybenga
- Laboratory
of Biophysical Chemistry, University of Groningen, Nijenborgh
7, 9747 AG Groningen, The Netherlands
| | | | | | | | | | - Bauke W. Dijkstra
- Laboratory
of Biophysical Chemistry, University of Groningen, Nijenborgh
7, 9747 AG Groningen, The Netherlands
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31
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Nestl BM, Hammer SC, Nebel BA, Hauer B. New generation of biocatalysts for organic synthesis. Angew Chem Int Ed Engl 2014; 53:3070-95. [PMID: 24520044 DOI: 10.1002/anie.201302195] [Citation(s) in RCA: 230] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Indexed: 02/04/2023]
Abstract
The use of enzymes as catalysts for the preparation of novel compounds has received steadily increasing attention over the past few years. High demands are placed on the identification of new biocatalysts for organic synthesis. The catalysis of more ambitious reactions reflects the high expectations of this field of research. Enzymes play an increasingly important role as biocatalysts in the synthesis of key intermediates for the pharmaceutical and chemical industry, and new enzymatic technologies and processes have been established. Enzymes are an important part of the spectrum of catalysts available for synthetic chemistry. The advantages and applications of the most recent and attractive biocatalysts--reductases, transaminases, ammonia lyases, epoxide hydrolases, and dehalogenases--will be discussed herein and exemplified by the syntheses of interesting compounds.
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Affiliation(s)
- Bettina M Nestl
- Technische Biochemie, Universität Stuttgart, Stuttgart (Germany)
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32
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Nestl BM, Hammer SC, Nebel BA, Hauer B. Biokatalysatoren für die organische Synthese - die neue Generation. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201302195] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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33
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Wang K, Hou Q, Liu Y. Insight into the mechanism of aminomutase reaction: A case study of phenylalanine aminomutase by computational approach. J Mol Graph Model 2013; 46:65-73. [DOI: 10.1016/j.jmgm.2013.09.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 08/28/2013] [Accepted: 09/25/2013] [Indexed: 11/24/2022]
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34
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Wanninayake U, Walker KD. A Bacterial Tyrosine Aminomutase Proceeds through Retention or Inversion of Stereochemistry To Catalyze Its Isomerization Reaction. J Am Chem Soc 2013; 135:11193-204. [DOI: 10.1021/ja403918w] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Udayanga Wanninayake
- Department
of Chemistry, and ‡Department of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
| | - Kevin D. Walker
- Department
of Chemistry, and ‡Department of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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35
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A new member of the 4-methylideneimidazole-5-one-containing aminomutase family from the enediyne kedarcidin biosynthetic pathway. Proc Natl Acad Sci U S A 2013; 110:8069-74. [PMID: 23633564 DOI: 10.1073/pnas.1304733110] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
4-Methylideneimidazole-5-one (MIO)-containing aminomutases catalyze the conversion of L-α-amino acids to β-amino acids with either an (R) or an (S) configuration. L-phenylalanine and L-tyrosine are the only two natural substrates identified to date. The enediyne chromophore of the chromoprotein antitumor antibiotic kedarcidin (KED) harbors an (R)-2-aza-3-chloro-β-tyrosine moiety reminiscent of the (S)-3-chloro-5-hydroxy-β-tyrosine moiety of the C-1027 enediyne chromophore, the biosynthesis of which uncovered the first known MIO-containing aminomutase, SgcC4. Comparative analysis of the KED and C-1027 biosynthetic gene clusters inspired the proposal for (R)-2-aza-3-chloro-β-tyrosine biosynthesis starting from 2-aza-L-tyrosine, featuring KedY4 as a putative MIO-containing aminomutase. Here we report the biochemical characterization of KedY4, confirming its proposed role in KED biosynthesis. KedY4 is an MIO-containing aminomutase that stereospecifically catalyzes the conversion of 2-aza-L-tyrosine to (R)-2-aza-β-tyrosine, exhibiting no detectable activity toward 2-aza-L-phenylalanine or L-tyrosine as an alternative substrate. In contrast, SgcC4, which stereospecifically catalyzes the conversion of L-tyrosine to (S)-β-tyrosine in C-1027 biosynthesis, exhibits minimal activity with 2-aza-L-tyrosine as an alternative substrate but generating (S)-2-aza-β-tyrosine, a product with the opposite stereochemistry of KedY4. This report of KedY4 broadens the scope of known substrates for the MIO-containing aminomutase family, and comparative studies of KedY4 and SgcC4 provide an outstanding opportunity to examine how MIO-containing aminomutases control substrate specificity and product enantioselectivity.
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36
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Bartsch S, Wybenga GG, Jansen M, Heberling MM, Wu B, Dijkstra BW, Janssen DB. Redesign of a Phenylalanine Aminomutase into a Phenylalanine Ammonia Lyase. ChemCatChem 2013. [DOI: 10.1002/cctc.201200871] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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37
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Heberling MM, Wu B, Bartsch S, Janssen DB. Priming ammonia lyases and aminomutases for industrial and therapeutic applications. Curr Opin Chem Biol 2013; 17:250-60. [PMID: 23557642 DOI: 10.1016/j.cbpa.2013.02.013] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 02/05/2013] [Indexed: 01/17/2023]
Abstract
Ammonia lyases (AL) and aminomutases (AM) are emerging in green synthetic routes to chiral amines and an AL is being explored as an enzyme therapeutic for treating phenylketonuria and cancer. Although the restricted substrate range of the wild-type enzymes limits their widespread application, the non-reliance on external cofactors and direct functionalization of an olefinic bond make ammonia lyases attractive biocatalysts for use in the synthesis of natural and non-natural amino acids, including β-amino acids. The approach of combining structure-guided enzyme engineering with efficient mutant library screening has extended the synthetic scope of these enzymes in recent years and has resolved important mechanistic issues for AMs and ALs, including those containing the MIO (4-methylideneimidazole-5-one) internal cofactor.
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Affiliation(s)
- Matthew M Heberling
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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38
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Abstract
Many natural products contain unusual aromatic β-amino acids or moieties derived therefrom. The biosynthesis of these β-amino acids was first elucidated during a biosynthetic study of the enediyne antitumor antibiotic C-1027, when an enzyme, SgcC4, was discovered to convert L-tyrosine to (S)-β-tyrosine. SgcC4 is similar in sequence and structure to 4-methylideneimidazole-5-one (MIO)-containing ammonia lyases. Whereas the ammonia lyases use the electrophilic power of the MIO group to catalyze the release of ammonia from aromatic amino acids to generate α,β-unsaturated carboxylic acids as final products, SgcC4 retains the α,β-unsaturated carboxylic acid and amine as intermediates and reappends the amino group to the β-carbon, affording a β-amino acid as the final product. The study of SgcC4 led to the subsequent discovery of other MIO-containing aminomutases with altered substrate specificity and product stereochemistry, including MdpC4 from the biosynthetic pathway of the enediyne antitumor antibiotic maduropeptin. This chapter describes protocols for the enzymatic and structural characterization of these MIO-containing aminomutases as exemplified by SgcC4 and MdpC4. These protocols are applicable to the study of other aminomutases.
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39
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Hao DC, Xiao PG, Ge GB, Liu M. Biological, Chemical, and Omics Research ofTaxusMedicinal Resources. Drug Dev Res 2012. [DOI: 10.1002/ddr.21040] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Da-Cheng Hao
- Biotechnology Institute/School of Environment; Dalian Jiaotong University; Dalian; China
| | | | - Guang-Bo Ge
- Pharmaceutical resource discovery; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian; China
| | - Ming Liu
- Biotechnology Institute/School of Environment; Dalian Jiaotong University; Dalian; China
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40
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Wanninayake U, Walker KD. Assessing the deamination rate of a covalent aminomutase adduct by burst phase analysis. Biochemistry 2012; 51:5226-8. [PMID: 22686417 DOI: 10.1021/bi300569r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Burst-phase kinetic analysis was used to evaluate the deamination rate of the aminated-methylidene imidazolone (NH(2)-MIO) adduct of a Taxus phenylalanine aminomutase. The kinetic parameters were interrogated by a non-natural substrate (S)-styryl-α-alanine that yielded a chromophoric styrylacrylate product upon deamination by the aminomutase. Transient inactivation of the enzyme by the NH(2)-MIO adduct intermediate resulted in an initial burst of product, with reactivation by deamination of the adduct. This study validated the rate constants of a kinetic model demonstrating that the NH(2)-MIO adduct and cinnamate intermediate are sufficiently retained to catalyze the natural α- to β-phenylalanine isomerization.
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41
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Pilbák S, Farkas Ö, Poppe L. Mechanism of the Tyrosine Ammonia Lyase Reaction-Tandem Nucleophilic and Electrophilic Enhancement by a Proton Transfer. Chemistry 2012; 18:7793-802. [DOI: 10.1002/chem.201103662] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 01/31/2012] [Indexed: 11/09/2022]
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42
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Guerra-Bubb J, Croteau R, Williams RM. The early stages of taxol biosynthesis: an interim report on the synthesis and identification of early pathway metabolites. Nat Prod Rep 2012; 29:683-96. [PMID: 22547034 DOI: 10.1039/c2np20021j] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The biosynthesis of the anti-cancer drug taxol (paclitaxel) has required the collaborative efforts of several research groups to tackle the synthesis and labeling of putative biosynthetic intermediates, in concert with the identification, cloning and functional expression of the biosynthetic genes responsible for the construction of this complex natural product. Based on a combination of precursor labeling and incorporation experiments, and metabolite isolation from Taxus spp., a picture of the complex matrix of pathway oxygenation reactions following formation of the first committed intermediate, taxa-4(5),11(12)-diene, is beginning to emerge. An overview of the current state of knowledge on the early-stages of taxol biosynthesis is presented.
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Affiliation(s)
- Jennifer Guerra-Bubb
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
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43
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Condurso HL, Bruner SD. Structure guided approaches toward exploiting and manipulating nonribosomal peptide and polyketide biosynthetic pathways. Curr Opin Chem Biol 2012; 16:162-9. [DOI: 10.1016/j.cbpa.2012.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 01/31/2012] [Accepted: 02/02/2012] [Indexed: 11/28/2022]
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44
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Strom S, Wanninayake U, Ratnayake ND, Walker KD, Geiger JH. Insights into the Mechanistic Pathway of thePantoea agglomeransPhenylalanine Aminomutase. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108525] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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45
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Strom S, Wanninayake U, Ratnayake ND, Walker KD, Geiger JH. Insights into the Mechanistic Pathway of thePantoea agglomeransPhenylalanine Aminomutase. Angew Chem Int Ed Engl 2012; 51:2898-902. [DOI: 10.1002/anie.201108525] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 01/26/2012] [Indexed: 11/11/2022]
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46
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Wu B, Szymański W, Wybenga GG, Heberling MM, Bartsch S, de Wildeman S, Poelarends GJ, Feringa BL, Dijkstra BW, Janssen DB. Mechanism-Inspired Engineering of Phenylalanine Aminomutase for Enhanced β-Regioselective Asymmetric Amination of Cinnamates. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201106372] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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47
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Wu B, Szymański W, Wybenga GG, Heberling MM, Bartsch S, de Wildeman S, Poelarends GJ, Feringa BL, Dijkstra BW, Janssen DB. Mechanism-Inspired Engineering of Phenylalanine Aminomutase for Enhanced β-Regioselective Asymmetric Amination of Cinnamates. Angew Chem Int Ed Engl 2011; 51:482-6. [DOI: 10.1002/anie.201106372] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 10/12/2011] [Indexed: 11/11/2022]
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48
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Wanninayake U, DePorre Y, Ondari M, Walker KD. (S)-Styryl-α-alanine Used To Probe the Intermolecular Mechanism of an Intramolecular MIO-Aminomutase. Biochemistry 2011; 50:10082-90. [DOI: 10.1021/bi2012299] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Udayanga Wanninayake
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yvonne DePorre
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Mark Ondari
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Kevin D. Walker
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824,
United States
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49
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Ratnayake ND, Wanninayake U, Geiger JH, Walker KD. Stereochemistry and mechanism of a microbial phenylalanine aminomutase. J Am Chem Soc 2011; 133:8531-3. [PMID: 21561099 DOI: 10.1021/ja2030728] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The stereochemistry of a phenylalanine aminomutase (PAM) on the andrimid biosynthetic pathway in Pantoea agglomerans (Pa) is reported. PaPAM is a member of the 4-methylidene-1H-imidazol-5(4H)-one (MIO)-dependent family of catalysts and isomerizes (2S)-α-phenylalanine to (3S)-β-phenylalanine, which is the enantiomer of the product made by the mechanistically similar aminomutase TcPAM from Taxus plants. The NH(2) and pro-(3S) hydrogen groups at C(α) and C(β), respectively, of the substrate are removed and interchanged completely intramolecularly with inversion of configuration at the migration centers to form β-phenylalanine. This is a contrast to the retention of configuration mechanism followed by TcPAM.
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