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Brack Y, Sun C, Yi D, Bornscheuer UT. Systematic Analysis of the MIO-forming Residues of Aromatic Ammonia Lyases. Chembiochem 2024; 25:e202400016. [PMID: 38323706 DOI: 10.1002/cbic.202400016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/01/2024] [Accepted: 02/07/2024] [Indexed: 02/08/2024]
Abstract
Aromatic ammonia lyases (AALs) and tyrosine/phenylalanine ammonia mutases (TAM/PAM) are 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO)-dependent enzymes. Usually, the MIO moiety is autocatalytically formed from the tripeptide Ala-Ser-Gly (ASG) and acts as an electrophile during the enzymatic reaction. However, the MIO-forming residues (ASG) have some diversity in this enzyme class. In this work, a systematic investigation on the variety of MIO-forming residues was carried out using in-depth sequence analyses. Several protein clusters of AAL-like enzymes with unusual MIO-forming residues such as ACG, TSG, SSG, and CSG were identified, including two novel histidine ammonia lyases and one PAM with CSG and TSG residues, respectively, as well as three novel ergothioneine trimethylammonia lyases without MIO motif. The mutagenesis of common MIO-groups confirmed the function of these MIO variants, which provides good starting points for future functional prediction and mutagenesis research of AALs.
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Affiliation(s)
- Yannik Brack
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 4, 17489, Greifswald, Germany
| | - Chenghai Sun
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 4, 17489, Greifswald, Germany
| | - Dong Yi
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 4, 17489, Greifswald, Germany
- National Key Laboratory of Lead Druggability Research, Research Center for Systems Biosynthesis, China State Institute of Pharmaceutical Industry, Gebaini Road 285, 201203, Shanghai, China
| | - Uwe T Bornscheuer
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 4, 17489, Greifswald, Germany
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2
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Fan S, Wei X, Lü R, Feng C, Zhang Q, Lü X, Jin Y, Yan M, Yang Z. Roles of the N-terminal motif in improving the activity and soluble expression of phenylalanine ammonia lyases in Escherichia coli. Int J Biol Macromol 2024; 262:130248. [PMID: 38367782 DOI: 10.1016/j.ijbiomac.2024.130248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 02/19/2024]
Abstract
Phenylalanine ammonia-lyase (PAL) has various applications in fine chemical manufacturing and the pharmaceutical industry. In particular, PAL derived from Anabaena variabilis (AvPAL) is used as a therapeutic agent to the treat phenylketonuria in clinical settings. In this study, we aligned the amino acid sequences of AvPAL and PAL derived from Nostoc punctiforme (NpPAL) to obtain several mutants with enhanced activity, expression yield, and thermal stability via amino acid substitution and saturation mutagenesis at the N-terminal position. Enzyme kinetic experiments revealed that the kcat values of NpPAL-N2K, NpPAL-I3T, and NpPAL-T4L mutants were increased to 3.2-, 2.8-, and 3.3-fold that of the wild-type, respectively. Saturation mutagenesis of the fourth amino acid in AvPAL revealed that the kcat values of AvPAL-L4N, AvPAL-L4P, AvPAL-L4Q and AvPAL-L4S increased to 4.0-, 3.7-, 3.6-, and 3.2-fold, respectively. Additionally, the soluble protein yield of AvPAL-L4K increased to approximately 14 mg/L, which is approximately 3.5-fold that of AvPAL. Molecular dynamics studies further revealed that maintaining the attacking state of the reaction and N-terminal structure increased the rate of catalytic reaction and improved the solubility of proteins. These findings provide new insights for the rational design of PAL in the future.
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Affiliation(s)
- Shuai Fan
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xiyu Wei
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Ruijie Lü
- School of Pharmacy, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Cuiyue Feng
- School of Pharmacy, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Qian Zhang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xudong Lü
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Yuanyuan Jin
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Maocai Yan
- School of Pharmacy, Jining Medical University, Rizhao 276800, Shandong, China.
| | - Zhaoyong Yang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.
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3
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Nikkel DJ, Wetmore SD. Distinctive Formation of a DNA-Protein Cross-Link during the Repair of DNA Oxidative Damage: Insights into Human Disease from MD Simulations and QM/MM Calculations. J Am Chem Soc 2023. [PMID: 37285289 DOI: 10.1021/jacs.3c01773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Reactive oxygen species damage DNA and result in health issues. The major damage product, 8-oxo-7,8-dihydroguanine (8oG), is repaired by human adenine DNA glycosylase homologue (MUTYH). Although MUTYH misfunction is associated with a genetic disorder called MUTYH-associated polyposis (MAP) and MUTYH is a potential target for cancer drugs, the catalytic mechanism required to develop disease treatments is debated in the literature. This study uses molecular dynamics simulations and quantum mechanics/molecular mechanics techniques initiated from DNA-protein complexes that represent different stages of the repair pathway to map the catalytic mechanism of the wild-type MUTYH bacterial homologue (MutY). This multipronged computational approach characterizes a DNA-protein cross-linking mechanism that is consistent with all previous experimental data and is a distinct pathway across the broad class of monofunctional glycosylase repair enzymes. In addition to clarifying how the cross-link is formed, accommodated by the enzyme, and hydrolyzed for product release, our calculations rationalize why cross-link formation is favored over immediate glycosidic bond hydrolysis, the accepted mechanism for all other monofunctional DNA glycosylases to date. Calculations on the Y126F mutant MutY highlight critical roles for active site residues throughout the reaction, while investigation of the N146S mutant rationalizes the connection between the analogous N224S MUTYH mutation and MAP. In addition to furthering our knowledge of the chemistry associated with a devastating disorder, the structural information gained about the distinctive MutY mechanism compared to other repair enzymes represents an important step for the development of specific and potent small-molecule inhibitors as cancer therapeutics.
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Affiliation(s)
- Dylan J Nikkel
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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Wang J, Zhang N, Huang Y, Li S, Zhang G. Simple and efficient enzymatic procedure for p-coumaric acid synthesis: Complete bioconversion and biocatalyst recycling under alkaline condition. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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5
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Corrado ML, Knaus T, Schwaneberg U, Mutti FG. High-Yield Synthesis of Enantiopure 1,2-Amino Alcohols from l-Phenylalanine via Linear and Divergent Enzymatic Cascades. Org Process Res Dev 2022; 26:2085-2095. [PMID: 35873603 PMCID: PMC9295148 DOI: 10.1021/acs.oprd.1c00490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Enantiomerically
pure 1,2-amino alcohols are important compounds
due to their biological activities and wide applications in chemical
synthesis. In this work, we present two multienzyme pathways for the
conversion of l-phenylalanine into either 2-phenylglycinol
or phenylethanolamine in the enantiomerically pure form. Both pathways
start with the two-pot sequential four-step conversion of l-phenylalanine into styrene via subsequent deamination, decarboxylation,
enantioselective epoxidation, and enantioselective hydrolysis. For
instance, after optimization, the multienzyme process could convert
507 mg of l-phenylalanine into (R)-1-phenyl-1,2-diol
in an overall isolated yield of 75% and >99% ee. The opposite enantiomer,
(S)-1-phenyl-1,2-diol, was also obtained in a 70%
yield and 98–99% ee following the same approach. At this stage,
two divergent routes were developed to convert the chiral diols into
either 2-phenylglycinol or phenylethanolamine. The former route consisted
of a one-pot concurrent interconnected two-step cascade in which the
diol intermediate was oxidized to 2-hydroxy-acetophenone by an alcohol
dehydrogenase and then aminated by a transaminase to give enantiomerically
pure 2-phenylglycinol. Notably, the addition of an alanine dehydrogenase
enabled the connection of the two steps and made the overall process
redox-self-sufficient. Thus, (S)-phenylglycinol was
isolated in an 81% yield and >99.4% ee starting from ca. 100 mg
of
the diol intermediate. The second route consisted of a one-pot concurrent
two-step cascade in which the oxidative and reductive steps were not
interconnected. In this case, the diol intermediate was oxidized to
either (S)- or (R)-2-hydroxy-2-phenylacetaldehyde
by an alcohol oxidase and then aminated by an amine dehydrogenase
to give the enantiomerically pure phenylethanolamine. The addition
of a formate dehydrogenase and sodium formate was required to provide
the reducing equivalents for the reductive amination step. Thus, (R)-phenylethanolamine was isolated in a 92% yield and >99.9%
ee starting from ca. 100 mg of the diol intermediate. In summary, l-phenylalanine was converted into enantiomerically pure 2-phenylglycinol
and phenylethanolamine in overall yields of 61% and 69%, respectively.
This work exemplifies how linear and divergent enzyme cascades can
enable the synthesis of high-value chiral molecules such as amino
alcohols from a renewable material such as l-phenylalanine
with high atom economy and improved sustainability.
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Affiliation(s)
- Maria L. Corrado
- Van’t Hoff Institute for Molecular Sciences, HIMS-Biocat, University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Tanja Knaus
- Van’t Hoff Institute for Molecular Sciences, HIMS-Biocat, University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, Aachen 52074, Germany
| | - Francesco G. Mutti
- Van’t Hoff Institute for Molecular Sciences, HIMS-Biocat, University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
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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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7
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Exploring the therapeutic potential of modern and ancestral phenylalanine/tyrosine ammonia-lyases as supplementary treatment of hereditary tyrosinemia. Sci Rep 2020; 10:1315. [PMID: 31992763 PMCID: PMC6987202 DOI: 10.1038/s41598-020-57913-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 01/07/2020] [Indexed: 12/01/2022] Open
Abstract
Phenylalanine/tyrosine ammonia-lyases (PAL/TALs) have been approved by the FDA for treatment of phenylketonuria and may harbour potential for complementary treatment of hereditary tyrosinemia Type I. Herein, we explore ancestral sequence reconstruction as an enzyme engineering tool to enhance the therapeutic potential of PAL/TALs. We reconstructed putative ancestors from fungi and compared their catalytic activity and stability to two modern fungal PAL/TALs. Surprisingly, most putative ancestors could be expressed as functional tetramers in Escherichia coli and thus retained their ability to oligomerize. All ancestral enzymes displayed increased thermostability compared to both modern enzymes, however, the increase in thermostability was accompanied by a loss in catalytic turnover. One reconstructed ancestral enzyme in particular could be interesting for further drug development, as its ratio of specific activities is more favourable towards tyrosine and it is more thermostable than both modern enzymes. Moreover, long-term stability assessment showed that this variant retained substantially more activity after prolonged incubation at 25 °C and 37 °C, as well as an increased resistance to incubation at 60 °C. Both of these factors are indicative of an extended shelf-life of biopharmaceuticals. We believe that ancestral sequence reconstruction has potential for enhancing the properties of enzyme therapeutics, especially with respect to stability. This work further illustrates that resurrection of putative ancestral oligomeric proteins is feasible and provides insight into the extent of conservation of a functional oligomerization surface area from ancestor to modern enzyme.
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8
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Barros J, Dixon RA. Plant Phenylalanine/Tyrosine Ammonia-lyases. TRENDS IN PLANT SCIENCE 2020; 25:66-79. [PMID: 31679994 DOI: 10.1016/j.tplants.2019.09.011] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/12/2019] [Accepted: 09/13/2019] [Indexed: 05/13/2023]
Abstract
Aromatic amino acid deaminases are key enzymes mediating carbon flux from primary to secondary metabolism in plants. Recent studies have uncovered a tyrosine ammonia-lyase that contributes to the typical characteristics of grass cell walls and contributes to about 50% of the total lignin synthesized by the plant. Grasses are currently preferred bioenergy feedstocks and lignin is the most important limiting factor in the conversion of plant biomass to liquid biofuels, as well as being an abundant renewable carbon source that can be industrially exploited. Further research on the structure, evolution, regulation, and biological function of functionally distinct ammonia-lyases has multiple implications for improving the economics of the agri-food and biofuel industries.
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Affiliation(s)
- Jaime Barros
- BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA; Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA; Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Richard A Dixon
- BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA; Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA; Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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9
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Sui Z, Luo J, Yao R, Huang C, Zhao Y, Kong L. Functional characterization and correlation analysis of phenylalanine ammonia-lyase (PAL) in coumarin biosynthesis from Peucedanum praeruptorum Dunn. PHYTOCHEMISTRY 2019; 158:35-45. [PMID: 30448740 DOI: 10.1016/j.phytochem.2018.11.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 11/06/2018] [Accepted: 11/08/2018] [Indexed: 06/09/2023]
Abstract
Coumarins exhibit many biological activities and are the main specialised metabolites of Peucedanum praeruptorum Dunn, an important plant used in traditional Chinese medicine. In preliminary studies, we cloned several genes involved in coumarin biosynthesis in P. praeruptorum, such as 4-coumarate: CoA ligase (4CL), p-coumaroyl CoA 2'-hydroxylase (C2'H), feruloyl CoA 6'-hydroxylase (F6'H) and bergaptol O-methyltransferase (BMT). However, phenylalanine ammonia-lyase (PAL) in P. praeruptorum (PpPAL) has not yet been studied. In the present study, we cloned one novel PpPAL gene. Subsequently, the relationship between gene and compounds was studied using quantitative real-time PCR (qRT-PCR) and High Performance Liquid Chromatography (HPLC) analysis. Then, enzyme function was analyzed with L-phenylalanine (L-Phe) as substrate. These experiments showed that the coumarin content could be upregulated by methyl jasmonate (MeJA), UV irradiation and cold, which was consistent with increased expression levels of PpPAL. In addition, correlation analysis indicated that coumarins were partially related to PpPAL. And the recombinant protein could catalyze the conversion of L-Phe to trans-cinnamic acid (t-CA) with a Km of 120 ± 33 μM and a Kcat of 117 ± 32 min-1. Besides, Tyr110, Phe116, Gly117, Ser206, Leu209, Leu259, Tyr354, Arg357, Asn387 and Phe403 were essential for enzymatic activity based on three-dimensional modeling and site-directed mutagenesis experiments. Altogether these results highlight the importance of PpPAL in abiotically induced coumarin biosynthesis and provide further insights regarding the structure-function relationships of this protein.
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Affiliation(s)
- Ziwei Sui
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Jun Luo
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Ruolan Yao
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Chuanlong Huang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Yucheng Zhao
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China.
| | - Lingyi Kong
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China.
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10
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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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11
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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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12
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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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13
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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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14
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Lin CI, McCarty RM, Liu HW. The Enzymology of Organic Transformations: A Survey of Name Reactions in Biological Systems. Angew Chem Int Ed Engl 2017; 56:3446-3489. [PMID: 27505692 PMCID: PMC5477795 DOI: 10.1002/anie.201603291] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 01/05/2023]
Abstract
Chemical reactions that are named in honor of their true, or at least perceived, discoverers are known as "name reactions". This Review is a collection of biological representatives of named chemical reactions. Emphasis is placed on reaction types and catalytic mechanisms that showcase both the chemical diversity in natural product biosynthesis as well as the parallels with synthetic organic chemistry. An attempt has been made, whenever possible, to describe the enzymatic mechanisms of catalysis within the context of their synthetic counterparts and to discuss the mechanistic hypotheses for those reactions that are currently active areas of investigation. This Review has been categorized by reaction type, for example condensation, nucleophilic addition, reduction and oxidation, substitution, carboxylation, radical-mediated, and rearrangements, which are subdivided by name reactions.
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Affiliation(s)
- Chia-I Lin
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin, Austin, TX, 78731, USA
| | - Reid M McCarty
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin, Austin, TX, 78731, USA
| | - Hung-Wen Liu
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin, Austin, TX, 78731, USA
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15
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Lin C, McCarty RM, Liu H. Die Enzymologie organischer Umwandlungen: Namensreaktionen in biologischen Systemen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201603291] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Chia‐I. Lin
- Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, and Department of Chemistry University of Texas at Austin Austin TX 78731 USA
| | - Reid M. McCarty
- Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, and Department of Chemistry University of Texas at Austin Austin TX 78731 USA
| | - Hung‐wen Liu
- Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, and Department of Chemistry University of Texas at Austin Austin TX 78731 USA
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16
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Bencze LC, Filip A, Bánóczi G, Toşa MI, Irimie FD, Gellért Á, Poppe L, Paizs C. Expanding the substrate scope of phenylalanine ammonia-lyase from Petroselinum crispum towards styrylalanines. Org Biomol Chem 2017; 15:3717-3727. [DOI: 10.1039/c7ob00562h] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The substrate scope of phenylalanine ammonia-lyase from Petroselinum crispum (PcPAL) towards the l-enantiomers of racemic styrylalanines rac-1a–d were extended by reshaping the aromatic binding pocket of the active site of PcPAL by point mutations of F137.
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Affiliation(s)
- László Csaba Bencze
- Biocatalysis and Biotransformation Research Centre
- Faculty of Chemistry and Chemical Engineering
- Babeş-Bolyai University of Cluj-Napoca
- RO-400028 Cluj-Napoca
- Romania
| | - Alina Filip
- Biocatalysis and Biotransformation Research Centre
- Faculty of Chemistry and Chemical Engineering
- 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
| | - Monica Ioana Toşa
- Biocatalysis and Biotransformation Research Centre
- Faculty of Chemistry and Chemical Engineering
- Babeş-Bolyai University of Cluj-Napoca
- RO-400028 Cluj-Napoca
- Romania
| | - Florin Dan Irimie
- Biocatalysis and Biotransformation Research Centre
- Faculty of Chemistry and Chemical Engineering
- 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
| | - László Poppe
- Biocatalysis and Biotransformation Research Centre
- Faculty of Chemistry and Chemical Engineering
- Babeş-Bolyai University of Cluj-Napoca
- RO-400028 Cluj-Napoca
- Romania
| | - Csaba Paizs
- Biocatalysis and Biotransformation Research Centre
- Faculty of Chemistry and Chemical Engineering
- Babeş-Bolyai University of Cluj-Napoca
- RO-400028 Cluj-Napoca
- Romania
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17
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Busto E, Simon RC, Richter N, Kroutil W. One-Pot, Two-Module Three-Step Cascade To Transform Phenol Derivatives to Enantiomerically Pure (R)- or (S)-p-Hydroxyphenyl Lactic Acids. ACS Catal 2016. [DOI: 10.1021/acscatal.6b00030] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Eduardo Busto
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, A-8010-Graz, Austria
| | - Robert C. Simon
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, A-8010-Graz, Austria
| | - Nina Richter
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, A-8010-Graz, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), Petersgasse 14, 8010 Graz, Austria
| | - Wolfgang Kroutil
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, A-8010-Graz, Austria
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18
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Busto E, Gerstmann M, Tobola F, Dittmann E, Wiltschi B, Kroutil W. Systems biocatalysis: para-alkenylation of unprotected phenols. Catal Sci Technol 2016. [DOI: 10.1039/c6cy01947a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Commercially available phenol derivatives were transformed with pyruvate to form a new C–C bond leading to the correspondingpara-coumaric acids and only one molecule of water as an innocent side product in buffer.
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Affiliation(s)
- Eduardo Busto
- Department of Chemistry
- NAWI Graz
- BioTechMed Graz
- University of Graz
- 8010 Graz
| | | | - Felix Tobola
- Austrian Centre of Industrial Biotechnology (ACIB)
- 8010 Graz
- Austria
| | - Edmund Dittmann
- Austrian Centre of Industrial Biotechnology (ACIB)
- 8010 Graz
- Austria
| | - Birgit Wiltschi
- Austrian Centre of Industrial Biotechnology (ACIB)
- 8010 Graz
- Austria
| | - Wolfgang Kroutil
- Department of Chemistry
- NAWI Graz
- BioTechMed Graz
- University of Graz
- 8010 Graz
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19
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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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20
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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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21
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Pinto GP, Ribeiro AJ, Ramos MJ, Fernandes PA, Toscano M, Russo N. New insights in the catalytic mechanism of tyrosine ammonia-lyase given by QM/MM and QM cluster models. Arch Biochem Biophys 2015; 582:107-15. [DOI: 10.1016/j.abb.2015.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/16/2015] [Accepted: 03/03/2015] [Indexed: 11/25/2022]
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22
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Busto E, Simon RC, Kroutil W. Vinylation of Unprotected Phenols Using a Biocatalytic System. Angew Chem Int Ed Engl 2015; 54:10899-902. [DOI: 10.1002/anie.201505696] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Indexed: 11/10/2022]
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23
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Busto E, Simon RC, Kroutil W. Vinylation of Unprotected Phenols Using a Biocatalytic System. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505696] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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24
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Highly Active and Specific Tyrosine Ammonia-Lyases from Diverse Origins Enable Enhanced Production of Aromatic Compounds in Bacteria and Saccharomyces cerevisiae. Appl Environ Microbiol 2015; 81:4458-76. [PMID: 25911487 DOI: 10.1128/aem.00405-15] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 04/20/2015] [Indexed: 11/20/2022] Open
Abstract
Phenylalanine and tyrosine ammonia-lyases form cinnamic acid and p-coumaric acid, which are precursors of a wide range of aromatic compounds of biotechnological interest. Lack of highly active and specific tyrosine ammonia-lyases has previously been a limitation in metabolic engineering approaches. We therefore identified 22 sequences in silico using synteny information and aiming for sequence divergence. We performed a comparative in vivo study, expressing the genes intracellularly in bacteria and yeast. When produced heterologously, some enzymes resulted in significantly higher production of p-coumaric acid in several different industrially important production organisms. Three novel enzymes were found to have activity exclusively for phenylalanine, including an enzyme from the low-GC Gram-positive bacterium Brevibacillus laterosporus, a bacterial-type enzyme from the amoeba Dictyostelium discoideum, and a phenylalanine ammonia-lyase from the moss Physcomitrella patens (producing 230 μM cinnamic acid per unit of optical density at 600 nm [OD600]) in the medium using Escherichia coli as the heterologous host). Novel tyrosine ammonia-lyases having higher reported substrate specificity than previously characterized enzymes were also identified. Enzymes from Herpetosiphon aurantiacus and Flavobacterium johnsoniae resulted in high production of p-coumaric acid in Escherichia coli (producing 440 μM p-coumaric acid OD600 unit(-1) in the medium) and in Lactococcus lactis. The enzymes were also efficient in Saccharomyces cerevisiae, where p-coumaric acid accumulation was improved 5-fold over that in strains expressing previously characterized tyrosine ammonia-lyases.
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25
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Zhu L, Zhou L, Cui W, Liu Z, Zhou Z. Mechanism-based site-directed mutagenesis to shift the optimum pH of the phenylalanine ammonia-lyase from Rhodotorula glutinis JN-1. ACTA ACUST UNITED AC 2014. [PMID: 28626644 PMCID: PMC5466100 DOI: 10.1016/j.btre.2014.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phenylalanine ammonia-lyase (RgPAL) from Rhodotorula glutinis JN-1 stereoselectively catalyzes the conversion of the l-phenylalanine into trans-cinnamic acid and ammonia, and was used in chiral resolution of dl-phenylalanine to produce the d-phenylalanine under acidic condition. However, the optimum pH of RgPAL is 9 and the RgPAL exhibits low catalytic efficiency at acidic side. Therefore, a mutant RgPAL with a lower optimum pH is expected. Based on catalytic mechanism and structure analysis, we constructed a mutant RgPAL-Q137E by site-directed mutagenesis, and found that this mutant had an extended optimum pH 7-9 with activity of 1.8-fold higher than that of the wild type at pH 7. As revealed by Friedel-Crafts-type mechanism of RgPAL, the improvement of the RgPAL-Q137E might be due to the negative charge of Glu137 which could stabilize the intermediate transition states through electrostatic interaction. The RgPAL-Q137E mutant was used to resolve the racemic dl-phenylalanine, and the conversion rate and the eeD value of d-phenylalanine using RgPAL-Q137E at pH 7 were increased by 29% and 48%, and achieved 93% and 86%, respectively. This work provides an effective strategy to shift the optimum pH which is favorable to further applications of RgPAL.
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Affiliation(s)
- Longbao Zhu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Li Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhongmei Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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26
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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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27
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Lovelock SL, Lloyd RC, Turner NJ. Phenylalanine Ammonia Lyase Catalyzed Synthesis of Amino Acids by an MIO-Cofactor Independent Pathway. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201311061] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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28
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Lovelock SL, Lloyd RC, Turner NJ. Phenylalanine Ammonia Lyase Catalyzed Synthesis of Amino Acids by an MIO-Cofactor Independent Pathway. Angew Chem Int Ed Engl 2014; 53:4652-6. [DOI: 10.1002/anie.201311061] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Indexed: 11/08/2022]
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29
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Hou Q, Sheng X, Liu Y. QM/MM studies of the mechanism of unusual bifunctional fructose-1,6-bisphosphate aldolase/phosphatase. Phys Chem Chem Phys 2014; 16:11366-73. [DOI: 10.1039/c3cp55263b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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30
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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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31
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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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32
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Toşa MI, Brem J, Mantu A, Irimie FD, Paizs C, Rétey J. The Interaction of Nitrophenylalanines with Wild Type and Mutant 4-Methylideneimidazole-5-one-less Phenylalanine Ammonia Lyase. ChemCatChem 2013. [DOI: 10.1002/cctc.201200536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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