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Wu T, Chen Y, Wei W, Song W, Wu J, Wen J, Hu G, Li X, Gao C, Chen X, Liu L. Mechanism-Guided Computational Design Drives meso-Diaminopimelate Dehydrogenase to Efficient Synthesis of Aromatic d-amino Acids. ACS Synth Biol 2024; 13:1879-1892. [PMID: 38847341 DOI: 10.1021/acssynbio.4c00176] [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] [Indexed: 06/22/2024]
Abstract
Aromatic d-amino acids (d-AAs) play a pivotal role as important chiral building blocks and key intermediates in fine chemical and drug synthesis. Meso-diaminopimelate dehydrogenase (DAPDH) serves as an excellent biocatalyst in the synthesis of d-AAs and their derivatives. However, its strict substrate specificity and the lack of efficient engineering methods have hindered its widespread application. Therefore, this study aims to elucidate the catalytic mechanism underlying DAPDH from Proteus vulgaris (PvDAPDH) through the examination of its crystallographic structure, computational simulations of potential energies and molecular dynamics simulations, and site-directed mutagenesis. Mechanism-guided computational design showed that the optimal mutant PvDAPDH-M3 increased specific activity and catalytic efficiency (kcat/Km) for aromatic keto acids up to 124-fold and 92.4-fold, respectively, compared to that of the wild type. Additionally, it expanded the substrate scope to 10 aromatic keto acid substrates. Finally, six high-value-added aromatic d-AAs and their derivatives were synthesized using a one-pot three-enzyme cascade reaction, exhibiting a good conversion rate ranging from 32 to 84% and excellent stereoselectivity (enantiomeric excess >99%). These findings provide a potential synthetic pathway for the green industrial production of aromatic d-AAs.
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Affiliation(s)
- Tianfu Wu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Yihan Chen
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Wanqing Wei
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Jian Wen
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Guipeng Hu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Xiaomin Li
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
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Tian S, Zhao G, Lv G, Wu C, Su R, Wang F, Wang Z, Liu Y, Chen N, Li Y. Efficient Fermentative Production of d-Alanine and Other d-Amino Acids by Metabolically Engineered Corynebacterium glutamicum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8039-8051. [PMID: 38545740 DOI: 10.1021/acs.jafc.4c00914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
d-Amino acids (d-AAs) have wide applications in industries such as pharmaceutical, food, and cosmetics due to their unique properties. Currently, the production of d-AAs has relied on chemical synthesis or enzyme catalysts, and it is challenging to produce d-AAs via direct fermentation from glucose. We observed that Corynebacterium glutamicum exhibits a remarkable tolerance to high concentrations of d-Ala, a crucial characteristic for establishing a successful fermentation process. By optimizing meso-diaminopilmelate dehydrogenases in different C. glutamicum strains and successively deleting l-Ala biosynthetic pathways, we developed an efficient d-Ala fermentation system. The d-Ala titer was enhanced through systems metabolic engineering, which involved strengthening glucose assimilation and pyruvate supply, reducing the formation of organic acid byproducts, and attenuating the TCA cycle. During fermentation in a 5-L bioreactor, a significant accumulation of l-Ala was observed in the broth, which was subsequently diminished by introducing an l-amino acid deaminase. Ultimately, the engineered strain DA-11 produced 85 g/L d-Ala with a yield of 0.30 g/g glucose, accompanied by an optical purity exceeding 99%. The fermentation platform has the potential to be extended for the synthesis of other d-AAs, as demonstrated by the production of d-Val and d-Glu.
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Affiliation(s)
- Siyu Tian
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Guihong Zhao
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Gengcheng Lv
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Chen Wu
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Rui Su
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Feiao Wang
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Zeting Wang
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Yuexiang Liu
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Ning Chen
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Yanjun Li
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
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Tomoiagă RB, Ursu M, Boros K, Nagy LC, Bencze LC. Ancestral l-amino acid oxidase: From substrate scope exploration to phenylalanine ammonia-lyase assay. J Biotechnol 2023; 377:43-52. [PMID: 37890533 DOI: 10.1016/j.jbiotec.2023.10.006] [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: 06/07/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 10/29/2023]
Abstract
In this study we assessed the applicability of the recently reported ancestral l-amino acid oxidase (AncLAAO), for the development of an enzyme-coupled phenylalanine ammonia-lyase (PAL) activity assay. Firstly, the expression and isolation of the AncLAAO-N1 was optimized, followed by activity tests of the obtained octameric N-terminal His-tagged enzyme towards various phenylalanine analogues to assess the compatibility of its substrate scope with that of the well-characterized PALs. AncLAAO-N1 showed high catalytic efficiency towards phenylalanines mono-, di-, or multiple-substituted in the meta- or para-positions, with ortho- substituted substrates being poorly transformed, these results highlighting the significant overlap between its substrate scope and those of PALs. After successful set-up of the AncLAAO-PAL coupled solid phase assay, in a 'proof of concept' approach we demonstrated its applicability for the high-throughput activity screens of PAL-libraries, by screening the saturation mutagenesis-derived I460NNK variant library of PAL from Petroselinum crispum, using p-MeO-phenylalanine as model substrate. Notably, the hits revealed by the coupled assay comprised all the active PAL variants: I460V, I460T, I460S, I460L, previously identified from the tested PAL-library by other assays. Our results validate the applicability of AncLAAO for coupled enzyme systems with phenylalanine ammonia-lyases, including cell-based assays suitable for the high-throughput screening of directed evolution-derived PAL-libraries.
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Affiliation(s)
- Raluca Bianca Tomoiagă
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Arany János Street 11, Cluj-Napoca RO-400028, Romania
| | - Marcel Ursu
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Arany János Street 11, Cluj-Napoca RO-400028, Romania
| | - Krisztina Boros
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Arany János Street 11, Cluj-Napoca RO-400028, Romania
| | - Levente Csaba Nagy
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Arany János Street 11, Cluj-Napoca RO-400028, Romania
| | - László Csaba Bencze
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Arany János Street 11, Cluj-Napoca RO-400028, Romania.
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Liu HL, Wu JM, Deng XT, Yu L, Yi PH, Liu ZQ, Xue YP, Jin LQ, Zheng YG. Development of an aminotransferase-driven biocatalytic cascade for deracemization of d,l-phosphinothricin. Biotechnol Bioeng 2023; 120:2940-2952. [PMID: 37227020 DOI: 10.1002/bit.28432] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/29/2023] [Accepted: 05/07/2023] [Indexed: 05/26/2023]
Abstract
2-oxo-4-[(hydroxy)(methyl)phosphinoyl]butyric acid (PPO) is the essential precursor keto acid for the asymmetric biosynthesis of herbicide l-phosphinothricin (l-PPT). Developing a biocatalytic cascade for PPO production with high efficiency and low cost is highly desired. Herein, a d-amino acid aminotransferase from Bacillus sp. YM-1 (Ym DAAT) with high activity (48.95 U/mg) and affinity (Km = 27.49 mM) toward d-PPT was evaluated. To circumvent the inhibition of by-product d-glutamate (d-Glu), an amino acceptor (α-ketoglutarate) regeneration cascade was constructed as a recombinant Escherichia coli (E. coli D), by coupling Ym d-AAT, d-aspartate oxidase from Thermomyces dupontii (TdDDO) and catalase from Geobacillus sp. CHB1. Moreover, the regulation of the ribosome binding site was employed to overcome the limiting step of expression toxic protein TdDDO in E. coli BL21(DE3). The aminotransferase-driven whole-cell biocatalytic cascade (E. coli D) showed superior catalytic efficiency for the synthesis of PPO from d,l-phosphinothricin (d,l-PPT). It revealed the production of PPO exhibited high space-time yield (2.59 g L-1 h-1 ) with complete conversion of d-PPT to PPO at high substrate concentration (600 mM d,l-PPT) in 1.5 L reaction system. This study first provides the synthesis of PPO from d,l-PPT employing an aminotransferase-driven biocatalytic cascade.
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Affiliation(s)
- Han-Lin Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Jia-Min Wu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Xin-Tong Deng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Lan Yu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Pu-Hong Yi
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Zhi-Qiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Ya-Ping Xue
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Li-Qun Jin
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Yu-Guo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
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Bakunova AK, Kostyukov AA, Kuzmin VA, Popov VO, Bezsudnova EY. Mechanistic aspects of the transamination reactions catalyzed by D-amino acid transaminase from Haliscomenobacter hydrossis. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140886. [PMID: 36496204 DOI: 10.1016/j.bbapap.2022.140886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/17/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022]
Abstract
Pyridoxal-5'-phosphate-(PLP-) dependent D-amino acid transaminases (DAATs) catalyze stereoselective reversible transfer of the amino group between D-amino acids and keto acids. In vivo DAATs are commonly known to synthesize D-glutamate for cell wall peptidoglycans. Today DAATs meet increasing attention for application in the synthesis of D-amino acids, whereas little is known about the mechanism of substrate recognition and catalytic steps of the D-amino acids conversion by DAATs. In this work, the pre-steady-state kinetics of the half-reactions of DAAT from Haliscomenobacter hydrossis with D-glutamate, D-alanine, D-leucine, and D-phenylalanine was examined at two wavelengths, 416 and 330 nm, using a stopped-flow technique. Monophasic kinetics was observed with specific substrates D-glutamate and D-alanine, whereas half-reactions with D-leucine and D-phenylalanine exhibited biphasic kinetics. All half-reactions proceeded until the complete conversion of PLP due to the release of the pyridoxamine-5'-phosphate form of cofactor from the holoenzyme . Comparison of kinetic parameters of half-reactions and the overall transamination reactions for D-leucine, D-phenylalanine revealed the increase in the rates of deamination of these substrates in the overall reaction with α-ketoglutarate. In the overall transamination reaction, the catalytic turnover rates for D-leucine and D-phenylalanine increased by 260 and 60 times, correspondingly, comparing with the slowest step rate constants in the half-reactions. We suggested the activating effect by a specific substrate α-ketoglutarate in the overall transamination reaction. The study of half-reactions helped to quantify the specificity of DAAT from H. hydrossis for D-amino acids with different properties. The results obtained are the first detailed analysis of half-reactions catalyzed by DAAT.
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Affiliation(s)
- Alina K Bakunova
- A.N.Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russian Federation
| | - Alexey A Kostyukov
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin st., 4, 119334 Moscow, Russian Federation
| | - Vladimir A Kuzmin
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin st., 4, 119334 Moscow, Russian Federation
| | - Vladimir O Popov
- A.N.Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russian Federation
| | - Ekaterina Yu Bezsudnova
- A.N.Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russian Federation.
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Asymmetric Synthesis of Enantiomerically Pure Aliphatic and Aromatic D-Amino Acids Catalyzed by Transaminase from Haliscomenobacter hydrossis. Catalysts 2022. [DOI: 10.3390/catal12121551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
D-amino acids are valuable building blocks for the synthesis of biologically active compounds and pharmaceuticals. The asymmetric synthesis of chiral amino acids from prochiral ketones using stereoselective enzymes is a well-known but far from exhausted approach for large-scale production. Herein, we investigated a pyridoxal-5′-phosphate-dependent D-amino acid transaminase from Haliscomenobacter hydrossis as a potential biocatalyst for the enzymatic asymmetric synthesis of optically pure aliphatic and aromatic D-amino acids. We studied the catalytic efficiency and stereoselectivity of transaminase from H. hydrossis in the amination of aliphatic and aromatic α-keto acids, using D-glutamate as a source of the amino group. We constructed a one-pot three-enzyme system, which included transaminase and two auxiliary enzymes, hydroxyglutarate dehydrogenase, and glucose dehydrogenase, to produce D-amino acids with a product yield of 95–99% and an enantiomeric excess of more than 99%. We estimated the stability of the transaminase and the cofactor leakage under reaction conditions. It was found that a high concentration of α-keto acids as well as a low reaction temperature (30 °C) can reduce the cofactor leakage under reaction conditions. The obtained results demonstrated the efficiency of transaminase from H. hydrossis in the asymmetric synthesis of enantiomerically pure D-amino acids.
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Williams V, Cui Y, Jiang X, Zhang C, Zhao J, Zhang N. Co-immobilized Multienzyme System for the Cofactor-Driven Cascade Synthesis of ( R) -2-Amino-3-(2-bromophenyl)propanoic Acid: A Model Reaction. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.2c00119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Vyasa Williams
- Center of Biosynthesis Technology, Asymchem Life Science (Tianjin) Co., Ltd., Tianjin 300457, P. R. China
| | - Yuxia Cui
- Center of Biosynthesis Technology, Asymchem Life Science (Tianjin) Co., Ltd., Tianjin 300457, P. R. China
| | - Xiangjun Jiang
- Center of Biosynthesis Technology, Asymchem Life Science (Tianjin) Co., Ltd., Tianjin 300457, P. R. China
| | - Chunyue Zhang
- Center of Biosynthesis Technology, Asymchem Life Science (Tianjin) Co., Ltd., Tianjin 300457, P. R. China
| | - Jiadong Zhao
- Center of Biosynthesis Technology, Asymchem Life Science (Tianjin) Co., Ltd., Tianjin 300457, P. R. China
| | - Na Zhang
- Center of Biosynthesis Technology, Asymchem Life Science (Tianjin) Co., Ltd., Tianjin 300457, P. R. China
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Jeon H, Pagar AD, Kang H, Giri P, Nadarajan SP, Sarak S, Khobragade TP, Lim S, Patil MD, Lee SG, Yun H. Creation of a ( R)-β-Transaminase by Directed Evolution of d-Amino Acid Aminotransferase. ACS Catal 2022. [DOI: 10.1021/acscatal.2c04221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hyunwoo Jeon
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Amol D. Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Hyeona Kang
- Department of Chemical and Biomolecular Engineering, Pusan National University, 63 Busan Daehak-ro, Beon-gil, Busan 46241, Korea
| | - Pritam Giri
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Saravanan P. Nadarajan
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Sharad Sarak
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Taresh P. Khobragade
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Seonga Lim
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Mahesh D. Patil
- Department of Nanomaterials and Application Technology, Center of Innovative and Applied Bioprocessing (CIAB), Sector-81, PO Manauli, S.A.S. Nagar, Mohali, Punjab 140306, India
| | - Sun-Gu Lee
- Department of Chemical and Biomolecular Engineering, Pusan National University, 63 Busan Daehak-ro, Beon-gil, Busan 46241, Korea
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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Han SW, Choi Y, Jang Y, Kim JS, Shin JS. One-pot biosynthesis of aromatic D-amino acids and neuroactive monoamines via enantioselective decarboxylation under in situ product removal using ion exchange resin. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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10
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Semi-Rational Design of Proteus mirabilis l-Amino Acid Deaminase for Expanding Its Substrate Specificity in α-Keto Acid Synthesis from l-Amino Acids. Catalysts 2022. [DOI: 10.3390/catal12020175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
l-amino acid deaminases (LAADs) are flavoenzymes that catalyze the stereospecific oxidative deamination of l-amino acids into α-keto acids, which are widely used in the pharmaceutical, food, chemical, and cosmetic industries. However, the substrate specificity of available LAADs is limited, and most substrates are concentrated on several bulky or basic l-amino acids. In this study, we employed a LAAD from Proteus mirabilis (PmiLAAD) and broadened its substrate specificity using a semi-rational design strategy. Molecular docking and alanine scanning identified F96, Q278, and E417 as key residues around the substrate-binding pocket of PmiLAAD. Site-directed saturation mutagenesis identified E417 as the key site for substrate specificity expansion. Expansion of the substrate channel with mutations of E417 (E417L, E417A) improved activity toward the bulky substrate l-Trp, and mutation of E417 to basic amino acids (E417K, E417H, E417R) enhanced the universal activity toward various l-amino acid substrates. The variant PmiLAADE417K showed remarkable catalytic activity improvement on seven substrates (l-Ala, l-Asp, l-Ile, l-Leu, l-Phe, l-Trp, and l-Val). The catalytic efficiency improvement obtained by E417 mutation may be attributed to the expansion of the entrance channel and its electrostatic interactions. These PmiLAAD variants with a broadened substrate spectrum can extend the application potential of LAADs.
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Bakunova AK, Nikolaeva AY, Rakitina TV, Isaikina TY, Khrenova MG, Boyko KM, Popov VO, Bezsudnova EY. The Uncommon Active Site of D-Amino Acid Transaminase from Haliscomenobacter hydrossis: Biochemical and Structural Insights into the New Enzyme. Molecules 2021; 26:molecules26165053. [PMID: 34443642 PMCID: PMC8401098 DOI: 10.3390/molecules26165053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 02/02/2023] Open
Abstract
Among industrially important pyridoxal-5’-phosphate (PLP)-dependent transaminases of fold type IV D-amino acid transaminases are the least studied. However, the development of cascade enzymatic processes, including the synthesis of D-amino acids, renewed interest in their study. Here, we describe the identification, biochemical and structural characterization of a new D-amino acid transaminase from Haliscomenobacter hydrossis (Halhy). The new enzyme is strictly specific towards D-amino acids and their keto analogs; it demonstrates one of the highest rates of transamination between D-glutamate and pyruvate. We obtained the crystal structure of the Halhy in the holo form with the protonated Schiff base formed by the K143 and the PLP. Structural analysis revealed a novel set of the active site residues that differ from the key residues forming the active sites of the previously studied D-amino acids transaminases. The active site of Halhy includes three arginine residues, one of which is unique among studied transaminases. We identified critical residues for the Halhy catalytic activity and suggested functions of the arginine residues based on the comparative structural analysis, mutagenesis, and molecular modeling simulations. We suggested a strong positive charge in the O-pocket and the unshaped P-pocket as a structural code for the D-amino acid specificity among transaminases of PLP fold type IV. Characteristics of Halhy complement our knowledge of the structural basis of substrate specificity of D-amino acid transaminases and the sequence-structure-function relationships in these enzymes.
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Affiliation(s)
- Alina K. Bakunova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia; (A.K.B.); (A.Y.N.); (T.V.R.); (T.Y.I.); (M.G.K.); (K.M.B.); (V.O.P.)
| | - Alena Yu. Nikolaeva
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia; (A.K.B.); (A.Y.N.); (T.V.R.); (T.Y.I.); (M.G.K.); (K.M.B.); (V.O.P.)
| | - Tatiana V. Rakitina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia; (A.K.B.); (A.Y.N.); (T.V.R.); (T.Y.I.); (M.G.K.); (K.M.B.); (V.O.P.)
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia
| | - Tatiana Y. Isaikina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia; (A.K.B.); (A.Y.N.); (T.V.R.); (T.Y.I.); (M.G.K.); (K.M.B.); (V.O.P.)
| | - Maria G. Khrenova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia; (A.K.B.); (A.Y.N.); (T.V.R.); (T.Y.I.); (M.G.K.); (K.M.B.); (V.O.P.)
- Chemistry Department, Lomonosov Moscow State University, Leninskiye Gory 1/3, 119991 Moscow, Russia
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia; (A.K.B.); (A.Y.N.); (T.V.R.); (T.Y.I.); (M.G.K.); (K.M.B.); (V.O.P.)
| | - Vladimir O. Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia; (A.K.B.); (A.Y.N.); (T.V.R.); (T.Y.I.); (M.G.K.); (K.M.B.); (V.O.P.)
| | - Ekaterina Yu. Bezsudnova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia; (A.K.B.); (A.Y.N.); (T.V.R.); (T.Y.I.); (M.G.K.); (K.M.B.); (V.O.P.)
- Correspondence: author E-mail:
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12
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Martínez-Rodríguez S, Torres JM, Sánchez P, Ortega E. Overview on Multienzymatic Cascades for the Production of Non-canonical α-Amino Acids. Front Bioeng Biotechnol 2020; 8:887. [PMID: 32850740 PMCID: PMC7431475 DOI: 10.3389/fbioe.2020.00887] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/09/2020] [Indexed: 12/11/2022] Open
Abstract
The 22 genetically encoded amino acids (AAs) present in proteins (the 20 standard AAs together with selenocysteine and pyrrolysine), are commonly referred as proteinogenic AAs in the literature due to their appearance in ribosome-synthetized polypeptides. Beyond the borders of this key set of compounds, the rest of AAs are generally named imprecisely as non-proteinogenic AAs, even when they can also appear in polypeptide chains as a result of post-transductional machinery. Besides their importance as metabolites in life, many of D-α- and L-α-"non-canonical" amino acids (NcAAs) are of interest in the biotechnological and biomedical fields. They have found numerous applications in the discovery of new medicines and antibiotics, drug synthesis, cosmetic, and nutritional compounds, or in the improvement of protein and peptide pharmaceuticals. In addition to the numerous studies dealing with the asymmetric synthesis of NcAAs, many different enzymatic pathways have been reported in the literature allowing for the biosynthesis of NcAAs. Due to the huge heterogeneity of this group of molecules, this review is devoted to provide an overview on different established multienzymatic cascades for the production of non-canonical D-α- and L-α-AAs, supplying neophyte and experienced professionals in this field with different illustrative examples in the literature. Whereas the discovery of new or newly designed enzymes is of great interest, dusting off previous enzymatic methodologies by a "back and to the future" strategy might accelerate the implementation of new or improved multienzymatic cascades.
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13
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Pollegioni L, Rosini E, Molla G. Advances in Enzymatic Synthesis of D-Amino Acids. Int J Mol Sci 2020; 21:E3206. [PMID: 32369969 PMCID: PMC7247363 DOI: 10.3390/ijms21093206] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 01/02/2023] Open
Abstract
In nature, the D-enantiomers of amino acids (D-AAs) are not used for protein synthesis and during evolution acquired specific and relevant physiological functions in different organisms. This is the reason for the surge in interest and investigations on these "unnatural" molecules observed in recent years. D-AAs are increasingly used as building blocks to produce pharmaceuticals and fine chemicals. In past years, a number of methods have been devised to produce D-AAs based on enantioselective enzymes. With the aim to increase the D-AA derivatives generated, to improve the intrinsic atomic economy and cost-effectiveness, and to generate processes at low environmental impact, recent studies focused on identification, engineering and application of enzymes in novel biocatalytic processes. The aim of this review is to report the advances in synthesis of D-AAs gathered in the past few years based on five main classes of enzymes. These enzymes have been combined and thus applied to multi-enzymatic processes representing in vitro pathways of alternative/exchangeable enzymes that allow the generation of an artificial metabolism for D-AAs synthetic purposes.
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Affiliation(s)
| | | | - Gianluca Molla
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy; (L.P.); (E.R.)
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14
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Voss M, Xiang C, Esque J, Nobili A, Menke MJ, André I, Höhne M, Bornscheuer UT. Creation of ( R)-Amine Transaminase Activity within an α-Amino Acid Transaminase Scaffold. ACS Chem Biol 2020; 15:416-424. [PMID: 31990173 DOI: 10.1021/acschembio.9b00888] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The enzymatic transamination of ketones into (R)-amines represents an important route for accessing a range of pharmaceuticals or building blocks. Although many publications have dealt with enzyme discovery, protein engineering, and the application of (R)-selective amine transaminases [(R)-ATA] in biocatalysis, little is known about the actual in vivo role and how these enzymes have evolved from the ubiquitous α-amino acid transaminases (α-AATs). Here, we show the successful introduction of an (R)-transaminase activity in an α-amino acid aminotransferase with one to six amino acid substitutions in the enzyme's active site. Bioinformatic analysis combined with computational redesign of the d-amino acid aminotransferase (DATA) led to the identification of a sextuple variant having a specific activity of 326 milliunits mg-1 in the conversion of (R)-phenylethylamine and pyruvate to acetophenone and d-alanine. This value is similar to those of natural (R)-ATAs, which typically are in the range of 250 milliunits mg-1. These results demonstrate that (R)-ATAs can evolve from α-AAT as shown here for the DATA scaffold.
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Affiliation(s)
- Moritz Voss
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
| | - Chao Xiang
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
| | - Jérémy Esque
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, 135, Avenue de Rangueil, F-31077 Toulouse cedex 04, France
| | - Alberto Nobili
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
| | - Marian J. Menke
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
| | - Isabelle André
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, 135, Avenue de Rangueil, F-31077 Toulouse cedex 04, France
| | - Matthias Höhne
- Protein Biochemistry, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
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15
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Non‐Enzymatic Hybrid Catalysis for Stereoconversion ofl‐Amino Acid Derivatives tod‐Isomers. ASIAN J ORG CHEM 2020. [DOI: 10.1002/ajoc.202000067] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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16
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The production of L- and D-phenylalanines using engineered phenylalanine ammonia lyases from Petroselinum crispum. Sci Rep 2019; 9:20123. [PMID: 31882791 PMCID: PMC6934771 DOI: 10.1038/s41598-019-56554-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/12/2019] [Indexed: 12/17/2022] Open
Abstract
The biocatalytic synthesis of l- and d-phenylalanine analogues of high synthetic value have been developed using as biocatalysts mutant variants of phenylalanine ammonia lyase from Petroselinum crispum (PcPAL), specifically tailored towards mono-substituted phenylalanine and cinnamic acid substrates. The catalytic performance of the engineered PcPAL variants was optimized within the ammonia elimination and ammonia addition reactions, focusing on the effect of substrate concentration, biocatalyst:substrate ratio, reaction buffer and reaction time, on the conversion and enantiomeric excess values. The optimal conditions provided an efficient preparative scale biocatalytic procedure of valuable phenylalanines, such as (S)-m-methoxyphenylalanine (Y = 40%, ee > 99%), (S)-p-bromophenylalanine (Y = 82%, ee > 99%), (S)-m-(trifluoromethyl)phenylalanine (Y = 26%, ee > 99%), (R)-p-methylphenylalanine, (Y = 49%, ee = 95%) and (R)-m-(trifluoromethyl)phenylalanine (Y = 34%, ee = 93%).
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Parmeggiani F, Rué Casamajo A, Walton CJW, Galman JL, Turner NJ, Chica RA. One-Pot Biocatalytic Synthesis of Substituted d-Tryptophans from Indoles Enabled by an Engineered Aminotransferase. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00739] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Fabio Parmeggiani
- Manchester Institute of Biotechnology (MIB), School of Chemistry, University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Arnau Rué Casamajo
- Manchester Institute of Biotechnology (MIB), School of Chemistry, University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Curtis J. W. Walton
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, K1N 6N5, Ottawa, Ontario, Canada
- Centre for Catalysis Research and Innovation, University of Ottawa, 30 Marie-Curie, K1N 6N5, Ottawa, Ontario, Canada
| | - James L. Galman
- Manchester Institute of Biotechnology (MIB), School of Chemistry, University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Nicholas J. Turner
- Manchester Institute of Biotechnology (MIB), School of Chemistry, University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Roberto A. Chica
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, K1N 6N5, Ottawa, Ontario, Canada
- Centre for Catalysis Research and Innovation, University of Ottawa, 30 Marie-Curie, K1N 6N5, Ottawa, Ontario, Canada
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18
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Zhang D, Jing X, Zhang W, Nie Y, Xu Y. Highly selective synthesis of d-amino acids from readily available l-amino acids by a one-pot biocatalytic stereoinversion cascade. RSC Adv 2019; 9:29927-29935. [PMID: 35531513 PMCID: PMC9072125 DOI: 10.1039/c9ra06301c] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 09/16/2019] [Indexed: 11/21/2022] Open
Abstract
d-Amino acids are key intermediates required for the synthesis of important pharmaceuticals. However, establishing a universal enzymatic method for the general synthesis of d-amino acids from cheap and readily available precursors with few by-products is challenging. In this study, we constructed and optimized a cascade enzymatic route involving l-amino acid deaminase and d-amino acid dehydrogenase for the biocatalytic stereoinversions of l-amino acids into d-amino acids. Using l-phenylalanine (l-Phe) as a model substrate, this artificial biocatalytic cascade stereoinversion route first deaminates l-Phe to phenylpyruvic acid (PPA) through catalysis involving recombinant Escherichia coli cells that express l-amino acid deaminase from Proteus mirabilis (PmLAAD), followed by stereoselective reductive amination with recombinant meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum (StDAPDH) to produce d-phenylalanine (d-Phe). By incorporating a formate dehydrogenase-based NADPH-recycling system, d-Phe was obtained in quantitative yield with an enantiomeric excess greater than 99%. In addition, the cascade reaction system was also used to stereoinvert a variety of aromatic and aliphatic l-amino acids to the corresponding d-amino acids by combining the PmLAAD whole-cell biocatalyst with the StDAPDH variant. Hence, this method represents a concise and efficient route for the asymmetric synthesis of d-amino acids from the corresponding l-amino acids. An efficient one-pot biocatalytic cascade was developed for synthesis of d-amino acids from readily available l-amino acids via stereoinversion.![]()
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Affiliation(s)
- Danping Zhang
- School of Biotechnology
- Key Laboratory of Industrial Biotechnology
- Ministry of Education
- Jiangnan University
- Wuxi 214122
| | - Xiaoran Jing
- School of Biotechnology
- Key Laboratory of Industrial Biotechnology
- Ministry of Education
- Jiangnan University
- Wuxi 214122
| | - Wenli Zhang
- School of Biotechnology
- Key Laboratory of Industrial Biotechnology
- Ministry of Education
- Jiangnan University
- Wuxi 214122
| | - Yao Nie
- School of Biotechnology
- Key Laboratory of Industrial Biotechnology
- Ministry of Education
- Jiangnan University
- Wuxi 214122
| | - Yan Xu
- School of Biotechnology
- Key Laboratory of Industrial Biotechnology
- Ministry of Education
- Jiangnan University
- Wuxi 214122
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19
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Walton CJW, Thiebaut F, Brunzelle JS, Couture JF, Chica RA. Structural Determinants of the Stereoinverting Activity of Pseudomonas stutzeri d-Phenylglycine Aminotransferase. Biochemistry 2018; 57:5437-5446. [PMID: 30153007 DOI: 10.1021/acs.biochem.8b00767] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aromatic d-amino acids are key precursors for the production of many small molecule therapeutics. Therefore, the development of biocatalytic methods for their synthesis is of great interest. An enzyme that has great potential as a biocatalyst for the synthesis of d-amino acids is the stereoinverting d-phenylglycine aminotransferase (DPAT) from Pseudomonas stutzeri ST-201. This enzyme catalyzes a unique l to d transamination reaction that produces d-phenylglycine and α-ketoglutarate from benzoylformate and l-glutamate, via a mechanism that is poorly understood. Here, we present the crystal structure of DPAT, which shows that the enzyme folds into a two-domain structure representative of class III aminotransferases. Guided by the crystal structure, we performed saturation mutagenesis to probe the substrate binding pockets of the enzyme. These experiments helped us identify two arginine residues (R34 and R407), one in each binding pocket, that are essential to catalysis. Together with kinetic analyses using a library of amino acid substrates, our mutagenesis and structural studies allow us to propose a binding model that explains the dual l/d specificity of DPAT. Our kinetic analyses also demonstrate that DPAT can catalyze the transamination of β- and γ-amino acids, reclassifying this enzyme as an ω-aminotransferase. Collectively, our studies highlight that the DPAT active site is amenable to protein engineering for expansion of its substrate scope, which offers the opportunity to generate new biocatalysts for the synthesis of a variety of valuable optically pure d-amino acids from inexpensive and abundant l-amino acids.
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Affiliation(s)
- Curtis J W Walton
- Department of Chemistry and Biomolecular Sciences , University of Ottawa , Ottawa , Ontario , Canada K1N 6N5.,Centre for Catalysis Research and Innovation , University of Ottawa , Ottawa , Ontario , Canada K1N 6N5
| | - Frédéric Thiebaut
- Department of Chemistry and Biomolecular Sciences , University of Ottawa , Ottawa , Ontario , Canada K1N 6N5.,Centre for Catalysis Research and Innovation , University of Ottawa , Ottawa , Ontario , Canada K1N 6N5
| | - Joseph S Brunzelle
- Life Science Collaborative Access Team, Northwestern Synchrotron Research Centers , Northwestern University , Argonne , Illinois 60439 , United States
| | - Jean-François Couture
- Centre for Catalysis Research and Innovation , University of Ottawa , Ottawa , Ontario , Canada K1N 6N5.,Department of Biochemistry, Microbiology and Immunology, and Ottawa Institute of Systems Biology , University of Ottawa , Ottawa , Ontario , Canada K1H 8M5
| | - Roberto A Chica
- Department of Chemistry and Biomolecular Sciences , University of Ottawa , Ottawa , Ontario , Canada K1N 6N5.,Centre for Catalysis Research and Innovation , University of Ottawa , Ottawa , Ontario , Canada K1N 6N5
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