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Chen Q, Wang J, Zhang S, Chen X, Hao J, Wu Q, Zhu D. Discovery and directed evolution of C-C bond formation enzymes for the biosynthesis of β-hydroxy-α-amino acids and derivatives. Crit Rev Biotechnol 2024:1-20. [PMID: 38566472 DOI: 10.1080/07388551.2024.2332295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/16/2024] [Indexed: 04/04/2024]
Abstract
β-Hydroxy-α-amino acids (β-HAAs) have extensive applications in the pharmaceutical, chemical synthesis, and food industries. The development of synthetic methodologies aimed at producing optically pure β-HAAs has been driven by practical applications. Among the various synthetic methods, biocatalytic asymmetric synthesis is considered a sustainable approach due to its capacity to generate two stereogenic centers from simple prochiral precursors in a single step. Therefore, extensive efforts have been made in recent years to search for effective enzymes which enable such biotransformation. This review provides an overview on the discovery and engineering of C-C bond formation enzymes for the biocatalytic synthesis of β-HAAs. We highlight examples where the use of threonine aldolases, threonine transaldolases, serine hydroxymethyltransferases, α-methylserine aldolases, α-methylserine hydroxymethyltransferases, and engineered alanine racemases facilitated the synthesis of β-HAAs. Additionally, we discuss the potential future advancements and persistent obstacles in the enzymatic synthesis of β-HAAs.
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Affiliation(s)
- Qijia Chen
- College of Food Science and Biology, University of Science and Technology, Shijiazhuang, China
| | - Jingmin Wang
- College of Food Science and Biology, University of Science and Technology, Shijiazhuang, China
| | - Sisi Zhang
- College of Food Science and Biology, University of Science and Technology, Shijiazhuang, China
| | - Xi Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jianxiong Hao
- College of Food Science and Biology, University of Science and Technology, Shijiazhuang, China
| | - Qiaqing Wu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Dunming Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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Hirato Y, Goto M, Mizobuchi T, Muramatsu H, Tanigawa M, Nishimura K. Structure of pyridoxal 5'-phosphate-bound D-threonine aldolase from Chlamydomonas reinhardtii. Acta Crystallogr F Struct Biol Commun 2023; 79:31-37. [PMID: 36748339 PMCID: PMC9903138 DOI: 10.1107/s2053230x23000304] [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: 09/06/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023] Open
Abstract
D-Threonine aldolase (DTA) is a pyridoxal-5'-phosphate-dependent enzyme which catalyzes the reversible aldol reaction of glycine with a corresponding aldehyde to yield the D-form β-hydroxy-α-amino acid. This study produced and investigated the crystal structure of DTA from Chlamydomonas reinhardtii (CrDTA) at 1.85 Å resolution. To our knowledge, this is the first report on the crystal structure of eukaryotic DTA. Compared with the structure of bacterial DTA, CrDTA has a similar arrangement of active-site residues. On the other hand, we speculated that some non-conserved residues alter the affinity for substrates and inhibitors. The structure of CrDTA could provide insights into the structural framework for structure-guided protein engineering studies to modify reaction selectivity.
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Affiliation(s)
- Yuki Hirato
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Masaru Goto
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Taichi Mizobuchi
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Hisashi Muramatsu
- Multidisciplinary Science Cluster, Research and Education Faculty, Kochi University, B200 Monobe, Nankoku, Kochi 783-8502, Japan
| | - Minoru Tanigawa
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, Building No. 2, 1-5-1 Kanda Surugadai, Chiyoda, Tokyo 101-0062, Japan
| | - Katsushi Nishimura
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, Building No. 2, 1-5-1 Kanda Surugadai, Chiyoda, Tokyo 101-0062, Japan
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Cai B, Bocola M, Zhou A, Sun F, Xu Q, Yang J, Shen T, Zhang Z, Sun L, Ji Y, Bong YK, Daussmann T, Chen H. Computer-aided directed evolution ofl-threonine aldolase for asymmetric biocatalytic synthesis of a chloramphenicol intermediate. Bioorg Med Chem 2022; 68:116880. [PMID: 35714535 DOI: 10.1016/j.bmc.2022.116880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 11/29/2022]
Abstract
l-Threonine aldolases (LTAs) employing pyridoxal phosphate (PLP) as cofactor can convert low-cost achiral substrates glycine and aldehyde directly into valuable β-hydroxy-α-amino acids such as (2R,3S)-2-amino-3-hydroxy-3-(4-nitrophenyl) propanoic acid ((R,S)-AHNPA), which is utilized broadly as crucial chiral intermediates for bioactive compounds. However, LTAs' stereospecificity towards the β carbon is rather moderate and their activity and stability at high substrate load is low, which limits their industrial application. Here, computer-aided directed evolution was applied to improve overall activity, selectivity and stability under desired process conditions of a l-threonine aldolase in the asymmetric synthesis of (R,S)-AHNPA. Selectivity and stability determining regions were computationally identified for structure-guided directed evolution of LTA-variants under efficient biocatalytic process conditions using 40% ethanol as cosolvent. We applied molecular modeling to rationalize selectivity improvement and design focused libraries targeting the substrate binding pocket, and we also used MD simulations in nonaqueous process environment as an effective and promising method to predict potential unstable loop regions near the tetramer interface which are hot-spots for cosolvent resistance. An excellent LTA variant EM-ALDO031 with 18 mutations was obtained, which showed ∼ 30-fold stability improvement in 40% ethanol and diastereoselectivity (de) raised from 31.5% to 85% through a three-phase evolution campaign. Our fast and efficient data-driven methodology utilizing a combination of experimental and computational tools enabled us to evolve an aldolase variant to achieve the target of 90% conversion at up to 150 g/L substrate load in 40% ethanol, enabling the biocatalytic production of β-hydroxy-α-amino acids from cheap achiral precursors at multi-ton scale.
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Affiliation(s)
- Baoqin Cai
- Enzymaster (Ningbo) Bio-engineering Co., Ltd, Zhejiang Innovation Center, No.2646 East Zhongshan Road, Ningbo 31500, China
| | - Marco Bocola
- Enzymaster Deutschland GmbH, Neusser Str. 39, Düsseldorf 40219, Germany
| | - Ameng Zhou
- Enzymaster (Ningbo) Bio-engineering Co., Ltd, Zhejiang Innovation Center, No.2646 East Zhongshan Road, Ningbo 31500, China
| | - Fenshuai Sun
- Enzymaster (Ningbo) Bio-engineering Co., Ltd, Zhejiang Innovation Center, No.2646 East Zhongshan Road, Ningbo 31500, China
| | - Qing Xu
- Enzymaster (Ningbo) Bio-engineering Co., Ltd, Zhejiang Innovation Center, No.2646 East Zhongshan Road, Ningbo 31500, China
| | - Jiadong Yang
- Enzymaster (Ningbo) Bio-engineering Co., Ltd, Zhejiang Innovation Center, No.2646 East Zhongshan Road, Ningbo 31500, China
| | - Tianran Shen
- Enzymaster (Ningbo) Bio-engineering Co., Ltd, Zhejiang Innovation Center, No.2646 East Zhongshan Road, Ningbo 31500, China
| | - Zhaoqi Zhang
- Enzymaster (Ningbo) Bio-engineering Co., Ltd, Zhejiang Innovation Center, No.2646 East Zhongshan Road, Ningbo 31500, China
| | - Lei Sun
- Enzymaster (Ningbo) Bio-engineering Co., Ltd, Zhejiang Innovation Center, No.2646 East Zhongshan Road, Ningbo 31500, China
| | - Yaoyao Ji
- Enzymaster (Ningbo) Bio-engineering Co., Ltd, Zhejiang Innovation Center, No.2646 East Zhongshan Road, Ningbo 31500, China
| | - Yong Koy Bong
- Enzymaster (Ningbo) Bio-engineering Co., Ltd, Zhejiang Innovation Center, No.2646 East Zhongshan Road, Ningbo 31500, China
| | - Thomas Daussmann
- Enzymaster Deutschland GmbH, Neusser Str. 39, Düsseldorf 40219, Germany
| | - Haibin Chen
- Enzymaster (Ningbo) Bio-engineering Co., Ltd, Zhejiang Innovation Center, No.2646 East Zhongshan Road, Ningbo 31500, China.
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Zheng W, Pu Z, Xiao L, Xu G, Yang LR, Yu H, Wu J. Substrate access path-guided engineering of L-threonine aldolase for improving diastereoselectivity. Chem Commun (Camb) 2022; 58:8258-8261. [DOI: 10.1039/d2cc02644a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The L-threonine aldolase from Leishmania major was engineered to improve diastereoselectivity by a CAST/ISM strategy, providing insights into the relationship between physico -chemical properties of substrate access path and diastereoselectivity....
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