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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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Nieto-Domínguez M, Sako A, Enemark-Rasmussen K, Gotfredsen CH, Rago D, Nikel PI. Enzymatic synthesis of mono- and trifluorinated alanine enantiomers expands the scope of fluorine biocatalysis. Commun Chem 2024; 7:104. [PMID: 38724655 PMCID: PMC11082193 DOI: 10.1038/s42004-024-01188-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/24/2024] [Indexed: 05/12/2024] Open
Abstract
Fluorinated amino acids serve as an entry point for establishing new-to-Nature chemistries in biological systems, and novel methods are needed for the selective synthesis of these building blocks. In this study, we focused on the enzymatic synthesis of fluorinated alanine enantiomers to expand fluorine biocatalysis. The alanine dehydrogenase from Vibrio proteolyticus and the diaminopimelate dehydrogenase from Symbiobacterium thermophilum were selected for in vitro production of (R)-3-fluoroalanine and (S)-3-fluoroalanine, respectively, using 3-fluoropyruvate as the substrate. Additionally, we discovered that an alanine racemase from Streptomyces lavendulae, originally selected for setting an alternative enzymatic cascade leading to the production of these non-canonical amino acids, had an unprecedented catalytic efficiency in β-elimination of fluorine from the monosubstituted fluoroalanine. The in vitro enzymatic cascade based on the dehydrogenases of V. proteolyticus and S. thermophilum included a cofactor recycling system, whereby a formate dehydrogenase from Pseudomonas sp. 101 (either native or engineered) coupled formate oxidation to NAD(P)H formation. Under these conditions, the reaction yields for (R)-3-fluoroalanine and (S)-3-fluoroalanine reached >85% on the fluorinated substrate and proceeded with complete enantiomeric excess. The selected dehydrogenases also catalyzed the conversion of trifluoropyruvate into trifluorinated alanine as a first-case example of fluorine biocatalysis with amino acids carrying a trifluoromethyl group.
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Affiliation(s)
- Manuel Nieto-Domínguez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Aboubakar Sako
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | | | - Daniela Rago
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
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Ma Q, Wang X, Luan F, Han P, Zheng X, Yin Y, Zhang X, Zhang Y, Gao X. Functional Studies on an Indel Loop between the Subtypes of meso-Diaminopimelate Dehydrogenase. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Qinyuan Ma
- School of Life Science and Medicine, Shandong University of Technology, Zibo 255000, China
| | - Xiaoxiao Wang
- School of Life Science and Medicine, Shandong University of Technology, Zibo 255000, China
| | - Fang Luan
- School of Life Science and Medicine, Shandong University of Technology, Zibo 255000, China
| | - Ping Han
- School of Life Science and Medicine, Shandong University of Technology, Zibo 255000, China
| | - Xue Zheng
- School of Life Science and Medicine, Shandong University of Technology, Zibo 255000, China
| | - Yanmiao Yin
- School of Life Science and Medicine, Shandong University of Technology, Zibo 255000, China
| | - Xianghe Zhang
- School of Life Science and Medicine, Shandong University of Technology, Zibo 255000, China
| | - Yàning Zhang
- School of Life Science and Medicine, Shandong University of Technology, Zibo 255000, China
| | - Xiuzhen Gao
- School of Life Science and Medicine, Shandong University of Technology, Zibo 255000, China
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Wang X, Ma Q, Shen J, Wang B, Gao X, Zhao L. Application Fields, Positions, and Bioinformatic Mining of Non-active Sites: A Mini-Review. Front Chem 2021; 9:661008. [PMID: 34136463 PMCID: PMC8201498 DOI: 10.3389/fchem.2021.661008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/21/2021] [Indexed: 11/22/2022] Open
Abstract
Active sites of enzymes play a vital role in catalysis, and researchhas been focused on the interactions between active sites and substrates to understand the biocatalytic process. However, the active sites distal to the catalytic cavity also participate in catalysis by maintaining the catalytic conformations. Therefore, some researchers have begun to investigate the roles of non-active sites in proteins, especially for enzyme families with different functions. In this mini-review, we focused on recent progress in research on non-active sites of enzymes. First, we outlined two major research methodswith non-active sites as direct targets, including understanding enzymatic mechanisms and enzyme engineering. Second, we classified the positions of reported non-active sites in enzyme structures and studied the molecular mechanisms underlying their functions, according to the literature on non-active sites. Finally, we summarized the results of bioinformatic analysisof mining non-active sites as targets for protein engineering.
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Affiliation(s)
- Xiaoxiao Wang
- School of Life Science, Shandong University of Technology, Zibo, China
| | - Qinyuan Ma
- School of Life Science, Shandong University of Technology, Zibo, China
| | - Jian Shen
- Shandong Jincheng Pharmaceutical Group Co.LTD, Zibo, China
| | - Bin Wang
- Shandong Jincheng Pharmaceutical Group Co.LTD, Zibo, China
| | - Xiuzhen Gao
- School of Life Science, Shandong University of Technology, Zibo, China
| | - Liming Zhao
- School of Life Science, Shandong University of Technology, Zibo, China.,Shandong Jincheng Pharmaceutical Group Co.LTD, Zibo, China.,State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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Tan X, Zhang S, Song W, Liu J, Gao C, Chen X, Liu L, Wu J. A multi-enzyme cascade for efficient production of D-p-hydroxyphenylglycine from L-tyrosine. BIORESOUR BIOPROCESS 2021; 8:41. [PMID: 38650231 PMCID: PMC10991500 DOI: 10.1186/s40643-021-00394-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/10/2021] [Indexed: 11/10/2022] Open
Abstract
In this study, a four-enzyme cascade pathway was developed and reconstructed in vivo for the production of D-p-hydroxyphenylglycine (D-HPG), a valuable intermediate used to produce β-lactam antibiotics and in fine-chemical synthesis, from L-tyrosine. In this pathway, catalytic conversion of the intermediate 4-hydroxyphenylglyoxalate by meso-diaminopimelate dehydrogenase from Corynebacterium glutamicum (CgDAPDH) was identified as the rate-limiting step, followed by application of a mechanism-guided "conformation rotation" strategy to decrease the hydride-transfer distance d(C6HDAP-C4NNADP) and increase CgDAPDH activity. Introduction of the best variant generated by protein engineering (CgDAPDHBC621/D120S/W144S/I169P with 5.32 ± 0.85 U·mg-1 specific activity) into the designed pathway resulted in a D-HPG titer of 42.69 g/L from 50-g/L L-tyrosine in 24 h, with 92.5% conversion, 71.5% isolated yield, and > 99% enantiomeric excess in a 3-L fermenter. This four-enzyme cascade provides an efficient enzymatic approach for the industrial production of D-HPG from cheap amino acids.
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Affiliation(s)
- Xu Tan
- School of Pharmaceutical Science, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Sheng Zhang
- Zhejiang Tianrui Chemical Co., Ltd, Quzhou, 324400, China
| | - Wei Song
- School of Pharmaceutical Science, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Jing Wu
- School of Pharmaceutical Science, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.
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Characterization of an NAD(P) +-dependent meso-diaminopimelate dehydrogenase from Thermosyntropha lipolytica. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140476. [PMID: 32599299 DOI: 10.1016/j.bbapap.2020.140476] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 11/22/2022]
Abstract
meso-Diaminopimelate dehydrogenase (meso-DAPDH) catalyzes the reversible NADP+-dependent oxidative deamination of meso-2,6-diaminopimelate (meso-DAP) to produce l-2-amino-6-oxopimelate. meso-DAPDH is divided into two major clusters, types I and II, based on substrate specificity and structural characteristic. Here, we describe a novel type II meso-DAPDH from Thermosyntropha lipolytica (TlDAPDH). The gene encoding a putative TlDAPDH was expressed in Escherichia coli cells, and then the enzyme was purified 7.3-fold to homogeneity from the crude cell extract. The molecule of TlDAPDH seemed to form a hexamer, which is the typical structural characteristic of type II meso-DAPDHs. The purified enzyme exhibited oxidative deamination activity toward meso-DAP with both NADP+ and NAD+ as coenzymes. TlDAPDH exhibited reductive amination activity of corresponding 2-oxo acid to produce d-amino acid. In particular, the productivities for d-aspartate and d-glutamate have not been reported in the type II enzymes. The optimum pH and temperature for oxidative deamination of meso-DAP were 10.5 and 55°C, respectively. TlDAPDH retained more than 80% of its activity after incubation for 30 min at temperatures between 50°C and 65°C and in the pH range of 4.5-9.5. Moreover, the coenzyme and substrate recognition mechanisms of TlDAPDH were elucidated based on a multiple sequence alignment and the homology model. The results of these analyses suggested that the molecular mechanisms for coenzyme and substrate recognition of TlDAPDH were similar to those of meso-DAPDH from S. thermophilum, which is the representative type II enzyme. Based on the kinetic characteristics and structural comparison, TlDAPDH was considered to be a novel type II meso-DAPDH.
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Akita H, Nakamichi Y, Morita T, Matsushika A. Identification and functional characterization of NAD(P) + -dependent meso-diaminopimelate dehydrogenase from Numidum massiliense. Microbiologyopen 2020; 9:e1059. [PMID: 32485072 PMCID: PMC7424261 DOI: 10.1002/mbo3.1059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/23/2020] [Accepted: 04/28/2020] [Indexed: 02/06/2023] Open
Abstract
meso‐Diaminopimelate dehydrogenase (meso‐DAPDH) catalyzes the reversible NADP+‐dependent oxidative deamination of meso‐2,6‐diaminopimelate (meso‐DAP) to produce l‐2‐amino‐6‐oxopimelate. Moreover, d‐amino acid dehydrogenase (d‐AADHs) derived from protein‐engineered meso‐DAPDH is useful for one‐step synthesis of d‐amino acids with high optical purity. Here, we report the identification and functional characterization of a novel NAD(P)+‐dependent meso‐DAPDH from Numidum massiliense (NmDAPDH). After the gene encoding the putative NmDAPDH was expressed in recombinant Escherichia coli cells, the enzyme was purified 4.0‐fold to homogeneity from the crude extract through five purification steps. Although the previously known meso‐DAPDHs use only NADP+ as a coenzyme, NmDAPDH was able to use both NADP+ and NAD+ as coenzymes. When NADP+ was used as a coenzyme, NmDAPDH exhibited an approximately 2 times higher kcat/Km value toward meso‐DAP than that of meso‐DAPDH from Symbiobacterium thermophilum (StDAPDH). NmDAPDH also catalyzed the reductive amination of corresponding 2‐oxo acids to produce acidic d‐amino acids such as d‐aspartate and d‐glutamate. The optimum pH and temperature for the oxidative deamination of meso‐DAP were about 10.5 and 75°C, respectively. Like StDAPDH, NmDAPDH exhibited high stability: it retained more than 75% of its activity after 30 min at 60°C (pH 7.2) or at pHs ranging from 5.5 to 13.0 (50°C). Alignment of the amino acid sequences of NmDAPDH and the known meso‐DAPDHs suggested NmDAPDH has a hexameric structure. Given its specificity for both NADP+ and NAD+, high stability, and a broad range of reductive amination activity toward 2‐oxo acids, NmDAPDH appears to offer advantages for engineering a more effective d‐AADH.
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Affiliation(s)
- Hironaga Akita
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Hiroshima, Japan
| | - Yusuke Nakamichi
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Hiroshima, Japan
| | - Tomotake Morita
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Akinori Matsushika
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Hiroshima, Japan.,Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
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Altered Cofactor Preference of Thermostable StDAPDH by a Single Mutation at K159. Int J Mol Sci 2020; 21:ijms21051788. [PMID: 32150965 PMCID: PMC7084900 DOI: 10.3390/ijms21051788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 11/16/2022] Open
Abstract
D-amino acid production from 2-keto acid by reductive amination is an attractive pathway because of its high yield and environmental safety. StDAPDH, a meso-diaminopimelate dehydrogenase (meso-DAPDH) from Symbiobacterium thermophilum, was the first meso-DAPDH to show amination of 2-keto acids. Furthermore, StDAPDH shows excellent thermostability compared to other meso-DAPDHs. However, the cofactor of StDAPDH is NADP(H), which is less common than NAD(H) in industrial applications. Therefore, cofactor engineering for StDAPDH is needed. In this study, the highly conserved cofactor binding sites around the adenosine moiety of NADPH were targeted to determine cofactor specificity. Lysine residues within a loop were found to be critical for the cofactor specificity of StDAPDH. Replacement of lysine with arginine resulted in the activity of pyruvic acid with NADH as the cofactor. The affinity of K159R to pyruvic acid was equal with NADH or NADPH as the cofactor, regardless of the mutation. Molecular dynamics simulations revealed that the large steric hindrance of arginine and the interaction of the salt bridge between NADH and arginine may have restricted the free movement of NADH, which prompted the formation of a stable active conformation of mutant K159R. These results provide further understanding of the catalytic mechanism of StDAPDH and guidance for the cofactor engineering of StDAPDH.
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Sechovcová H, Kulhavá L, Fliegerová K, Trundová M, Morais D, Mrázek J, Kopečný J. Comparison of enzymatic activities and proteomic profiles of Butyrivibrio fibrisolvens grown on different carbon sources. Proteome Sci 2019; 17:2. [PMID: 31168299 PMCID: PMC6545216 DOI: 10.1186/s12953-019-0150-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 05/15/2019] [Indexed: 01/12/2023] Open
Abstract
Background The rumen microbiota is one of the most complex consortia of anaerobes, involving archaea, bacteria, protozoa, fungi and phages. They are very effective at utilizing plant polysaccharides, especially cellulose and hemicelluloses. The most important hemicellulose decomposers are clustered with the genus Butyrivibrio. As the related species differ in their range of hydrolytic activities and substrate preferences, Butyrivibrio fibrisolvens was selected as one of the most effective isolates and thus suitable for proteomic studies on substrate comparisons in the extracellular fraction. The B. fibrisolvens genome is the biggest in the butyrivibria cluster and is focused on “environmental information processing” and “carbohydrate metabolism”. Methods The study of the effect of carbon source on B. fibrisolvens 3071 was based on cultures grown on four substrates: xylose, glucose, xylan, xylan with 25% glucose. The enzymatic activities were studied by spectrophotometric and zymogram methods. Proteomic study was based on genomics, 2D electrophoresis and nLC/MS (Bruker Daltonics) analysis. Results Extracellular β-endoxylanase as well as xylan β-xylosidase activities were induced with xylan. The presence of the xylan polymer induced hemicellulolytic enzymes and increased the protein fraction in the interval from 40 to 80 kDa. 2D electrophoresis with nLC/MS analysis of extracellular B. fibrisolvens 3071 proteins found 14 diverse proteins with significantly different expression on the tested substrates. Conclusion The comparison of four carbon sources resulted in the main significant changes in B. fibrisolvens proteome occurring outside the fibrolytic cluster of proteins. The affected proteins mainly belonged to the glycolysis and protein synthesis cluster. Electronic supplementary material The online version of this article (10.1186/s12953-019-0150-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hana Sechovcová
- 1Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, 142 20 Prague, Czech Republic.,5Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technická 5, 166 286 Prague, Czech Republic
| | - Lucie Kulhavá
- 2Institute of Physiology, CAS, v.v.i., Vídeňská 1083, 142 20 Prague, Czech Republic.,4Department of Analytical Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843 Prague 2, Czech Republic
| | - Kateřina Fliegerová
- 1Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Mária Trundová
- 3Institute of Biotechnology, CAS, v.v.i., Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Daniel Morais
- 6Institute of Microbiology, CAS, v.v.i., Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Jakub Mrázek
- 1Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Jan Kopečný
- 1Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, 142 20 Prague, Czech Republic
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Gao X, Ma Q, Chen M, Dong M, Pu Z, Zhang X, Song Y. Insight into the Highly Conserved and Differentiated Cofactor-Binding Sites of meso-Diaminopimelate Dehydrogenase StDAPDH. J Chem Inf Model 2019; 59:2331-2338. [PMID: 30807172 DOI: 10.1021/acs.jcim.8b00879] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
meso-Diaminopimelate dehydrogenase ( meso-DAPDH) is a good candidate for one-step synthesis of d-amino acid from 2-keto acids. Our previous research revealed the classification of meso-DAPDH family and showed that type II meso-DAPDH, such as the meso-DAPDH from Symbiobacterium thermophilum (StDAPDH), could catalyze reductive amination. In this article, seven residues of StDAPDH, which are highly conserved in each subfamily but are different between two subfamilies, were targeted to explore the relationships between structure and function. Determination of kinetic parameters showed that the amino acid residues, including P69, K159, V68, S90, V14, and V156, played very important roles in the catalytic function of StDAPDH. Molecular dynamics simulation revealed that these point mutations reduced the productive conformations by the newly formed or eliminated interactions between the residues and ligands. These results strengthen our understanding of the catalytic mechanism and evolution of meso-DAPDH and can aid future endeavors in enzyme engineering.
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Affiliation(s)
- Xiuzhen Gao
- School of Life Science , Shandong University of Technology , Zibo 255000 , People's Republic of China
| | - Qinyuan Ma
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science &Technology), Ministry of Education, Tianjin Key Lab of Industrial Microbiology, College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , People's Republic of China
| | - Meiling Chen
- School of Agricultural Engineering and Food Science , Shandong University of Technology , Zibo 255000 , People's Republic of China
| | - Miaomiao Dong
- School of Life Science , Shandong University of Technology , Zibo 255000 , People's Republic of China
| | - Zhongji Pu
- School of Life Science and Biotechnology , Dalian University of Technology , Dalian 116024 , People's Republic of China
| | - Xianhai Zhang
- School of Life Science , Shandong University of Technology , Zibo 255000 , People's Republic of China
| | - Yuanda Song
- School of Agricultural Engineering and Food Science , Shandong University of Technology , Zibo 255000 , People's Republic of China
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Xu JZ, Ruan HZ, Liu LM, Wang LP, Zhang WG. Overexpression of thermostable meso-diaminopimelate dehydrogenase to redirect diaminopimelate pathway for increasing L-lysine production in Escherichia coli. Sci Rep 2019; 9:2423. [PMID: 30787467 PMCID: PMC6382763 DOI: 10.1038/s41598-018-37974-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 12/11/2018] [Indexed: 11/29/2022] Open
Abstract
Dehydrogenase pathway, one of diaminopimelate pathway, is important to the biosynthesis of L-lysine and peptidoglycan via one single reaction catalyzed by meso-diaminopimelate dehydrogenase (DapDH). In this study, the thermostable DapDH was introduced into diaminopimelate pathway that increased the final titer (from 71.8 to 119.5 g/L), carbon yield (from 35.3% to 49.1%) and productivity (from 1.80 to 2.99 g/(L∙h)) of L-lysine by LATR12-2∆rpiB::ddhSt in fed-batch fermentation. To do this, the kinetic properties and the effects of different DapDHs on L-lysine production were investigated, and the results indicated that overexpression of StDapDH in LATR12-2 was beneficial to construct an L-lysine producer with good productive performance because it exhibited the best of kinetic characteristics and optimal temperature as well as thermostability in reductive amination. Furthermore, ammonium availability was optimized, and found that 20 g/L of (NH4)2SO4 was the optimal ammonium concentration for improving the efficiency of L-lysine production by LATR12-2∆rpiB::ddhSt. Metabolomics analysis showed that introducing the StDapDH significantly enhanced carbon flux into pentose phosphate pathway and L-lysine biosynthetic pathway, thus increasing the levels of NADPH and precursors for L-lysine biosynthesis. This is the first report of a rational modification of diaminopimelate pathway that improves the efficiency of L-lysine production through overexpression of thermostable DapDH in E. coli.
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Affiliation(s)
- Jian-Zhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi, 214122, People's Republic of China.
| | - Hao-Zhe Ruan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi, 214122, People's Republic of China
| | - Li-Ming Liu
- State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi, 214122, People's Republic of China
| | - Lu-Ping Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi, 214122, People's Republic of China
| | - Wei-Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi, 214122, People's Republic of China
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Zhang C, Song W, Liu J, Chen X, Liu L. Production of enantiopure (R)- or (S)-2-hydroxy-4-(methylthio)butanoic acid by multi-enzyme cascades. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0244-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Song W, Wang JH, Wu J, Liu J, Chen XL, Liu LM. Asymmetric assembly of high-value α-functionalized organic acids using a biocatalytic chiral-group-resetting process. Nat Commun 2018; 9:3818. [PMID: 30232330 PMCID: PMC6145935 DOI: 10.1038/s41467-018-06241-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 08/24/2018] [Indexed: 11/21/2022] Open
Abstract
The preparation of α-functionalized organic acids can be greatly simplified by adopting a protocol involving the catalytic assembly of achiral building blocks. However, the enzymatic assembly of small amino acids and aldehydes to form numerous α-functionalized organic acids is highly desired and remains a significant challenge. Herein, we report an artificially designed chiral-group-resetting biocatalytic process, which uses simple achiral glycine and aldehydes to synthesize stereodefined α-functionalized organic acids. This cascade biocatalysis comprises a basic module and three different extender modules and operates in a modular assembly manner. The engineered Escherichia coli catalysts, which contained different module(s), provide access to α-keto acids, α-hydroxy acids, and α-amino acids with excellent conversion and enantioselectivities. Therefore, this biocatalytic process provides an attractive strategy for the conversion of low-cost achiral starting materials to high-value α-functionalized organic acids. Alpha-functionalized organic acids are building blocks of many bioactive compounds. Here, the authors developed a toolbox-like, modular set of enzymes that reset chiral groups, turning achiral glycine and simple aldehydes into stereodefined α-keto acids, α-hydroxy acids, and α-amino acids.
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Affiliation(s)
- Wei Song
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jin-Hui Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jing Wu
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Xiu-Lai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Li-Ming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China. .,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China. .,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China.
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14
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Zhang Y, Ma Q, Dong M, Zhang X, Chen Y, Gao X, Song Y. Essential role of amino acid position 71 in substrate preference by meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum IAM14863. Enzyme Microb Technol 2018; 111:57-62. [PMID: 29421037 DOI: 10.1016/j.enzmictec.2018.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 12/19/2017] [Accepted: 01/01/2018] [Indexed: 10/18/2022]
Abstract
meso--Diaminopimelate dehydrogenase (meso-DAPDH) catalyzes the reversible oxidative deamination of the d-configuration of meso-2,6-diaminopimelate (meso-DAP) and is thought to have substrate specificity toward meso-DAP. The discovery of the meso-DAPDH from Symbiobacterium thermophilum IAM14863 (StDAPDH) revealed meso-DAPDH members with broad substrate specificity. In order to elucidate the substrate-preference mechanism of StDAPDH, it is necessary to identify the key residues related to this mechanism. Our previous work suggested that the non-active-site R71 of StDAPDH was related to substrate preference. Here, we report the key roles of the non-active site on the catalysis of StDAPDH. In order to explore the mechanism through which non-active-site R71 only affected the amination activity of StDAPDH, we performed molecular dynamic simulations and investigated the functional role of R71 in the type II meso-DAPDH StDAPDH. Site-directed mutagenesis with the allelic site A69 of CgDAPDH as a target proved that when replaced by Arg at position 71 of StDAPDH, the CgA69R mutant showed higher catalytic efficiencies toward a series of 2-keto acids, ranging from 1.2- to 1.5-fold. These findings provide some guidelines for improving our understanding of the broad substrate specificity of StDAPDH.
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Affiliation(s)
- Yanan Zhang
- School of Life Science, Shandong University of Technology, Zibo 255000, People's Republic of China
| | - Qinyuan Ma
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin 300457, People's Republic of China; Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Miaomiao Dong
- School of Life Science, Shandong University of Technology, Zibo 255000, People's Republic of China
| | - Xianhai Zhang
- School of Life Science, Shandong University of Technology, Zibo 255000, People's Republic of China
| | - Yichu Chen
- School of Life Science, Shandong University of Technology, Zibo 255000, People's Republic of China
| | - Xiuzhen Gao
- School of Life Science, Shandong University of Technology, Zibo 255000, People's Republic of China.
| | - Yuanda Song
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255000, People's Republic of China
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15
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Cheng X, Chen X, Feng J, Wu Q, Zhu D. Structure-guided engineering ofmeso-diaminopimelate dehydrogenase for enantioselective reductive amination of sterically bulky 2-keto acids. Catal Sci Technol 2018. [DOI: 10.1039/c8cy01426d] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structure-guided reshaping the substrate-binding pocket of ameso-diaminopimelate dehydrogenase (StDAPDH) led to a mutant W121L/H227I, which catalyzed the enantioselective reductive amination of some sterically bulky 2-keto acids.
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Affiliation(s)
- Xinkuan Cheng
- University of Chinese Academy of Sciences
- Beijing 100049
- PR China
- National Engineering Laboratory for Industrial Enzymes and
- Tianjin Engineering Research Center of Biocatalytic Technology
| | - Xi Chen
- University of Chinese Academy of Sciences
- Beijing 100049
- PR China
- National Engineering Laboratory for Industrial Enzymes and
- Tianjin Engineering Research Center of Biocatalytic Technology
| | - Jinhui Feng
- University of Chinese Academy of Sciences
- Beijing 100049
- PR China
- National Engineering Laboratory for Industrial Enzymes and
- Tianjin Engineering Research Center of Biocatalytic Technology
| | - Qiaqing Wu
- University of Chinese Academy of Sciences
- Beijing 100049
- PR China
- National Engineering Laboratory for Industrial Enzymes and
- Tianjin Engineering Research Center of Biocatalytic Technology
| | - Dunming Zhu
- University of Chinese Academy of Sciences
- Beijing 100049
- PR China
- National Engineering Laboratory for Industrial Enzymes and
- Tianjin Engineering Research Center of Biocatalytic Technology
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16
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Xue YP, Cao CH, Zheng YG. Enzymatic asymmetric synthesis of chiral amino acids. Chem Soc Rev 2018; 47:1516-1561. [DOI: 10.1039/c7cs00253j] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
This review summarizes the progress achieved in the enzymatic asymmetric synthesis of chiral amino acids from prochiral substrates.
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Affiliation(s)
- Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Cheng-Hao Cao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
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