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Hu B, Xi X, Xiao F, Bai X, Gong Y, Li Y, Qiao X, Tang C, Huang J. Significantly enhanced specific activity of Bacillus subtilis (2,3)-butanediol dehydrogenase through computer-aided refinement of its substrate-binding pocket. Int J Biol Macromol 2024; 281:136443. [PMID: 39389503 DOI: 10.1016/j.ijbiomac.2024.136443] [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: 06/10/2024] [Revised: 09/04/2024] [Accepted: 10/07/2024] [Indexed: 10/12/2024]
Abstract
(2,3)-Butanediol dehydrogenases (BDHs) are widely utilized for the stereoselective interconversion between α-hydroxy ketones and vicinal diols to produce various functional building blocks. In this study, to enhance the specific activity towards (R)-phenyl-1,2-ethanediol (1a) for 2-hydroxyacetophenone (1b), the substrate-binding pocket of a Bacillus subtilis BDH (BsBDHA) was refined through site-directed mutagenesis. Based on molecular docking simulations, 14 residues were identified and subjected to alanine scanning mutagenesis. After screening, two residues, His42 and Gly292, were singled out for partial site-saturation mutagenesis. The results revealed that BsBDHAH42A and BsBDHAG292A displayed high activities of 3.21 and 1.97 U/mg, respectively. Employing combinatorial mutagenesis, a superior mutant, BsBDHAI49L/V266L/G292A, was developed, exhibiting significantly enhanced specific activity and catalytic efficiency towards (R)-1a, achieving 14.81 U/mg and 4.47 mM-1 s-1, respectively, which were 27.4- and 55.9-fold higher than those of BsBDHA. Further substrate spectrum analysis revealed that the superior mutant displayed increased specific activities for (R)-2a-6a by 1.4- to 10.3-fold. The integration of BsBDHAI49L/V266L/G292A into a three-enzymatic cascade for the synthesis of 1b effectively elevated the yield from 58.1 to 82.4%. Molecular mechanism analysis indicated that the mutation-induced changes in intermolecular forces resulted in a higher frequency of reactive conformations for (R)-1a in BsBDHAI49L/V266L/G292A compared to BsBDHA.
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Affiliation(s)
- Bochun Hu
- Henan Key Laboratory of Biomarker Based Rapid-detection Technology for Food Safety, Food and Pharmacy College, Xuchang University, Xuchang 461000, PR China
| | - Xiaoqi Xi
- Henan Key Laboratory of Biomarker Based Rapid-detection Technology for Food Safety, Food and Pharmacy College, Xuchang University, Xuchang 461000, PR China; Henan Provincial Engineering Laboratory of Insect Bio-reactor and College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, PR China
| | - Fugang Xiao
- Henan Key Laboratory of Biomarker Based Rapid-detection Technology for Food Safety, Food and Pharmacy College, Xuchang University, Xuchang 461000, PR China
| | - Xiaomeng Bai
- Henan Key Laboratory of Biomarker Based Rapid-detection Technology for Food Safety, Food and Pharmacy College, Xuchang University, Xuchang 461000, PR China
| | - Yuanyuan Gong
- Henan Key Laboratory of Biomarker Based Rapid-detection Technology for Food Safety, Food and Pharmacy College, Xuchang University, Xuchang 461000, PR China
| | - Yifan Li
- Henan Key Laboratory of Biomarker Based Rapid-detection Technology for Food Safety, Food and Pharmacy College, Xuchang University, Xuchang 461000, PR China
| | - Xueqin Qiao
- Henan Key Laboratory of Biomarker Based Rapid-detection Technology for Food Safety, Food and Pharmacy College, Xuchang University, Xuchang 461000, PR China
| | - Cunduo Tang
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, PR China.
| | - Jihong Huang
- Henan Key Laboratory of Biomarker Based Rapid-detection Technology for Food Safety, Food and Pharmacy College, Xuchang University, Xuchang 461000, PR China.
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Li Y, Zhao X, Yao M, Yang W, Han Y, Liu L, Zhang J, Liu J. Mechanism of microbial production of acetoin and 2,3-butanediol optical isomers and substrate specificity of butanediol dehydrogenase. Microb Cell Fact 2023; 22:165. [PMID: 37644496 PMCID: PMC10466699 DOI: 10.1186/s12934-023-02163-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/31/2023] [Indexed: 08/31/2023] Open
Abstract
3-Hydroxybutanone (Acetoin, AC) and 2,3-butanediol (BD) are two essential four-carbon platform compounds with numerous pharmaceutical and chemical synthesis applications. AC and BD have two and three stereoisomers, respectively, while the application of the single isomer product in chemical synthesis is superior. AC and BD are glucose overflow metabolites produced by biological fermentation from a variety of microorganisms. However, the AC or BD produced by microorganisms using glucose is typically a mixture of various stereoisomers. This was discovered to be due to the simultaneous presence of multiple butanediol dehydrogenases (BDHs) in microorganisms, and AC and BD can be interconverted under BDH catalysis. In this paper, beginning with the synthesis pathways of microbial AC and BD, we review in detail the studies on the formation mechanisms of different stereoisomers of AC and BD, summarize the properties of different types of BDH that have been tabulated, and analyze the structural characteristics and affinities of different types of BDH by comparing them using literature and biological database data. Using microorganisms, recent research on the production of optically pure AC or BD was also reviewed. Limiting factors and possible solutions for chiral AC and BD production are discussed.
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Affiliation(s)
- Yuchen Li
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology, Shandong Academy of Sciences), Jinan, 250013, China
- School of Food Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Xiangying Zhao
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology, Shandong Academy of Sciences), Jinan, 250013, China.
- School of Food Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China.
| | - Mingjing Yao
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology, Shandong Academy of Sciences), Jinan, 250013, China
| | - Wenli Yang
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology, Shandong Academy of Sciences), Jinan, 250013, China
- School of Food Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Yanlei Han
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology, Shandong Academy of Sciences), Jinan, 250013, China
| | - Liping Liu
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology, Shandong Academy of Sciences), Jinan, 250013, China
- School of Food Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Jiaxiang Zhang
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology, Shandong Academy of Sciences), Jinan, 250013, China
- School of Food Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Jianjun Liu
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology, Shandong Academy of Sciences), Jinan, 250013, China
- School of Food Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
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Hu BC, Li MR, Li YY, Yuan XS, Hu YY, Xiao FG. Engineering a BsBDHA substrate-binding pocket entrance for the improvement in catalytic performance toward (R)-phenyl-1,2-ethanediol based on the computer-aided design. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2023.108907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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Wang X, Jia L, Ji F. Structural and enzymatic characterization of Bacillus subtilis R,R-2,3-butanediol dehydrogenase. Biochim Biophys Acta Gen Subj 2023; 1867:130326. [PMID: 36781054 DOI: 10.1016/j.bbagen.2023.130326] [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: 09/11/2022] [Revised: 12/22/2022] [Accepted: 02/07/2023] [Indexed: 02/13/2023]
Abstract
2,3-butanediol dehydrogenase (BDH, EC 1.1.1.76) also known as acetoin reductase (AR, EC 1.1.1.4) is the key enzyme converting acetoin (AC) into 2,3-butanediol (BD) and undertaking the irreversible conversion of diacetyl to acetoin in various microorganisms. The existence of three BDHs (R,R-, meso-, and S,S-BDH) product different BD isomers. Catalyzing mechanisms of meso- and S,S-BDH have been understood with the assistance of their X-ray crystal structures. However, the lack of structural data for R,R-BDH restricts the integral understanding of the catalytic mechanism of BDHs. In this study, we successfully crystallized and solved the X-ray crystal structure of Bacillus subtilis R,R-BDH. A zinc ion was found locating in the catalytic center and coordinated by Cys37, His70 and Glu152, helping to stabilize the chiral substrates observed in the predicted molecular docking model. The interaction patterns of different chiral substrates in the molecular docking model explained the react priority measured by the enzyme activity assay of R,R-BDH. Site-directed mutation experiments determined that the amino acids Cys37, Thr244, Ile268 and Lys340 are important in the catalytically active center. The structural information of R,R-BDH presented in this study accomplished the understanding of BDHs catalytic mechanism and more importantly provides useful guidance for the directional engineering of R,R-BDH to obtain high-purity monochiral BD and AC.
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Affiliation(s)
- Xiaofei Wang
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, PR China
| | - Lingyun Jia
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, PR China
| | - Fangling Ji
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, PR China.
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Choi Y, Kim YH. Regulatory role of cysteines in (2R, 3R)-butanediol dehydrogenase BdhA of Bacillus velezensis strain GH1-13. J Microbiol 2022; 60:411-418. [DOI: 10.1007/s12275-022-2018-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 01/28/2022] [Accepted: 02/03/2022] [Indexed: 11/29/2022]
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