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Bihani SC, Nagar V, Kumar M. Mechanistic and evolutionary insights into alkaline phosphatase superfamily through structure-function studies on Sphingomonas alkaline phosphatase. Arch Biochem Biophys 2023; 736:109524. [PMID: 36716801 DOI: 10.1016/j.abb.2023.109524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 12/20/2022] [Accepted: 01/20/2023] [Indexed: 01/28/2023]
Abstract
Alkaline phosphatases (APs), represented by E. coli AP (ECAP), employ an arginine residue to stabilize the phosphoryl group in the active site; whereas, AP from Sphingomonas (SPAP) shows a unique combination of substrate-binding residues; Thr89, Asn110, Lys171, and Arg173. Although such combination has been observed only in SPAP, these residues are present separately in different members of the AP superfamily. Here, we establish the presence of two distinct classes of APs; ECAP-type and SPAP-type. Bioinformatic analyses show that SPAP-type of APs are widely distributed in the bacterial kingdom. The role of active site residues in the catalytic mechanism has been delineated through a set of crystal structures reported here. These structures, representing different stages of the reaction pathway provide wealth of information for the catalytic mechanism. Despite critical differences in the substrate binding residues, SPAP follows a mechanism similar to that of ECAP-type of APs. Structure-based phylogenetic analysis suggests that SPAP and ECAP may have diverged very early during the evolution from a common ancestor. Moreover, it is proposed that the SPAP-type of APs are fundamental members of the AP superfamily and are more closely related to other members of the superfamily as compared to the ECAP-type of APs.
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Affiliation(s)
- Subhash C Bihani
- Protein Crystallography Section, Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India.
| | - Vandan Nagar
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India; Food Microbiology Group, Food Technology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - Mukesh Kumar
- Protein Crystallography Section, Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India
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Wohlgemuth R. Advances in the Synthesis and Analysis of Biologically Active Phosphometabolites. Int J Mol Sci 2023; 24:3150. [PMID: 36834560 PMCID: PMC9961378 DOI: 10.3390/ijms24043150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/01/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
Phosphorus-containing metabolites cover a large molecular diversity and represent an important domain of small molecules which are highly relevant for life and represent essential interfaces between biology and chemistry, between the biological and abiotic world. The large but not unlimited amount of phosphate minerals on our planet is a key resource for living organisms on our planet, while the accumulation of phosphorus-containing waste is associated with negative effects on ecosystems. Therefore, resource-efficient and circular processes receive increasing attention from different perspectives, from local and regional levels to national and global levels. The molecular and sustainability aspects of a global phosphorus cycle have become of much interest for addressing the phosphorus biochemical flow as a high-risk planetary boundary. Knowledge of balancing the natural phosphorus cycle and the further elucidation of metabolic pathways involving phosphorus is crucial. This requires not only the development of effective new methods for practical discovery, identification, and high-information content analysis, but also for practical synthesis of phosphorus-containing metabolites, for example as standards, as substrates or products of enzymatic reactions, or for discovering novel biological functions. The purpose of this article is to review the advances which have been achieved in the synthesis and analysis of phosphorus-containing metabolites which are biologically active.
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Affiliation(s)
- Roland Wohlgemuth
- MITR, Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego Street 116, 90-924 Lodz, Poland; or
- Swiss Coordination Committee Biotechnology (SKB), 8021 Zurich, Switzerland
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The Power of Biocatalysts for Highly Selective and Efficient Phosphorylation Reactions. Catalysts 2022. [DOI: 10.3390/catal12111436] [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
Reactions involving the transfer of phosphorus-containing groups are of key importance for maintaining life, from biological cells, tissues and organs to plants, animals, humans, ecosystems and the whole planet earth. The sustainable utilization of the nonrenewable element phosphorus is of key importance for a balanced phosphorus cycle. Significant advances have been achieved in highly selective and efficient biocatalytic phosphorylation reactions, fundamental and applied aspects of phosphorylation biocatalysts, novel phosphorylation biocatalysts, discovery methodologies and tools, analytical and synthetic applications, useful phosphoryl donors and systems for their regeneration, reaction engineering, product recovery and purification. Biocatalytic phosphorylation reactions with complete conversion therefore provide an excellent reaction platform for valuable analytical and synthetic applications.
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Hsu C, Tsai HY, Chang CF, Yang CC, Su NW. Discovery of a novel phosphotransferase from Bacillus subtilis that phosphorylates a broad spectrum of flavonoids. Food Chem 2022; 400:134001. [DOI: 10.1016/j.foodchem.2022.134001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/18/2022] [Accepted: 08/20/2022] [Indexed: 11/17/2022]
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Wohlgemuth R, Littlechild J. Complexity reduction and opportunities in the design, integration and intensification of biocatalytic processes for metabolite synthesis. Front Bioeng Biotechnol 2022; 10:958606. [PMID: 35935499 PMCID: PMC9355135 DOI: 10.3389/fbioe.2022.958606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
The biosynthesis of metabolites from available starting materials is becoming an ever important area due to the increasing demands within the life science research area. Access to metabolites is making essential contributions to analytical, diagnostic, therapeutic and different industrial applications. These molecules can be synthesized by the enzymes of biological systems under sustainable process conditions. The facile synthetic access to the metabolite and metabolite-like molecular space is of fundamental importance. The increasing knowledge within molecular biology, enzyme discovery and production together with their biochemical and structural properties offers excellent opportunities for using modular cell-free biocatalytic systems. This reduces the complexity of synthesizing metabolites using biological whole-cell approaches or by classical chemical synthesis. A systems biocatalysis approach can provide a wealth of optimized enzymes for the biosynthesis of already identified and new metabolite molecules.
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Affiliation(s)
- Roland Wohlgemuth
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Lodz, Poland
- Swiss Coordination Committee for Biotechnology, Zurich, Switzerland
| | - Jennifer Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
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Alcántara AR, Domínguez de María P, Littlechild JA, Schürmann M, Sheldon RA, Wohlgemuth R. Biocatalysis as Key to Sustainable Industrial Chemistry. CHEMSUSCHEM 2022; 15:e202102709. [PMID: 35238475 DOI: 10.1002/cssc.202102709] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/10/2022] [Indexed: 06/14/2023]
Abstract
The role and power of biocatalysis in sustainable chemistry has been continuously brought forward step by step to its present outstanding position. The problem-solving capabilities of biocatalysis have been realized by numerous substantial achievements in biology, chemistry and engineering. Advances and breakthroughs in the life sciences and interdisciplinary cooperation with chemistry have clearly accelerated the implementation of biocatalytic synthesis in modern chemistry. Resource-efficient biocatalytic manufacturing processes have already provided numerous benefits to sustainable chemistry as well as customer-centric value creation in the pharmaceutical, food, flavor, fragrance, vitamin, agrochemical, polymer, specialty, and fine chemical industries. Biocatalysis can make significant contributions not only to manufacturing processes, but also to the design of completely new value-creation chains. Biocatalysis can now be considered as a key enabling technology to implement sustainable chemistry.
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Affiliation(s)
- Andrés R Alcántara
- Department of Chemistry in Pharmaceutical Sciences (QUICIFARM), Complutense University of Madrid (UCM), 28040-, Madrid, Spain
| | - Pablo Domínguez de María
- Sustainable Momentum, SL, Av. Ansite 3, 4-6, 35011, Las Palmas de Gran Canaria, Canary Is., Spain
| | - Jennifer A Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | | | - Roger A Sheldon
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Braamfontein, Johannesburg, South Africa
| | - Roland Wohlgemuth
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, 90-537, Lodz, Poland
- Swiss Coordination Committee for Biotechnology, 8021, Zurich, Switzerland
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Song W, Zheng K, Xu X, Gao C, Guo L, Liu J, Chen X, Liu L, Hu G, Wu J. Enzymatic Production of Ascorbic Acid-2-Phosphate by Engineered Pseudomonas aeruginosa Acid Phosphatase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:14215-14221. [PMID: 34786944 DOI: 10.1021/acs.jafc.1c04685] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
l-Ascorbic acid-2-phosphate (AsA-2P) is stable in aqueous solution and at high temperatures and is widely used in foods, pharmaceuticals, cosmetics, and fodders; however, practical application of enzymatic synthesis methods to promote industrial-scale production of AsA-2P remains a major challenge. In this study, we enhanced the phosphorylation efficiency of Pseudomonas aeruginosa acid phosphatase (APase; EC 3.1.3.2) for AsA-2P production via protein engineering. Among the mutants obtained, we selected the most efficient mutant (Var5; G125E/D135T/S136N), which exhibited an increased kcat of 18.6 s-1 and a Km for AsA of 223.9 mM. In addition, Var5 exhibited a maximum enzyme activity of 2080.4 U/L after 10 h of fermentation, which was 80% higher than the wild-type enzyme. Furthermore, under optimal conditions, Var5 showed a maximal conversion of 48.6% and achieved a final AsA-2P titer of 61.5 g/L at 8 h, which is considerably higher than that reported for other similar biocatalytic approaches. These findings demonstrate the potential of this method for the large-scale production of AsA-2P.
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Affiliation(s)
- Wei Song
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Kai Zheng
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, China
| | - Xin Xu
- 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
| | - Liang Guo
- 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
| | - 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
| | - Guipeng Hu
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jing Wu
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, China
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Xu X, Yan S, Hou X, Song W, Wang L, Wu T, Qi M, Wu J, Rao Y, Wang B, Liu L. Local Electric Field Modulated Reactivity of Pseudomonas aeruginosa Acid Phosphatase for Enhancing Phosphorylation of l-Ascorbic Acid. ACS Catal 2021. [DOI: 10.1021/acscatal.1c04200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Xin Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Shengheng Yan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen University, Xiamen 360015, P. R. China
| | - Xiaodong Hou
- State Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
| | - Wei Song
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, P. R. China
| | - Lei Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Tianfu Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Mengya Qi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Jing Wu
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, P. R. China
| | - Yijian Rao
- State Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen University, Xiamen 360015, P. R. China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
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Abstract
Biocatalysis has undergone a remarkable transition in the last two decades, from being considered a niche technology to playing a much more relevant role in organic synthesis today. Advances in molecular biology and bioinformatics, and the decreasing costs for gene synthesis and sequencing contribute to the growing success of engineered biocatalysts in industrial applications. However, the incorporation of biocatalytic process steps in new or established manufacturing routes is not always straightforward. To realize the full synthetic potential of biocatalysis for the sustainable manufacture of chemical building blocks, it is therefore important to regularly analyze the success factors and existing hurdles for the implementation of enzymes in large scale small molecule synthesis. Building on our previous analysis of biocatalysis in the Swiss manufacturing environment, we present a follow-up study on how the industrial biocatalysis situation in Switzerland has evolved in the last four years. Considering the current industrial landscape, we record recent advances in biocatalysis in Switzerland as well as give suggestions where enzymatic transformations may be valuably employed to address some of the societal challenges we face today, particularly in the context of the current Coronavirus disease 2019 (COVID-19) pandemic.
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