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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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Ganjoo A, Babu V. Recombinant Amidases: Recent Insights and its Applications in the Production of Industrially Important Fine Chemicals. Mol Biotechnol 2024:10.1007/s12033-024-01123-8. [PMID: 38598092 DOI: 10.1007/s12033-024-01123-8] [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: 11/30/2023] [Accepted: 02/27/2024] [Indexed: 04/11/2024]
Abstract
The current research for the synthesis of industrially important fine chemicals is more inclined towards developing enzyme-based processes. The biotransformation reactions wherein microbial cells/enzymes are used, have become essential in making the process efficient, green, and economical. Amongst industrially important enzymes, amidase is one of the most versatile tools in biocatalysis and biotransformation reactions. It shows broad substrate specificity and sturdy functional characteristics because of its promiscuous nature. Further, advancement in the area led to the development of amidase recombinant systems, which are developed using biotechnology and enzyme engineering tools. Additionally, recombinant amidases may be instrumental in commercializing the synthesis of fine chemicals such as hydroxamic acids that have a significant pharmaceutical market. Hence, the present review focuses on highlighting and assimilating the tools and techniques used in developing recombinant systems followed by their applications.
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Affiliation(s)
- Ananta Ganjoo
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vikash Babu
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Du Y, Li J, Chen S, Xia Y, Jin K. Pathogenicity analysis and comparative genomics reveal the different infection strategies between the generalist Metarhizium anisopliae and the specialist Metarhizium acridum. PEST MANAGEMENT SCIENCE 2024; 80:820-836. [PMID: 37794279 DOI: 10.1002/ps.7812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 08/28/2023] [Accepted: 09/30/2023] [Indexed: 10/06/2023]
Abstract
BACKGROUND The fungal genera Metarhizium contain many important multiple species that are used as biocontrol agents and as model organisms for exploring insect-fungal interactions. Metarhizium spp. exhibit different traits of pathogenicity, suggesting that the pathogenesis can be quite distinctive. However, the underlying differences in their pathogenesis remain poorly understood. RESULTS Pathogenicity analysis showed that Metarhizium anisopliae (strain CQMa421) displayed higher virulence against oriental migratory locusts, Locusta migratoria manilensis (Meyen), than the acridid-specific specie Metarhizium acridum (strain CQMa102). Relative to M. acridum, M. anisopliae possessed a higher conidial hydrophobicity, increased ability to penetrate the host, accelerated growth under hypoxia and enhanced ability for the utilization of different carbon sources. Different distributions of carbohydrate epitopes at cell wall surface of M. anisopliae might also contribute to successful evasion of host immune defenses. Comparative genomics showed that M. anisopliae has 98 more virulence-related secreted proteins (133) than M. acridum (35), which can be functionally classified as hydrolases, virulence effectors, cell wall degradation and stress tolerance-related proteins, and helpful to the cuticle penetration and host internal environment adaption. In addition, differences in genomic clusters specifically related to secondary metabolites, including the clusters of Indole-NRPS hybrid, T1PKS-NRPS like hybrid, Betalactone, Fungal-Ripp and NRPS-Terpene hybrid, may lead to differences in core virulence-related secondary metabolite genes in M. acridum (18) and M. anisopliae (36). CONCLUSION The comparative study provided new insights into the different infection strategies between M. anisopliae and M. acridum, and further facilitate the identification of virulence-related genes for the improvement of mycoinsecticides. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Yanru Du
- School of Life Sciences, Chongqing University, Chongqing, P. R. China
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing, P. R. China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing, P. R. China
| | - Jun Li
- School of Life Sciences, Chongqing University, Chongqing, P. R. China
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing, P. R. China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing, P. R. China
| | - Shaopeng Chen
- Tobacco Leaf Branch of Chongqing Tobacco Company of China Tobacco Corporation, Chongqing, P. R. China
| | - Yuxian Xia
- School of Life Sciences, Chongqing University, Chongqing, P. R. China
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing, P. R. China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing, P. R. China
| | - Kai Jin
- School of Life Sciences, Chongqing University, Chongqing, P. R. China
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing, P. R. China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing, P. R. China
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Jiang H, Yuan P, Ding J, Wu H, Wang L, Chen K, Jiang N, Dai Y. Novel biodegradation pathway of insecticide flonicamid mediated by an amidase and its unusual substrate spectrum. JOURNAL OF HAZARDOUS MATERIALS 2023; 441:129952. [PMID: 36116312 DOI: 10.1016/j.jhazmat.2022.129952] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/20/2022] [Accepted: 09/06/2022] [Indexed: 06/15/2023]
Abstract
The insecticide flonicamid (FLO) and its main degradation intermediate 4-trifluoromethylnicotinamide (TFNA-AM) are hazardous to the environment and animals. Microbial transformation of FLO has been well studied, but no study has yet reported on TFNA-AM degradation by a microorganism. Here, Pseudomonas stutzeri CGMCC 22915 effectively degraded TFNA-AM to 5-trifluoromethylnicotinic acid (TFNA). P. stutzeri CGMCC 22915 degraded 60.0% of TFNA-AM (1154.44 μmol/L) within 6 h with a half-life of just 4.5 h. Moreover, P. stutzeri CGMCC 22915 significantly promoted TFNA-AM decomposition in surface water. The reaction was catalyzed by an amidase, PsAmiA. PsAmiA is encoded in a novel nitrile-converting enzyme gene cluster. The enzyme shared only 20-44% identities with previously characterized signature amidases. PsAmiA was successfully expressed in Escherichia coli and its enzymatic properties were investigated using TFNA-AM as the substrate. PsAmiA was more active toward amides without hydrophilic groups, and did not hydrolyze another amide metabolite of FLO, N-(4-trifluoromethylnicotinoyl)glycinamide (TFNG-AM), which is structurally very similar to TFNA-AM. Molecular docking of PsAmiA and TFNA-AM indicated that hydrophobic residues Leu148, Ala150, Ala195, Ile225, Trp341, Leu460, and Ile463 may affect its substrate spectrum. This study provides new insights of the environmental fate of FLO at the molecular level and the structure-function relationships of amidases.
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Affiliation(s)
- Huoyong Jiang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Panpan Yuan
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Jianjun Ding
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Hongkai Wu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Li Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Kexin Chen
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Nengdang Jiang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Yijun Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
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Li W, Lu J, Yang C, Arildsen K, Li X, Xia S. An Amidase Contributes to Full Virulence of Sclerotinia sclerotiorum. Int J Mol Sci 2022; 23:11207. [PMID: 36232508 PMCID: PMC9570306 DOI: 10.3390/ijms231911207] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/17/2022] [Accepted: 09/20/2022] [Indexed: 11/25/2022] Open
Abstract
Sclerotinia sclerotiorum is one of the most notorious and ubiquitous soilborne plant pathogens, causing serious economic losses to a large number of hosts worldwide. Although virulence factors have been identified in this filamentous fungus, including various cell-wall-degrading enzymes, toxins, oxalic acids and effectors, our understanding of its virulence strategies is far from complete. To explore novel factors contributing to disease, a new pipeline combining forward genetic screening and next-generation sequencing was utilized in this study. Analysis of a hypovirulent mutant revealed that a mutation in an amidase-encoding gene, Sscle_10g079050, resulted in reduced virulence. This is a first report on the contribution of an amidase to fungal virulence, likely through affecting oxalic acid homeostasis.
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Affiliation(s)
- Wei Li
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- College of Life Science, Chongqing Normal University, Chongqing 401331, China
| | - Junxing Lu
- College of Life Science, Chongqing Normal University, Chongqing 401331, China
| | - Chenghuizi Yang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Kate Arildsen
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Shitou Xia
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
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Xi L, Tan W, Li J, Qu J, Liu J. Cloning and characterization of a novel thermostable amidase, Xam, from Xinfangfangia sp. DLY26. Biotechnol Lett 2021; 43:1395-1402. [PMID: 33811594 DOI: 10.1007/s10529-021-03124-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 03/26/2021] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Identification and characterization of a novel thermostable amidase (Xam) with wide pH tolerance and broad-spectrum substrate specificity. RESULTS Xam was identified from non-thermophilic Xinfangfangia sp. DLY26 and its acyl transfer activity was investigated. Recombinant Xam was optimally active at 60 °C and pH 9.0. The enzyme had a half life of 18 h at 55 °C and maintained more than 60 % of its maximum activity in the range of pH 3.0-11.0. Additionally, Xam exhibited broad substrate specificity towards aliphatic, aromatic, and heterocyclic amides. CONCLUSIONS These unique properties make Xam a promising biocatalyst for production of important hydroxamic acids at elevated temperatures.
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Affiliation(s)
- Lijun Xi
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Wenfei Tan
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Jing Li
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Jianbo Qu
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Jianguo Liu
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China.
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Tan W, Liu J, Li Z, Xu Z, Xin W, Xi L. Cloning, expression and biochemical characterization of a novel amidase from Thauera sinica K11. Protein Expr Purif 2020; 177:105751. [PMID: 32931916 DOI: 10.1016/j.pep.2020.105751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/14/2020] [Accepted: 09/10/2020] [Indexed: 11/17/2022]
Abstract
A novel amidase (TAM) was identified and cloned from the genome of Thauera sinica K11. The recombinant protein was purified to homogeneity by one-step affinity chromatography for up to 26.4-fold with a yield of 38.1%. Gel filtration chromatography and SDS-PAGE revealed that the enzyme was a tetramer with a subunit of approximately 37.5 kDa. The amidase exhibited the maximum acyl transfer activity at 45 °C and pH 7.0, and it was highly stable over a wide pH range of 6.0-11.0. Inhibition of enzyme activity was observed in the presence of metal ions, thiol reagents and organic solvents. TAM showed a broad substrate spectrum toward aliphatic, aromatic and heterocyclic amides. For linear aliphatic monoamides, the acyl transfer activity of TAM was decreased with the extension of the carbon chain length, and thus the highest activity of 228.2 U/mg was obtained when formamide was used as substrate. This distinct selectivity of amidase to linear aliphatic monoamides expanded the findings of signature amidases to substrate specificity.
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Affiliation(s)
- Wenfei Tan
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Jianguo Liu
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China.
| | - Ziyi Li
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Zhenzhen Xu
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Wen Xin
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Lijun Xi
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China.
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Wu Z, Liu C, Zhang Z, Zheng R, Zheng Y. Amidase as a versatile tool in amide-bond cleavage: From molecular features to biotechnological applications. Biotechnol Adv 2020; 43:107574. [PMID: 32512219 DOI: 10.1016/j.biotechadv.2020.107574] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 12/27/2022]
Abstract
Amidases (EC 3. 5. 1. X) are versatile biocatalysts for synthesis of chiral carboxylic acids, α-amino acids and amides due to their hydrolytic and acyl transfer activity towards the C-N linkages. They have been extensively exploited and studied during the past years for their high specific activity and excellent enantioselectivity involved in various biotechnological applications in pharmaceutical and agrochemical industries. Additionally, they have attracted considerable attentions in biodegradation and bioremediation owing to environmental pressures. Motivated by industrial demands, crystallographic investigations and catalytic mechanisms of amidases based on structural biology have witnessed a dramatic promotion in the last two decades. The protein structures showed that different types of amidases have their typical stuctural elements, such as the conserved AS domains in signature amidases and the typical architecture of metal-associated active sites in acetamidase/formamidase family amidases. This review provides an overview of recent research advances in various amidases, with a focus on their structural basis of phylogenetics, substrate specificities and catalytic mechanisms as well as their biotechnological applications. As more crystal structures of amidases are determined, the structure/function relationships of these enzymes will also be further elucidated, which will facilitate molecular engineering and design of amidases to meet industrial requirements.
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Affiliation(s)
- Zheming Wu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Changfeng Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Zhaoyu Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Renchao Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China.
| | - Yuguo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
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Lauterbach A, Geissler AJ, Eisenbach L, Behr J, Vogel RF. Novel diagnostic marker genes differentiate Saccharomyces
with respect to their potential application. JOURNAL OF THE INSTITUTE OF BREWING 2018. [DOI: 10.1002/jib.525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Alexander Lauterbach
- Lehrstuhl für Technische Mikrobiologie; Technische Universität München; Gregor-Mendel Str. 4 85354 Freising Germany
| | - Andreas J. Geissler
- Lehrstuhl für Technische Mikrobiologie; Technische Universität München; Gregor-Mendel Str. 4 85354 Freising Germany
| | - Lara Eisenbach
- Lehrstuhl für Technische Mikrobiologie; Technische Universität München; Gregor-Mendel Str. 4 85354 Freising Germany
| | - Jürgen Behr
- Lehrstuhl für Technische Mikrobiologie; Technische Universität München; Gregor-Mendel Str. 4 85354 Freising Germany
- Bavarian Center for Biomolecular Mass Spectrometry; Gregor-Mendel Str. 4 85354 Freising Germany
| | - Rudi F. Vogel
- Lehrstuhl für Technische Mikrobiologie; Technische Universität München; Gregor-Mendel Str. 4 85354 Freising Germany
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Nelson DL, Applegate GA, Beio ML, Graham DL, Berkowitz DB. Human serine racemase structure/activity relationship studies provide mechanistic insight and point to position 84 as a hot spot for β-elimination function. J Biol Chem 2017; 292:13986-14002. [PMID: 28696262 DOI: 10.1074/jbc.m117.777904] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 06/26/2017] [Indexed: 11/06/2022] Open
Abstract
There is currently great interest in human serine racemase, the enzyme responsible for producing the NMDA co-agonist d-serine. Reported correlation of d-serine levels with disorders including Alzheimer's disease, ALS, and ischemic brain damage (elevated d-serine) and schizophrenia (reduced d-serine) has further piqued this interest. Reported here is a structure/activity relationship study of position Ser84, the putative re-face base. In the most extreme case of functional reprogramming, the S84D mutant displays a dramatic reversal of β-elimination substrate specificity in favor of l-serine over the normally preferred l-serine-O-sulfate (∼1200-fold change in kcat/Km ratios) and l (l-THA; ∼5000-fold change in kcat/Km ratios) alternative substrates. On the other hand, the S84T (which performs l-Ser racemization activity), S84A (good kcat but high Km for l-THA elimination), and S84N mutants (nearly WT efficiency for l-Ser elimination) displayed intermediate activity, all showing a preference for the anionic substrates, but generally attenuated compared with the native enzyme. Inhibition studies with l-erythro-β-hydroxyaspartate follow this trend, with both WT serine racemase and the S84N mutant being competitively inhibited, with Ki = 31 ± 1.5 μm and 1.5 ± 0.1 mm, respectively, and the S84D being inert to inhibition. Computational modeling pointed to a key role for residue Arg-135 in binding and properly positioning the l-THA and l-serine-O-sulfate substrates and the l-erythro-β-hydroxyaspartate inhibitor. Examination of available sequence data suggests that Arg-135 may have originated for l-THA-like β-elimination function in earlier evolutionary variants, and examination of available structural data suggests that a Ser84-H2O-Lys114 hydrogen-bonding network in human serine racemase lowers the pKa of the Ser84re-face base.
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Affiliation(s)
- David L Nelson
- From the Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588
| | - Greg A Applegate
- From the Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588
| | - Matthew L Beio
- From the Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588
| | - Danielle L Graham
- From the Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588
| | - David B Berkowitz
- From the Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588.
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