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Jiang Y, Yao M, Feng J, Niu H, Qiao B, Li B, Wang B, Xiao W, Dong M, Yuan Y. Molecular Insights into Converting Hydroxide Adenosyltransferase into Halogenase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12685-12695. [PMID: 38771136 DOI: 10.1021/acs.jafc.4c02581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Halogenation plays a unique role in the design of agrochemicals. Enzymatic halogenation reactions have attracted great attention due to their excellent specificity and mild reaction conditions. S-adenosyl-l-methionine (SAM)-dependent halogenases mediate the nucleophilic attack of halide ions (X-) to SAM to produce 5'-XDA. However, only 11 SAM-dependent fluorinases and 3 chlorinases have been reported, highlighting the desire for additional halogenases. SAM-dependent hydroxide adenosyltransferase (HATase) has a similar reaction mechanism as halogenases but uses water as a substrate instead of halide ions. Here, we explored a HATase from the thermophile Thermotoga maritima MSB8 and transformed it into a halogenase. We identified a key dyad W8L/V71T for the halogenation reaction. We also obtained the best performing mutants for each halogenation reaction: M1, M2 and M4 for Cl-, Br- and I-, respectively. The M4 mutant retained the thermostability of HATase in the iodination reaction at 80 °C, which surpasses the natural halogenase SalL. QM/MM revealed that these mutants bind halide ions with more suitable angles for nucleophilic attack of C5' of SAM, thus conferring halogenation capabilities. Our work achieved the halide ion specificity of halogenases and generated thermostable halogenases for the first time, which provides new opportunities to expand the halogenase repertoire from hydroxylase.
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Affiliation(s)
- Yixun Jiang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Mingdong Yao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Jianqiang Feng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Haoran Niu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Bin Qiao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Bingzhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Wenhai Xiao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- School of Life Sciences, Faculty of Medicine, Tianjin University, Tianjin 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
- Georgia Tech Shenzhen Institute, Tianjin University, Shenzhen 518071, China
| | - Min Dong
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yingjin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
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Jiang Y, Yao M, Niu H, Wang W, He J, Qiao B, Li B, Dong M, Xiao W, Yuan Y. Enzyme Engineering Renders Chlorinase the Activity of Fluorinase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:1203-1212. [PMID: 38179953 DOI: 10.1021/acs.jafc.3c08185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Organofluorine compounds have attracted substantial attention owing to their wide application in agrochemistry. Fluorinase (FlA) is a unique enzyme in nature that can incorporate fluorine into an organic molecule. Chlorinase (SalL) has a similar mechanism as fluorinase and can use chloride but not fluoride as a substrate to generate 5'-chloro-deoxyadenosine (5'-ClDA) from S-adenosyl-l-methionine (SAM). Therefore, identifying the features that lead to this selectivity for halide ions is highly important. Here, we engineered SalL to gain the function of FlA. We found that residue Tyr70 plays a key role in this conversion through alanine scanning. Site-saturation mutagenesis experiments demonstrated that Y70A/C/S/T/G all exhibited obvious fluorinase activity. The G131S mutant of SalL, in which the previously thought crucial residue Ser158 for fluoride binding in FlA was introduced, did not exhibit fluorination activity. Compared with the Y70T single mutant, the double mutant Y70T/W129F increased 5'-fluoro-5-deoxyadenosine (5'-FDA) production by 76%. The quantum mechanics (QM)/molecular mechanics (MM) calculations suggested that the lower energy barriers and shorter nucleophilic distance from F- to SAM in the mutants than in the SalL wild-type may contribute to the activity. Therefore, our study not only renders SalL the activity of FlA but also sheds light on the enzyme selectivity between fluoride versus chloride.
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Affiliation(s)
- Yixun Jiang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Mingdong Yao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Haoran Niu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Wenrui Wang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Jiale He
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Bin Qiao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Bingzhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Min Dong
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Wenhai Xiao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
- Georgia Tech Shenzhen Institute, Tianjin University, Shenzhen 518071, China
| | - Yingjin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
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Kornfuehrer T, Romanowski S, de Crécy-Lagard V, Hanson AD, Eustáquio AS. An Enzyme Containing the Conserved Domain of Unknown Function DUF62 Acts as a Stereoselective (R s ,S c )-S-Adenosylmethionine Hydrolase. Chembiochem 2020; 21:3495-3499. [PMID: 32776704 DOI: 10.1002/cbic.202000349] [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: 06/02/2020] [Revised: 08/07/2020] [Indexed: 11/09/2022]
Abstract
Homochirality is a signature of biological systems. The essential and ubiquitous cofactor S-adenosyl-l-methionine (SAM) is synthesized in cells from adenosine triphosphate and l-methionine to yield exclusively the (S,S)-SAM diastereomer. (S,S)-SAM plays a crucial role as the primary methyl donor in transmethylation reactions important to the development and homeostasis of all organisms from bacteria to humans. However, (S,S)-SAM slowly racemizes at the sulfonium center to yield the inactive (R,S)-SAM, which can inhibit methyltransferases. Control of SAM homochirality has been shown to involve homocysteine S-methyltransferases in plants, insects, worms, yeast, and in ∼18 % of bacteria. Herein, we show that a recombinant protein containing a domain of unknown function (DUF62) from the actinomycete bacterium Salinispora tropica functions as a stereoselective (R,S)-SAM hydrolase (adenosine-forming). DUF62 proteins are encoded in the genomes of 21 % of bacteria and 42 % of archaea and potentially represent a novel mechanism to remediate SAM damage.
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Affiliation(s)
- Taylor Kornfuehrer
- Department of Pharmaceutical Sciences and, Center for Biomolecular Sciences, University of Illinois, Chicago, IL 60607, USA
| | - Sean Romanowski
- Department of Pharmaceutical Sciences and, Center for Biomolecular Sciences, University of Illinois, Chicago, IL 60607, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science and, Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Alessandra S Eustáquio
- Department of Pharmaceutical Sciences and, Center for Biomolecular Sciences, University of Illinois, Chicago, IL 60607, USA
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Sooklal SA, De Koning C, Brady D, Rumbold K. Identification and characterisation of a fluorinase from Actinopolyspora mzabensis. Protein Expr Purif 2020; 166:105508. [DOI: 10.1016/j.pep.2019.105508] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/26/2019] [Accepted: 10/02/2019] [Indexed: 01/25/2023]
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Deng H, Ma L, Bandaranayaka N, Qin Z, Mann G, Kyeremeh K, Yu Y, Shepherd T, Naismith JH, O'Hagan D. Identification of fluorinases from Streptomyces sp MA37, Norcardia brasiliensis, and Actinoplanes sp N902-109 by genome mining. Chembiochem 2014; 15:364-8. [PMID: 24449539 DOI: 10.1002/cbic.201300732] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Indexed: 11/10/2022]
Abstract
The fluorinase is an enzyme that catalyses the combination of S-adenosyl-L-methionine (SAM) and a fluoride ion to generate 5'-fluorodeoxy adenosine (FDA) and L-methionine through a nucleophilic substitution reaction with a fluoride ion as the nucleophile. It is the only native fluorination enzyme that has been characterised. The fluorinase was isolated in 2002 from Streptomyces cattleya, and, to date, this has been the only source of the fluorinase enzyme. Herein, we report three new fluorinase isolates that have been identified by genome mining. The novel fluorinases from Streptomyces sp. MA37, Nocardia brasiliensis, and an Actinoplanes sp. have high homology (80-87 % identity) to the original S. cattleya enzyme. They all possess a characteristic 21-residue loop. The three newly identified genes were overexpressed in E. coli and shown to be fluorination enzymes. An X-ray crystallographic study of the Streptomyces sp. MA37 enzyme demonstrated that it is almost identical in structure to the original fluorinase. Culturing of the Streptomyces sp. MA37 strain demonstrated that it not only also elaborates the fluorometabolites, fluoroacetate and 4-fluorothreonine, similar to S. cattleya, but this strain also produces a range of unidentified fluorometabolites. These are the first new fluorinases to be reported since the first isolate, over a decade ago, and their identification extends the range of fluorination genes available for fluorination biotechnology.
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Affiliation(s)
- Hai Deng
- UK Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE (UK).
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Gulder TAM, Moore BS. Salinosporamide natural products: Potent 20 S proteasome inhibitors as promising cancer chemotherapeutics. Angew Chem Int Ed Engl 2010; 49:9346-67. [PMID: 20927786 PMCID: PMC3103133 DOI: 10.1002/anie.201000728] [Citation(s) in RCA: 171] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Proteasome inhibitors are rapidly evolving as potent treatment options in cancer therapy. One of the most promising drug candidates of this type is salinosporamide A from the bacterium Salinispora tropica. This marine natural product possesses a complex, densely functionalized γ-lactam-β-lactone pharmacophore, which is responsible for its irreversible binding to its target, the β subunit of the 20S proteasome. Salinosporamide A entered phase I clinical trials for the treatment of multiple myeloma only three years after its discovery. The strong biological activity and the challenging structure of this compound have fueled intense academic and industrial research in recent years, which has led to the development of more than ten syntheses, the elucidation of its biosynthetic pathway, and the generation of promising structure-activity relationships and oncological data. Salinosporamide A thus serves as an intriguing example of the successful interplay of modern drug discovery and biomedical research, medicinal chemistry and pharmacology, natural product synthesis and analysis, as well as biosynthesis and bioengineering.
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Affiliation(s)
- Tobias A. M. Gulder
- Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0204 (USA), Fax: (+1)858-534-1305, , Homepage: http://moorelab.ucsd.edu
| | - Bradley S. Moore
- Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0204 (USA), Fax: (+1)858-534-1305, , Homepage: http://moorelab.ucsd.edu
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Gulder TAM, Moore BS. Salinosporamid-Naturstoffe: potente Inhibitoren des 20S-Proteasoms als vielversprechende Krebs-Chemotherapeutika. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000728] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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David O'Hagan. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201002846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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David O'Hagan. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/anie.201002846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Deng H, McMahon SA, Eustáquio AS, Moore BS, Naismith JH, O'Hagan D. Mechanistic insights into water activation in SAM hydroxide adenosyltransferase (duf-62). Chembiochem 2009; 10:2455-9. [PMID: 19739191 PMCID: PMC3063057 DOI: 10.1002/cbic.200900369] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2009] [Indexed: 11/06/2022]
Affiliation(s)
- Hai Deng
- Centre for Biomolecular Sciences, School of Chemistry University of St. Andrews, St. Andrews, KY16 9ST (UK) Fax: (+44) 133-446-3808
| | - Stephen A. McMahon
- Centre for Biomolecular Sciences, School of Chemistry University of St. Andrews, St. Andrews, KY16 9ST (UK) Fax: (+44) 133-446-3808
| | - Alessandra S. Eustáquio
- Scripps Institution of Oceanography University of California in San Diego La Jolla, CA 92093-0204 (USA)
| | - Bradley S. Moore
- Scripps Institution of Oceanography University of California in San Diego La Jolla, CA 92093-0204 (USA)
- Skaggs School of Pharmacy and Pharmaceutical Sciences University of California at San Diego, La Jolla, CA 92093-0204 (USA) Fax: (+1)858-822-6652
| | - James H. Naismith
- Centre for Biomolecular Sciences, School of Chemistry University of St. Andrews, St. Andrews, KY16 9ST (UK) Fax: (+44) 133-446-3808
| | - David O'Hagan
- Centre for Biomolecular Sciences, School of Chemistry University of St. Andrews, St. Andrews, KY16 9ST (UK) Fax: (+44) 133-446-3808
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Eustáquio AS, Härle J, Noel JP, Moore BS. S-Adenosyl-L-methionine hydrolase (adenosine-forming), a conserved bacterial and archaeal protein related to SAM-dependent halogenases. Chembiochem 2009; 9:2215-9. [PMID: 18720493 PMCID: PMC2692205 DOI: 10.1002/cbic.200800341] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Alessandra S Eustáquio
- Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0204, USA
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