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Frazier CL, Deb D, Weeks AM. Engineered reactivity of a bacterial E1-like enzyme enables ATP-driven modification of protein C termini. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593989. [PMID: 38798401 PMCID: PMC11118369 DOI: 10.1101/2024.05.13.593989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
In biological systems, ATP provides an energetic driving force for peptide bond formation, but protein chemists lack tools that emulate this strategy. Inspired by the eukaryotic ubiquitination cascade, we developed an ATP-driven platform for C-terminal activation and peptide ligation based on E. coli MccB, a bacterial ancestor of ubiquitin-activating (E1) enzymes that natively catalyzes C-terminal phosphoramidate bond formation. We show that MccB can act on non-native substrates to generate an O-AMPylated electrophile that can react with exogenous nucleophiles to form diverse C-terminal functional groups including thioesters, a versatile class of biological intermediates that have been exploited for protein semisynthesis. To direct this activity towards specific proteins of interest, we developed the Thioesterification C-terminal Handle (TeCH)-tag, a sequence that enables high-yield, ATP-driven protein bioconjugation via a thioester intermediate. By mining the natural diversity of the MccB family, we developed two additional MccB/TeCH-tag pairs that are mutually orthogonal to each other and to the E. coli system, facilitating the synthesis of more complex bioconjugates. Our method mimics the chemical logic of peptide bond synthesis that is widespread in biology for high-yield in vitro manipulation of protein structure with molecular precision.
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Affiliation(s)
- Clara L. Frazier
- Department of Biochemistry, University of Wisconsin – Madison, Madison, WI, USA 53706
| | - Debashrito Deb
- Department of Biochemistry, University of Wisconsin – Madison, Madison, WI, USA 53706
| | - Amy M. Weeks
- Department of Biochemistry, University of Wisconsin – Madison, Madison, WI, USA 53706
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
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2
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Cheng X, Ma L. Enzymatic synthesis of fluorinated compounds. Appl Microbiol Biotechnol 2021; 105:8033-8058. [PMID: 34625820 PMCID: PMC8500828 DOI: 10.1007/s00253-021-11608-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/16/2021] [Accepted: 09/18/2021] [Indexed: 12/31/2022]
Abstract
Fluorinated compounds are widely used in the fields of molecular imaging, pharmaceuticals, and materials. Fluorinated natural products in nature are rare, and the introduction of fluorine atoms into organic compound molecules can give these compounds new functions and make them have better performance. Therefore, the synthesis of fluorides has attracted more and more attention from biologists and chemists. Even so, achieving selective fluorination is still a huge challenge under mild conditions. In this review, the research progress of enzymatic synthesis of fluorinated compounds is summarized since 2015, including cytochrome P450 enzymes, aldolases, fluoroacetyl coenzyme A thioesterases, lipases, transaminases, reductive aminases, purine nucleoside phosphorylases, polyketide synthases, fluoroacetate dehalogenases, tyrosine phenol-lyases, glycosidases, fluorinases, and multienzyme system. Of all enzyme-catalyzed synthesis methods, the direct formation of the C-F bond by fluorinase is the most effective and promising method. The structure and catalytic mechanism of fluorinase are introduced to understand fluorobiochemistry. Furthermore, the distribution, applications, and future development trends of fluorinated compounds are also outlined. Hopefully, this review will help researchers to understand the significance of enzymatic methods for the synthesis of fluorinated compounds and find or create excellent fluoride synthase in future research.Key points• Fluorinated compounds are distributed in plants and microorganisms, and are used in imaging, medicine, materials science.• Enzyme catalysis is essential for the synthesis of fluorinated compounds.• The loop structure of fluorinase is the key to forming the C-F bond.
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Affiliation(s)
- Xinkuan Cheng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Laboratory of Metabolic Control Fermentation Technology, College of Biotechnology, Tianjin University of Science & Technology, No. 29, Thirteenth Street, Binhai New District, Tianjin, 300457, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Laboratory of Metabolic Control Fermentation Technology, College of Biotechnology, Tianjin University of Science & Technology, No. 29, Thirteenth Street, Binhai New District, Tianjin, 300457, China.
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3
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Lyu Z, Zhao Y, Buuh ZY, Gorman N, Goldman AR, Islam MS, Tang HY, Wang RE. Steric-Free Bioorthogonal Labeling of Acetylation Substrates Based on a Fluorine-Thiol Displacement Reaction. J Am Chem Soc 2021; 143:1341-1347. [PMID: 33433199 PMCID: PMC8300487 DOI: 10.1021/jacs.0c05605] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We have developed a novel bioorthogonal reaction that can selectively displace fluorine substitutions alpha to amide bonds. This fluorine-thiol displacement reaction (FTDR) allows for fluorinated cofactors or precursors to be utilized as chemical reporters, hijacking acetyltransferase-mediated acetylation both in vitro and in live cells, which cannot be achieved with azide- or alkyne-based chemical reporters. The fluoroacetamide labels can be further converted to biotin or fluorophore tags using FTDR, enabling the general detection and imaging of acetyl substrates. This strategy may lead to a steric-free labeling platform for substrate proteins, expanding our chemical toolbox for functional annotation of post-translational modifications in a systematic manner.
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Affiliation(s)
- Zhigang Lyu
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Yue Zhao
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Zakey Yusuf Buuh
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Nicole Gorman
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Aaron R Goldman
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Md Shafiqul Islam
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Hsin-Yao Tang
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Rongsheng E Wang
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, Pennsylvania 19122, United States
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4
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Axer A, Jumde RP, Adam S, Faust A, Schäfers M, Fobker M, Koehnke J, Hirsch AKH, Gilmour R. Enhancing glycan stability via site-selective fluorination: modulating substrate orientation by molecular design. Chem Sci 2020; 12:1286-1294. [PMID: 34163891 PMCID: PMC8179167 DOI: 10.1039/d0sc04297h] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Single site OH → F substitution at the termini of maltotetraose leads to significantly improved hydrolytic stability towards α-amylase and α-glucosidase relative to the natural compound. To explore the effect of molecular editing, selectively modified oligosaccharides were prepared via a convergent α-selective strategy. Incubation experiments in purified α-amylase and α-glucosidase, and in human and murine blood serum, provide insight into the influence of fluorine on the hydrolytic stability of these clinically important scaffolds. Enhancements of ca. 1 order of magnitude result from these subtle single point mutations. Modification at the monosaccharide furthest from the probable enzymatic cleavage termini leads to the greatest improvement in stability. In the case of α-amylase, docking studies revealed that retentive C2-fluorination at the reducing end inverts the orientation in which the substrate is bound. A co-crystal structure of human α-amylase revealed maltose units bound at the active-site. In view of the evolving popularity of C(sp3)–F bioisosteres in medicinal chemistry, and the importance of maltodextrins in bacterial imaging, this discovery begins to reconcile the information-rich nature of carbohydrates with their intrinsic hydrolytic vulnerabilities. Single site OH → F substitution at the termini of maltotetraose leads to significantly improved hydrolytic stability towards α-amylase and α-glucosidase relative to the natural compound.![]()
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Affiliation(s)
- Alexander Axer
- Organisch Chemisches Institut, WWU Münster Corrensstraße 36 48149 Münster Germany
| | - Ravindra P Jumde
- Department of Drug Discovery and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) University Campus E8.1 66123 Saarbrücken Germany
| | - Sebastian Adam
- Workgroup Structural Biology of Biosynthetic Enzymes, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Institute for Infection Research (HZI) University Campus E8.1 66123 Saarbrücken Germany
| | - Andreas Faust
- European Institute for Molecular Imaging Münster Germany
| | - Michael Schäfers
- European Institute for Molecular Imaging Münster Germany.,Department of Nuclear Medicine, University Hospital (UKM) Münster Germany
| | - Manfred Fobker
- Center for Laboratory Medicine, WWU Münster Münster Germany
| | - Jesko Koehnke
- Workgroup Structural Biology of Biosynthetic Enzymes, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Institute for Infection Research (HZI) University Campus E8.1 66123 Saarbrücken Germany.,Department of Pharmacy, Saarland University 66123 Saarbrücken Germany
| | - Anna K H Hirsch
- Department of Drug Discovery and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) University Campus E8.1 66123 Saarbrücken Germany.,Department of Pharmacy, Saarland University 66123 Saarbrücken Germany
| | - Ryan Gilmour
- Organisch Chemisches Institut, WWU Münster Corrensstraße 36 48149 Münster Germany
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5
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Kuzmishin Nagy AB, Bakhtina M, Musier-Forsyth K. Trans-editing by aminoacyl-tRNA synthetase-like editing domains. Enzymes 2020; 48:69-115. [PMID: 33837712 DOI: 10.1016/bs.enz.2020.07.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Aminoacyl-tRNA synthetases (aaRS) are ubiquitous enzymes responsible for aminoacyl-tRNA (aa-tRNA) synthesis. Correctly formed aa-tRNAs are necessary for proper decoding of mRNA and accurate protein synthesis. tRNAs possess specific nucleobases that promote selective recognition by cognate aaRSs. Selecting the cognate amino acid can be more challenging because all amino acids share the same peptide backbone and several are isosteric or have similar side chains. Thus, aaRSs can misactivate non-cognate amino acids and produce mischarged aa-tRNAs. If left uncorrected, mischarged aa-tRNAs deliver their non-cognate amino acid to the ribosome resulting in misincorporation into the nascent polypeptide chain. This changes the primary protein sequence and potentially causes misfolding or formation of non-functional proteins that impair cell survival. A variety of proofreading or editing pathways exist to prevent and correct mistakes in aa-tRNA formation. Editing may occur before the amino acid transfer step of aminoacylation via hydrolysis of the aminoacyl-adenylate. Alternatively, post-transfer editing, which occurs after the mischarged aa-tRNA is formed, may be carried out via a distinct editing site on the aaRS where the mischarged aa-tRNA is deacylated. In recent years, it has become clear that most organisms also encode factors that lack aminoacylation activity but resemble aaRS editing domains and function to clear mischarged aa-tRNAs in trans. This review focuses on these trans-editing factors, which are encoded in all three domains of life and function together with editing domains present within aaRSs to ensure that the accuracy of protein synthesis is sufficient for cell survival.
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Affiliation(s)
- Alexandra B Kuzmishin Nagy
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Marina Bakhtina
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, United States.
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6
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Pseudomonas sp. AOB-7 utilizes PHA granules as a sustained-release carbon source and biofilm carrier for aerobic denitrification of aquaculture water. Appl Microbiol Biotechnol 2020; 104:3183-3192. [DOI: 10.1007/s00253-020-10452-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/01/2020] [Accepted: 02/06/2020] [Indexed: 12/13/2022]
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7
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Bentler P, Bergander K, Daniliuc CG, Mück‐Lichtenfeld C, Jumde RP, Hirsch AKH, Gilmour R. Inverting Small Molecule-Protein Recognition by the Fluorine Gauche Effect: Selectivity Regulated by Multiple H→F Bioisosterism. Angew Chem Int Ed Engl 2019; 58:10990-10994. [PMID: 31157945 PMCID: PMC6771710 DOI: 10.1002/anie.201905452] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/31/2019] [Indexed: 12/31/2022]
Abstract
Fluorinated motifs have a venerable history in drug discovery, but as C(sp3 )-F-rich 3D scaffolds appear with increasing frequency, the effect of multiple bioisosteric changes on molecular recognition requires elucidation. Herein we demonstrate that installation of a 1,3,5-stereotriad, in the substrate for a commonly used lipase from Pseudomonas fluorescens does not inhibit recognition, but inverts stereoselectivity. This provides facile access to optically active, stereochemically well-defined organofluorine compounds (up to 98 % ee). Whilst orthogonal recognition is observed with fluorine, the trend does not hold for the corresponding chlorinated substrates or mixed halogens. This phenomenon can be placed on a structural basis by considering the stereoelectronic gauche effect inherent to F-C-C-X systems (σ→σ*). Docking reveals that this change in selectivity (H versus F) with a common lipase results from inversion in the orientation of the bound substrate being processed as a consequence of conformation. This contrasts with the stereochemical interpretation of the biogenetic isoprene rule, whereby product divergence from a common starting material is also a consequence of conformation, albeit enforced by two discrete enzymes.
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Affiliation(s)
- Patrick Bentler
- Organisch Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstraße 4048149MünsterGermany
| | - Klaus Bergander
- Organisch Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstraße 4048149MünsterGermany
| | - Constantin G. Daniliuc
- Organisch Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstraße 4048149MünsterGermany
| | - Christian Mück‐Lichtenfeld
- Organisch Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstraße 4048149MünsterGermany
| | - Ravindra P. Jumde
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Department of Drug Design and OptimizationUniversity Campus E8.166123SaarbrückenGermany
| | - Anna K. H. Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Department of Drug Design and OptimizationUniversity Campus E8.166123SaarbrückenGermany
- Department of PharmacySaarland University66123SaarbrückenGermany
| | - Ryan Gilmour
- Organisch Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstraße 4048149MünsterGermany
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8
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Bentler P, Bergander K, Daniliuc CG, Mück‐Lichtenfeld C, Jumde RP, Hirsch AKH, Gilmour R. Inverting Small Molecule–Protein Recognition by the Fluorine
Gauche
Effect: Selectivity Regulated by Multiple H→F Bioisosterism. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905452] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Patrick Bentler
- Organisch Chemisches InstitutWestfälische Wilhelms-Universität Münster Corrensstraße 40 48149 Münster Germany
| | - Klaus Bergander
- Organisch Chemisches InstitutWestfälische Wilhelms-Universität Münster Corrensstraße 40 48149 Münster Germany
| | - Constantin G. Daniliuc
- Organisch Chemisches InstitutWestfälische Wilhelms-Universität Münster Corrensstraße 40 48149 Münster Germany
| | - Christian Mück‐Lichtenfeld
- Organisch Chemisches InstitutWestfälische Wilhelms-Universität Münster Corrensstraße 40 48149 Münster Germany
| | - Ravindra P. Jumde
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Department of Drug Design and Optimization University Campus E8.1 66123 Saarbrücken Germany
| | - Anna K. H. Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Department of Drug Design and Optimization University Campus E8.1 66123 Saarbrücken Germany
- Department of PharmacySaarland University 66123 Saarbrücken Germany
| | - Ryan Gilmour
- Organisch Chemisches InstitutWestfälische Wilhelms-Universität Münster Corrensstraße 40 48149 Münster Germany
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9
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Entropy drives selective fluorine recognition in the fluoroacetyl-CoA thioesterase from Streptomyces cattleya. Proc Natl Acad Sci U S A 2018; 115:E2193-E2201. [PMID: 29453276 DOI: 10.1073/pnas.1717077115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fluorinated small molecules play an important role in the design of bioactive compounds for a broad range of applications. As such, there is strong interest in developing a deeper understanding of how fluorine affects the interaction of these ligands with their targets. Given the small number of fluorinated metabolites identified to date, insights into fluorine recognition have been provided almost entirely by synthetic systems. The fluoroacetyl-CoA thioesterase (FlK) from Streptomyces cattleya thus provides a unique opportunity to study an enzyme-ligand pair that has been evolutionarily optimized for a surprisingly high 106 selectivity for a single fluorine substituent. In these studies, we synthesize a series of analogs of fluoroacetyl-CoA and acetyl-CoA to generate nonhydrolyzable ester, amide, and ketone congeners of the thioester substrate to isolate the role of fluorine molecular recognition in FlK selectivity. Using a combination of thermodynamic, kinetic, and protein NMR experiments, we show that fluorine recognition is entropically driven by the interaction of the fluorine substituent with a key residue, Phe-36, on the lid structure that covers the active site, resulting in an ∼5- to 20-fold difference in binding (KD). Although the magnitude of discrimination is similar to that found in designed synthetic ligand-protein complexes where dipolar interactions control fluorine recognition, these studies show that hydrophobic and solvation effects serve as the major determinant of naturally evolved fluorine selectivity.
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10
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Pal M, Easton NM, Yaphe H, Bearne SL. Potent dialkyl substrate-product analogue inhibitors and inactivators of α-methylacyl-coenzyme A racemase from Mycobacterium tuberculosis by rational design. Bioorg Chem 2018; 77:640-650. [PMID: 29502025 DOI: 10.1016/j.bioorg.2018.01.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/28/2018] [Accepted: 01/30/2018] [Indexed: 12/15/2022]
Abstract
Rational approaches for the design of enzyme inhibitors furnish powerful strategies for developing pharmaceutical agents and tools for probing biological mechanisms. A new strategy for the development of gem-disubstituted substrate-product analogues as inhibitors of racemases and epimerases is elaborated using α-methylacyl-coenzyme A racemase from Mycobacterium tuberculosis (MtMCR) as a model enzyme. MtMCR catalyzes the epimerization at C2 of acyl-CoA substrates, a key step in the metabolism of branched-chain fatty acids. Moreover, the human enzyme is a potential target for the development of therapeutic agents directed against prostate cancer. We show that rationally designed, N,N-dialkylcarbamoyl-CoA substrate-product analogues inactivate MtMCR. Binding greatly exceeds that of the substrate, (S)-ibuprofenoyl-CoA, up to ∼250-fold and is proportional to the alkyl chain length (4-12 carbons) with the N,N-didecyl and N,N-didodecyl species having competitive inhibition constants with values of 1.9 ± 0.2 μM and 0.42 ± 0.04 μM, respectively. The presence of two decyl chains enhanced binding over a single decyl chain by ∼204-fold. Overall, the results reveal that gem-disubstituted substrate-product analogues can yield extremely potent inhibitors of an epimerase with a capacious active site.
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Affiliation(s)
- Mohan Pal
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Nicole M Easton
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Hannah Yaphe
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Department of Chemistry, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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11
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Fluorothreonyl-tRNA deacylase prevents mistranslation in the organofluorine producer Streptomyces cattleya. Proc Natl Acad Sci U S A 2017; 114:11920-11925. [PMID: 29078362 DOI: 10.1073/pnas.1711482114] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Fluorine is an element with unusual properties that has found significant utility in the design of synthetic small molecules, ranging from therapeutics to materials. In contrast, only a few fluorinated compounds made by living organisms have been found to date, most of which derive from the fluoroacetate/fluorothreonine biosynthetic pathway first discovered in Streptomyces cattleya While fluoroacetate has long been known to act as an inhibitor of the tricarboxylic acid cycle, the fate of the amino acid fluorothreonine is still not well understood. Here, we show that fluorothreonine can be misincorporated into protein in place of the proteinogenic amino acid threonine. We have identified two conserved proteins from the organofluorine biosynthetic locus, FthB and FthC, that are involved in managing fluorothreonine toxicity. Using a combination of biochemical, genetic, physiological, and proteomic studies, we show that FthB is a trans-acting transfer RNA (tRNA) editing protein, which hydrolyzes fluorothreonyl-tRNA 670-fold more efficiently than threonyl-RNA, and assign a role to FthC in fluorothreonine transport. While trans-acting tRNA editing proteins have been found to counteract the misacylation of tRNA with commonly occurring near-cognate amino acids, their role has yet to be described in the context of secondary metabolism. In this regard, the recruitment of tRNA editing proteins to biosynthetic clusters may have enabled the evolution of pathways to produce specialized amino acids, thereby increasing the diversity of natural product structure while also attenuating the risk of mistranslation that would ensue.
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12
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Thuronyi BW, Privalsky TM, Chang MCY. Engineered Fluorine Metabolism and Fluoropolymer Production in Living Cells. Angew Chem Int Ed Engl 2017; 56:13637-13640. [PMID: 28861937 PMCID: PMC5818260 DOI: 10.1002/anie.201706696] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/15/2017] [Indexed: 12/19/2022]
Abstract
Fluorine has become an important element for the design of synthetic molecules for use in medicine, agriculture, and materials. Despite the many advantages provided by fluorine for tuning key molecular properties, it is rarely found in natural metabolism. We seek to expand the molecular space available for discovery through the development of new biosynthetic strategies that cross synthetic with natural compounds. Towards this goal, we engineered a microbial host for organofluorine metabolism and show that we can achieve the production of the fluorinated diketide 2-fluoro-3-hydroxybutyrate at approximately 50 % yield. This fluorinated diketide can be used as a monomer in vivo to produce fluorinated poly(hydroxyalkanoate) (PHA) bioplastics with fluorine substitutions ranging from around 5-15 %. This system provides a platform to produce mm flux through the key fluoromalonyl coenzyme A (CoA) building block, thereby offering the potential to generate a broad range of fluorinated small-molecule targets in living cells.
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Affiliation(s)
- B W Thuronyi
- Departments of Chemistry and Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, 94720-1460, USA
- Current address: Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Thomas M Privalsky
- Departments of Chemistry and Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, 94720-1460, USA
- Current address: Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Michelle C Y Chang
- Departments of Chemistry and Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, 94720-1460, USA
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13
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Khandokar YB, Srivastava P, Cowieson N, Sarker S, Aragao D, Das S, Smith KM, Raidal SR, Forwood JK. Structural insights into GDP-mediated regulation of a bacterial acyl-CoA thioesterase. J Biol Chem 2017; 292:20461-20471. [PMID: 28972175 DOI: 10.1074/jbc.m117.800227] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 09/12/2017] [Indexed: 11/06/2022] Open
Abstract
Thioesterases catalyze the cleavage of thioester bonds within many activated fatty acids and acyl-CoA substrates. They are expressed ubiquitously in both prokaryotes and eukaryotes and are subdivided into 25 thioesterase families according to their catalytic active site, protein oligomerization, and substrate specificity. Although many of these enzyme families are well-characterized in terms of function and substrate specificity, regulation across most thioesterase families is poorly understood. Here, we characterized a TE6 thioesterase from the bacterium Neisseria meningitidis Structural analysis with X-ray crystallographic diffraction data to 2.0-Å revealed that each protein subunit harbors a hot dog-fold and that the TE6 enzyme forms a hexamer with D3 symmetry. An assessment of thioesterase activity against a range of acyl-CoA substrates revealed the greatest activity against acetyl-CoA, and structure-guided mutagenesis of putative active site residues identified Asn24 and Asp39 as being essential for activity. Our structural analysis revealed that six GDP nucleotides bound the enzyme in close proximity to an intersubunit disulfide bond interactions that covalently link thioesterase domains in a double hot dog dimer. Structure-guided mutagenesis of residues within the GDP-binding pocket identified Arg93 as playing a key role in the nucleotide interaction and revealed that GDP is required for activity. All mutations were confirmed to be specific and not to have resulted from structural perturbations by X-ray crystallography. This is the first report of a bacterial GDP-regulated thioesterase and of covalent linkage of thioesterase domains through a disulfide bond, revealing structural similarities with ADP regulation in the human ACOT12 thioesterase.
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Affiliation(s)
| | | | - Nathan Cowieson
- the Life Sciences Division, Diamond Light Source, Didcot OX11 0DE, United Kingdom
| | - Subir Sarker
- the Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, Victoria 3086, Australia, and
| | - David Aragao
- the Australian National Synchrotron, Melbourne, Victoria 3168, Australia
| | - Shubagata Das
- School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia
| | | | - Shane R Raidal
- School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia
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14
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Thuronyi BW, Privalsky TM, Chang MCY. Engineered Fluorine Metabolism and Fluoropolymer Production in Living Cells. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706696] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Benjamin W. Thuronyi
- Departments of Chemistry and Molecular & Cell Biology University of California, Berkeley Berkeley CA 94720-1460 USA
- Current address: Department of Chemistry & Chemical Biology Harvard University Cambridge MA 02138 USA
| | - Thomas M. Privalsky
- Departments of Chemistry and Molecular & Cell Biology University of California, Berkeley Berkeley CA 94720-1460 USA
- Current address: Department of Chemistry Stanford University Stanford CA 94305 USA
| | - Michelle C. Y. Chang
- Departments of Chemistry and Molecular & Cell Biology University of California, Berkeley Berkeley CA 94720-1460 USA
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15
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Carvalho MF, Oliveira RS. Natural production of fluorinated compounds and biotechnological prospects of the fluorinase enzyme. Crit Rev Biotechnol 2017; 37:880-897. [PMID: 28049355 DOI: 10.1080/07388551.2016.1267109] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Fluorinated compounds are finding increasing uses in several applications. They are employed in almost all areas of modern society. These compounds are all produced by chemical synthesis and their abundance highly contrasts with fluorinated molecules of natural origin. To date, only some plants and a handful of actinomycetes species are known to produce a small number of fluorinated compounds that include fluoroacetate (FA), some ω-fluorinated fatty acids, nucleocidin, 4-fluorothreonine (4-FT), and the more recently identified (2R3S4S)-5-fluoro-2,3,4-trihydroxypentanoic acid. This largely differs from other naturally produced halogenated compounds, which totals more than 5000. The mechanisms underlying biological fluorination have been uncovered after discovering the first actinomycete species, Streptomyces cattleya, that is capable of producing FA and 4-FT, and a fluorinase has been identified as the enzyme responsible for the formation of the C-F bond. The discovery of this enzyme has opened new perspectives for the biotechnological production of fluorinated compounds and many advancements have been achieved in its application mainly as a biocatalyst for the synthesis of [18F]-labeled radiotracers for medical imaging. Natural fluorinated compounds may also be derived from abiogenic sources, such as volcanoes and rocks, though their concentrations and production mechanisms are not well known. This review provides an outlook of what is currently known about fluorinated compounds with natural origin. The paucity of these compounds and the biological mechanisms responsible for their production are addressed. Due to its relevance, special emphasis is given to the discovery, characterization and biotechnological potential of the unique fluorinase enzyme.
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Affiliation(s)
- Maria F Carvalho
- a CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto , Porto , Portugal
| | - Rui S Oliveira
- b Centre for Functional Ecology, Department of Life Sciences , University of Coimbra , Coimbra , Portugal.,c Department of Environmental Health , Research Centre on Health and Environment, School of Allied Health Sciences, Polytechnic Institute of Porto , Porto , Portugal
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16
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Abstract
The role of fluorine in drug design and development is expanding rapidly as we learn more about the unique properties associated with this unusual element and how to deploy it with greater sophistication. The judicious introduction of fluorine into a molecule can productively influence conformation, pKa, intrinsic potency, membrane permeability, metabolic pathways, and pharmacokinetic properties. In addition, (18)F has been established as a useful positron emitting isotope for use with in vivo imaging technology that potentially has extensive application in drug discovery and development, often limited only by convenient synthetic accessibility to labeled compounds. The wide ranging applications of fluorine in drug design are providing a strong stimulus for the development of new synthetic methodologies that allow more facile access to a wide range of fluorinated compounds. In this review, we provide an update on the effects of the strategic incorporation of fluorine in drug molecules and applications in positron emission tomography.
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Affiliation(s)
- Eric P Gillis
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development , 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Kyle J Eastman
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development , 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Matthew D Hill
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development , 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - David J Donnelly
- Discovery Chemistry Platforms, PET Radiochemical Synthesis, Bristol-Myers Squibb Research and Development , P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Nicholas A Meanwell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development , 5 Research Parkway, Wallingford, Connecticut 06492, United States
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17
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Pal M, Bearne SL. Synthesis of coenzyme A thioesters using methyl acyl phosphates in an aqueous medium. Org Biomol Chem 2015; 12:9760-3. [PMID: 25355071 DOI: 10.1039/c4ob02079k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Regioselective S-acylation of coenzyme A (CoA) is achieved under aqueous conditions using various aliphatic and aromatic carboxylic acids activated as their methyl acyl phosphate monoesters. Unlike many hydrophobic activating groups, the anionic methyl acyl phosphate mixed anhydride is more compatible with aqueous solvents, making it useful for conducting acylation reactions in an aqueous medium.
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Affiliation(s)
- Mohan Pal
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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18
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Walker MC, Chang MCY. Natural and engineered biosynthesis of fluorinated natural products. Chem Soc Rev 2015; 43:6527-36. [PMID: 24776946 DOI: 10.1039/c4cs00027g] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Both natural products and synthetic organofluorines play important roles in the discovery and design of pharmaceuticals. The combination of these two classes of molecules has the potential to be useful in the ongoing search for new bioactive compounds but our ability to produce site-selectively fluorinated natural products remains limited by challenges in compatibility between their high structural complexity and current methods for fluorination. Living systems provide an alternative route to chemical fluorination and could enable the production of organofluorine natural products through synthetic biology approaches. While the identification of biogenic organofluorines has been limited, the study of the native organisms and enzymes that utilize these compounds can help to guide efforts to engineer the incorporation of this unusual element into complex pharmacologically active natural products. This review covers recent advances in understanding both natural and engineered production of organofluorine natural products.
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Affiliation(s)
- Mark C Walker
- Departments of Chemistry and Molecular & Cell Biology, University of California, Berkeley, 125 Lewis, Berkeley, CA 94720-1460, USA.
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19
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Abstract
The catalytic diversity of living systems offers a broad range of opportunities for developing new methods to produce small molecule targets such as fuels, materials, and pharmaceuticals. In addition to providing cost-effective and renewable methods for large-scale commercial processes, the exploration of the unusual chemical phenotypes found in living organisms can also enable the expansion of chemical space for discovery of novel function by combining orthogonal attributes from both synthetic and biological chemistry. In this context, we have focused on the development of new fluorine chemistry using synthetic biology approaches. While fluorine has become an important feature in compounds of synthetic origin, the scope of biological fluorine chemistry in living systems is limited, with fewer than 20 organofluorine natural products identified to date. In order to expand the diversity of biosynthetically accessible organofluorines, we have begun to develop methods for the site-selective introduction of fluorine into complex natural products by engineering biosynthetic machinery to incorporate fluorinated building blocks. To gain insight into how both enzyme active sites and metabolic pathways can be evolved to manage and select for fluorinated compounds, we have studied one of the only characterized natural hosts for organofluorine biosynthesis, the soil microbe Streptomyces cattleya. This information provides a template for designing engineered organofluorine enzymes, pathways, and hosts and has allowed us to initiate construction of enzymatic and cellular pathways for the production of fluorinated polyketides.
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Affiliation(s)
- Benjamin W. Thuronyi
- University of California, Berkeley, Department of Chemistry, Berkeley, CA 94720-1460
| | - Michelle C. Y. Chang
- University of California, Berkeley, Department of Chemistry, Berkeley, CA 94720-1460
- University of California, Berkeley, Department of Molecular and Cell Biology, Berkeley, CA 94720-3200
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20
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O'Hagan D, Deng H. Enzymatic fluorination and biotechnological developments of the fluorinase. Chem Rev 2014; 115:634-49. [PMID: 25253234 DOI: 10.1021/cr500209t] [Citation(s) in RCA: 229] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- David O'Hagan
- EaStChem School of Chemistry, University of St Andrews , North Haugh, St Andrews KY169ST, United Kingdom
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21
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Latham JA, Chen D, Allen KN, Dunaway-Mariano D. Divergence of substrate specificity and function in the Escherichia coli hotdog-fold thioesterase paralogs YdiI and YbdB. Biochemistry 2014; 53:4775-87. [PMID: 24992697 PMCID: PMC4116150 DOI: 10.1021/bi500333m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The work described in this paper, and its companion paper (Wu, R., Latham, J. A., Chen, D., Farelli, J., Zhao, H., Matthews, K. Allen, K. N., and Dunaway-Mariano, D. (2014) Structure and Catalysis in the Escherichia coli Hotdog-fold Thioesterase Paralogs YdiI and YbdB. Biochemistry, DOI: 10.1021/bi500334v), focuses on the evolution of a pair of paralogous hotdog-fold superfamily thioesterases of E. coli, YbdB and YdiI, which share a high level of sequence identity but perform different biological functions (viz., proofreader of 2,3-dihydroxybenzoyl-holoEntB in the enterobactin biosynthetic pathway and catalyst of the 1,4-dihydoxynapthoyl-CoA hydrolysis step in the menaquinone biosynthetic pathway, respectively). In vitro substrate activity screening of a library of thioester metabolites showed that YbdB displays high activity with benzoyl-holoEntB and benzoyl-CoA substrates, marginal activity with acyl-CoA thioesters, and no activity with 1,4-dihydoxynapthoyl-CoA. YdiI, on the other hand, showed a high level of activity with its physiological substrate, significant activity toward a wide range of acyl-CoA thioesters, and minimal activity toward benzoyl-holoEntB. These results were interpreted as evidence for substrate promiscuity that facilitates YbdB and YdiI evolvability, and divergence in substrate preference, which correlates with their assumed biological function. YdiI support of the menaquinone biosynthetic pathway was confirmed by demonstrating reduced anaerobic growth of the E. coli ydiI-knockout mutant (vs wild-type E. coli) on glucose in the presence of the electron acceptor fumarate. Bioinformatic analysis revealed that a small biological range exists for YbdB orthologs (i.e., limited to Enterobacteriales) relative to that of YdiI orthologs. The divergence in YbdB and YdiI substrate specificity detailed in this paper set the stage for their structural analyses reported in the companion paper.
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Affiliation(s)
- John A Latham
- Department of Chemistry & Chemical Biology, University of New Mexico , Albuquerque, New Mexico 87131, United States
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22
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Weeks AM, Keddie NS, Wadoux RDP, O'Hagan D, Chang MCY. Molecular recognition of fluorine impacts substrate selectivity in the fluoroacetyl-CoA thioesterase FlK. Biochemistry 2014; 53:2053-63. [PMID: 24635371 PMCID: PMC3985765 DOI: 10.1021/bi4015049] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The fluoroacetate-producing bacterium Streptomyces cattleya has evolved a fluoroacetyl-CoA thioesterase
(FlK) that exhibits
a remarkably high level of discrimination for its cognate substrate
compared to the cellularly abundant analogue acetyl-CoA, which differs
only by the absence of the fluorine substitution. A major determinant
of FlK specificity derives from its ability to take advantage of the
unique properties of fluorine to enhance the reaction rate, allowing
fluorine discrimination under physiological conditions where both
substrates are likely to be present at saturating concentrations.
Using a combination of pH–rate profiles, pre-steady-state kinetic
experiments, and Taft analysis of wild-type and mutant FlKs with a
set of substrate analogues, we explore the role of fluorine in controlling
the enzyme acylation and deacylation steps. Further analysis of chiral
(R)- and (S)-[2H1]fluoroacetyl-CoA substrates demonstrates that a kinetic isotope
effect (1.7 ± 0.2) is observed for only the (R)-2H1 isomer, indicating that deacylation requires
recognition of the prochiral fluoromethyl group to position the α-carbon
for proton abstraction. Taken together, the selectivity for the fluoroacetyl-CoA
substrate appears to rely not only on the enhanced polarization provided
by the electronegative fluorine substitution but also on molecular
recognition of fluorine in both formation and breakdown of the acyl-enzyme
intermediate to control active site reactivity. These studies provide
insights into the basis of fluorine selectivity in a naturally occurring
enzyme–substrate pair, with implications for drug design and
the development of fluorine-selective biocatalysts.
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Affiliation(s)
- Amy M Weeks
- Department of Chemistry, University of California , Berkeley, California 94720-1460, United States
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23
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Wang Y, Deng Z, Qu X. Characterization of a SAM-dependent fluorinase from a latent biosynthetic pathway for fluoroacetate and 4-fluorothreonine formation in Nocardia brasiliensis. F1000Res 2014; 3:61. [PMID: 24795808 PMCID: PMC3999930 DOI: 10.12688/f1000research.3-61.v1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/18/2014] [Indexed: 11/20/2022] Open
Abstract
Fluorination has been widely used in chemical synthesis, but is rare in nature. The only known biological fluorination scope is represented by the
fl pathway from
Streptomyces cattleya that produces fluoroacetate (FAc) and 4-fluorothreonine (4-FT). Here we report the identification of a novel pathway for FAc and 4-FT biosynthesis from the actinomycetoma-causing pathogen
Nocardia brasiliensis ATCC 700358. The new pathway shares overall conservation with the
fl pathway in
S. cattleya. Biochemical characterization of the conserved domains revealed a novel fluorinase NobA that can biosynthesize 5’-fluoro-5’-deoxyadenosine (5’-FDA) from inorganic fluoride and
S-adenosyl-l-methionine (SAM). The NobA shows similar halide specificity and characteristics to the fluorination enzyme FlA of the
fl pathway. Kinetic parameters for fluoride (
K
m 4153 μM,
k
cat 0.073 min
-1) and SAM (
K
m 416 μM,
k
cat 0.139 min
-1) have been determined, revealing that NobA is slightly (2.3 fold) slower than FlA. Upon sequence comparison, we finally identified a distinct loop region in the fluorinases that probably accounts for the disparity of fluorination activity.
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Affiliation(s)
- Yaya Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Xudong Qu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
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24
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Huang S, Ma L, Tong MH, Yu Y, O'Hagan D, Deng H. Fluoroacetate biosynthesis from the marine-derived bacterium Streptomyces xinghaiensis NRRL B-24674. Org Biomol Chem 2014; 12:4828-31. [DOI: 10.1039/c4ob00970c] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Streptomyces xinghaiensis is the first fluorometabolite producing microorganism identified from the marine environment.
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Affiliation(s)
- Sheng Huang
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education)
- School of Pharmaceutical Sciences
- Wuhan University
- Wuhan 430071, P. R. China
| | - Long Ma
- School of Chemistry and Biomedical Sciences Research Centre
- University of St Andrews
- St Andrews KY169ST, UK
| | - Ming Him Tong
- Marine Biodiscovery Centre
- Department of Chemistry
- Meston Walk
- University of Aberdeen
- Aberdeen AB24 3UE, UK
| | - Yi Yu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education)
- School of Pharmaceutical Sciences
- Wuhan University
- Wuhan 430071, P. R. China
| | - David O'Hagan
- School of Chemistry and Biomedical Sciences Research Centre
- University of St Andrews
- St Andrews KY169ST, UK
| | - Hai Deng
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education)
- School of Pharmaceutical Sciences
- Wuhan University
- Wuhan 430071, P. R. China
- Marine Biodiscovery Centre
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25
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Affiliation(s)
- Annette D. Allen
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Thomas T. Tidwell
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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