1
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Liu K, Zhang J, Zhang G, Zhang L, Meng Z, Ma L, Zhang W, Xiong W, Zhu Y, Wang B, Zhang C. Deciphering Deoxynybomycin Biosynthesis Reveals Fe(II)/α-Ketoglutarate-Dependent Dioxygenase-Catalyzed Oxazoline Ring Formation and Decomposition. J Am Chem Soc 2023; 145:27886-27899. [PMID: 38055632 DOI: 10.1021/jacs.3c11772] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
The antibacterial agents deoxynybomycin (DNM) and nybomycin (NM) have a unique tetracyclic structure featuring an angularly fused 4-oxazoline ring. Here, we report the identification of key enzymes responsible for forming the 4-oxazoline ring in Embleya hyalina NBRC 13850 by comparative bioinformatics analysis of the biosynthetic gene clusters encoding structurally similar natural products DNM, deoxynyboquinone (DNQ), and diazaquinomycins (DAQs). The N-methyltransferase DnmS plays a crucial role in catalyzing the N-dimethylation of a tricyclic precursor prenybomycin to generate NM D; subsequently, the Fe(II)/α-ketoglutarate-dependent dioxygenase (Fe/αKGD) DnmT catalyzes the formation of a 4-oxazoline ring from NM D to produce DNM; finally, a second Fe/αKGD DnmU catalyzes the C-12 hydroxylation of DNM to yield NM. Strikingly, DnmT is shown to display unexpected functions to also catalyze the decomposition of the 4-oxazoline ring and the N-demethylation, thereby converting DNM back to prenybomycin, to putatively serve as a manner to control the intracellular yield of DNM. Structure modeling, site-directed mutagenesis, and quantum mechanics calculations provide mechanistic insights into the DnmT-catalyzed reactions. This work expands our understanding of the functional diversity of Fe/αKGDs in natural product biosynthesis.
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Affiliation(s)
- Kai Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, China-Sri Lanka Joint Center for Education and Research, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Jinyan Zhang
- 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
| | - Guangtao Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, China-Sri Lanka Joint Center for Education and Research, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, China-Sri Lanka Joint Center for Education and Research, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Meng
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, China-Sri Lanka Joint Center for Education and Research, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Liang Ma
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, China-Sri Lanka Joint Center for Education and Research, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Wenjun Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, China-Sri Lanka Joint Center for Education and Research, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Weiliang Xiong
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, China-Sri Lanka Joint Center for Education and Research, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, China-Sri Lanka Joint Center for Education and Research, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, 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
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, China-Sri Lanka Joint Center for Education and Research, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
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2
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Vennelakanti V, Li GL, Kulik HJ. Why Nonheme Iron Halogenases Do Not Fluorinate C-H Bonds: A Computational Investigation. Inorg Chem 2023; 62:19758-19770. [PMID: 37972340 DOI: 10.1021/acs.inorgchem.3c03215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Selective halogenation is necessary for a range of fine chemical applications, including the development of therapeutic drugs. While synthetic processes to achieve C-H halogenation require harsh conditions, enzymes such as nonheme iron halogenases carry out some types of C-H halogenation, i.e., chlorination or bromination, with ease, while others, i.e., fluorination, have never been observed in natural or engineered nonheme iron enzymes. Using density functional theory and correlated wave function theory, we investigate the differences in structural and energetic preferences of the smaller fluoride and the larger chloride or bromide intermediates throughout the catalytic cycle. Although we find that the energetics of rate-limiting hydrogen atom transfer are not strongly impacted by fluoride substitution, the higher barriers observed during the radical rebound reaction for fluoride relative to chloride and bromide contribute to the difficulty of C-H fluorination. We also investigate the possibility of isomerization playing a role in differences in reaction selectivity, and our calculations reveal crucial differences in terms of isomer energetics of the key ferryl intermediate between fluoride and chloride/bromide intermediates. While formation of monodentate isomers believed to be involved in selective catalysis is shown for chloride and bromide intermediates, we find that formation of the fluoride monodentate intermediate is not possible in our calculations, which lack additional stabilizing interactions with the greater protein environment. Furthermore, the shorter Fe-F bonds are found to increase isomerization reaction barriers, suggesting that incorporation of residues that form a halogen bond with F and elongate Fe-F bonds could make selective C-H fluorination possible in nonheme iron halogenases. Our work highlights the differences between the fluoride and chloride/bromide intermediates and suggests potential steps toward engineering nonheme iron halogenases to enable selective C-H fluorination.
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Affiliation(s)
- Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Grace L Li
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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3
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Slater JW, Lin CY, Neugebauer ME, McBride MJ, Sil D, Nair M, Katch BJ, Boal AK, Chang MC, Silakov A, Krebs C, Bollinger JM. Synergistic Binding of the Halide and Cationic Prime Substrate of l-Lysine 4-Chlorinase, BesD, in Both Ferrous and Ferryl States. Biochemistry 2023; 62:2480-2491. [PMID: 37542461 PMCID: PMC10829012 DOI: 10.1021/acs.biochem.3c00248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2023]
Abstract
An aliphatic halogenase requires four substrates: 2-oxoglutarate (2OG), halide (Cl- or Br-), the halogenation target ("prime substrate"), and dioxygen. In well-studied cases, the three nongaseous substrates must bind to activate the enzyme's Fe(II) cofactor for efficient capture of O2. Halide, 2OG, and (lastly) O2 all coordinate directly to the cofactor to initiate its conversion to a cis-halo-oxo-iron(IV) (haloferryl) complex, which abstracts hydrogen (H•) from the non-coordinating prime substrate to enable radicaloid carbon-halogen coupling. We dissected the kinetic pathway and thermodynamic linkage in binding of the first three substrates of the l-lysine 4-chlorinase, BesD. After addition of 2OG, subsequent coordination of the halide to the cofactor and binding of cationic l-Lys near the cofactor are associated with strong heterotropic cooperativity. Progression to the haloferryl intermediate upon the addition of O2 does not trap the substrates in the active site and, in fact, markedly diminishes cooperativity between halide and l-Lys. The surprising lability of the BesD•[Fe(IV)=O]•Cl•succinate•l-Lys complex engenders pathways for decay of the haloferryl intermediate that do not result in l-Lys chlorination, especially at low chloride concentrations; one identified pathway involves oxidation of glycerol. The mechanistic data imply (i) that BesD may have evolved from a hydroxylase ancestor either relatively recently or under weak selective pressure for efficient chlorination and (ii) that acquisition of its activity may have involved the emergence of linkage between l-Lys binding and chloride coordination following the loss of the anionic protein-carboxylate iron ligand present in extant hydroxylases.
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Affiliation(s)
- Jeffrey W. Slater
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Chi-Yun Lin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Monica E. Neugebauer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, United States
- Present address: Department of Systems Biology, Harvard Medical School, Boston, MA 02115, United States
| | - Molly J. McBride
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Present address: Alliance Pharma, New York, NY 10065, United States
| | - Debangsu Sil
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Present address: Department of Chemistry, Indian Institute of Science Education & Research (IISER)-Pune, Pune-411008, India
| | - Mrutyunjay Nair
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Bryce J. Katch
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Present address: Tri-Institutional MD-PhD Program, Weill Cornell Medical College and Cornell University, New York, NY 10065, United States
| | - Amie K. Boal
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| | - Michelle C.Y. Chang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, United States
- Departments of Chemistry and of Molecular and Cell Biology, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Alexey Silakov
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
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4
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Smithwick ER, Wilson RH, Chatterjee S, Pu Y, Dalluge JJ, Damodaran AR, Bhagi-Damodaran A. Electrostatically regulated active site assembly governs reactivity in non-heme iron halogenases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542349. [PMID: 37292651 PMCID: PMC10245910 DOI: 10.1101/2023.05.25.542349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Non-heme iron halogenases (NHFe-Hals) catalyze the direct insertion of a chloride/bromide ion at an unactivated carbon position using a high-valent haloferryl intermediate. Despite more than a decade of structural and mechanistic characterization, how NHFe-Hals preferentially bind specific anions and substrates for C-H functionalization remains unknown. Herein, using lysine halogenating BesD and HalB enzymes as model systems, we demonstrate strong positive cooperativity between anion and substrate binding to the catalytic pocket. Detailed computational investigations indicate that a negatively charged glutamate hydrogen-bonded to iron's equatorial-aqua ligand acts as an electrostatic lock preventing both lysine and anion binding in the absence of the other. Using a combination of UV-Vis spectroscopy, binding affinity studies, stopped-flow kinetics investigations, and biochemical assays, we explore the implication of such active site assembly towards chlorination, bromination, and azidation reactivities. Overall, our work highlights previously unknown features regarding how anion-substrate pair binding govern reactivity of iron halogenases that are crucial for engineering next-generation C-H functionalization biocatalysts.
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Affiliation(s)
- Elizabeth R. Smithwick
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - R. Hunter Wilson
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Sourav Chatterjee
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Yu Pu
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Joseph J. Dalluge
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Anoop Rama Damodaran
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
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5
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Slater JW, Neugebauer ME, McBride MJ, Sil D, Lin CY, Katch BJ, Boal AK, Chang MC, Silakov A, Krebs C, Bollinger JM. Synergistic Binding of the Halide and Cationic Prime Substrate of the l-Lysine 4-Chlorinase, BesD, in Both Ferrous and Ferryl States. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539147. [PMID: 37205437 PMCID: PMC10187165 DOI: 10.1101/2023.05.02.539147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
An aliphatic halogenase requires four substrates: 2-oxoglutarate (2OG), halide (Cl - or Br - ), the halogenation target ("prime substrate"), and dioxygen. In well-studied cases, the three non-gaseous substrates must bind to activate the enzyme's Fe(II) cofactor for efficient capture of O 2 . Halide, 2OG, and (lastly) O 2 all coordinate directly to the cofactor to initiate its conversion to a cis -halo-oxo-iron(IV) (haloferryl) complex, which abstracts hydrogen (H•) from the non-coordinating prime substrate to enable radicaloid carbon-halogen coupling. We dissected the kinetic pathway and thermodynamic linkage in binding of the first three substrates of the l -lysine 4-chlorinase, BesD. After 2OG adds, subsequent coordination of the halide to the cofactor and binding of cationic l -Lys near the cofactor are associated with strong heterotropic cooperativity. Progression to the haloferryl intermediate upon addition of O 2 does not trap the substrates in the active site and, in fact, markedly diminishes cooperativity between halide and l -Lys. The surprising lability of the BesD•[Fe(IV)=O]•Cl•succinate• l -Lys complex engenders pathways for decay of the haloferryl intermediate that do not result in l -Lys chlorination, especially at low chloride concentrations; one identified pathway involves oxidation of glycerol. The mechanistic data imply that (i) BesD may have evolved from a hydroxylase ancestor either relatively recently or under weak selective pressure for efficient chlorination and (ii) that acquisition of its activity may have involved the emergence of linkage between l -Lys binding and chloride coordination following loss of the anionic protein-carboxylate iron ligand present in extant hydroxylases.
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Affiliation(s)
- Jeffrey W. Slater
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Monica E. Neugebauer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
- Present address: Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Molly J. McBride
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Debangsu Sil
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Chi-Yun Lin
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Bryce J. Katch
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Amie K. Boal
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Michelle C.Y. Chang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
- Departments of Chemistry and of Molecular and Cell Biology, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alexey Silakov
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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6
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Vennelakanti V, Mehmood R, Kulik HJ. Are Vanadium Intermediates Suitable Mimics in Non-Heme Iron Enzymes? An Electronic Structure Analysis. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Rimsha Mehmood
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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7
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Liu X, Yuan Z, Su H, Hou X, Deng Z, Xu H, Guo B, Yin D, Sheng X, Rao Y. Molecular Basis of the Unusual Seven-Membered Methylenedioxy Bridge Formation Catalyzed by Fe(II)/α-KG-Dependent Oxygenase CTB9. ACS Catal 2022. [DOI: 10.1021/acscatal.1c04627] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Xuanzhong Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
| | - Zhenbo Yuan
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
| | - Hao Su
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences and National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P. R. China
| | - Xiaodong Hou
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
| | - Zhiwei Deng
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
| | - Huibin Xu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
| | - Baodang Guo
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
| | - Dejing Yin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
| | - Xiang Sheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences and National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P. R. China
| | - Yijian Rao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
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8
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Mehmood R, Vennelakanti V, Kulik HJ. Spectroscopically Guided Simulations Reveal Distinct Strategies for Positioning Substrates to Achieve Selectivity in Nonheme Fe(II)/α-Ketoglutarate-Dependent Halogenases. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03169] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Rimsha Mehmood
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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9
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Crowe C, Molyneux S, Sharma SV, Zhang Y, Gkotsi DS, Connaris H, Goss RJM. Halogenases: a palette of emerging opportunities for synthetic biology-synthetic chemistry and C-H functionalisation. Chem Soc Rev 2021; 50:9443-9481. [PMID: 34368824 PMCID: PMC8407142 DOI: 10.1039/d0cs01551b] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Indexed: 12/14/2022]
Abstract
The enzymatic generation of carbon-halogen bonds is a powerful strategy used by both nature and synthetic chemists to tune the bioactivity, bioavailability and reactivity of compounds, opening up the opportunity for selective C-H functionalisation. Genes encoding halogenase enzymes have recently been shown to transcend all kingdoms of life. These enzymes install halogen atoms into aromatic and less activated aliphatic substrates, achieving selectivities that are often challenging to accomplish using synthetic methodologies. Significant advances in both halogenase discovery and engineering have provided a toolbox of enzymes, enabling the ready use of these catalysts in biotransformations, synthetic biology, and in combination with chemical catalysis to enable late stage C-H functionalisation. With a focus on substrate scope, this review outlines the mechanisms employed by the major classes of halogenases, while in parallel, it highlights key advances in the utilisation of the combination of enzymatic halogenation and chemical catalysis for C-H activation and diversification.
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Affiliation(s)
- Charlotte Crowe
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Samuel Molyneux
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Sunil V. Sharma
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Ying Zhang
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Danai S. Gkotsi
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Helen Connaris
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Rebecca J. M. Goss
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
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10
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Mubarak MQE, Gérard EF, Blanford CF, Hay S, de Visser SP. How Do Vanadium Chloroperoxidases Generate Hypochlorite from Hydrogen Peroxide and Chloride? A Computational Study. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03490] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- M. Qadri E. Mubarak
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Emilie F. Gérard
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Christopher F. Blanford
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Materials, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Sam Hay
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Sam P. de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
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11
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Menon BRK, Richmond D, Menon N. Halogenases for biosynthetic pathway engineering: Toward new routes to naturals and non-naturals. CATALYSIS REVIEWS-SCIENCE AND ENGINEERING 2020. [DOI: 10.1080/01614940.2020.1823788] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Binuraj R. K. Menon
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, UK
| | - Daniel Richmond
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, UK
| | - Navya Menon
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, UK
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12
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Lopez S, Mayes DM, Crouzy S, Cavazza C, Leprêtre C, Moreau Y, Burzlaff N, Marchi-Delapierre C, Ménage S. A Mechanistic Rationale Approach Revealed the Unexpected Chemoselectivity of an Artificial Ru-Dependent Oxidase: A Dual Experimental/Theoretical Approach. ACS Catal 2020. [DOI: 10.1021/acscatal.9b04904] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Sarah Lopez
- Univ. Grenoble-Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France
- Univ. Grenoble-Alpes, DCM-SeRCO, F-38000 Grenoble, France
| | | | - Serge Crouzy
- Univ. Grenoble-Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France
| | - Christine Cavazza
- Univ. Grenoble-Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France
| | - Chloé Leprêtre
- Univ. Grenoble-Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France
| | - Yohann Moreau
- Univ. Grenoble-Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France
| | - Nicolai Burzlaff
- Department of Chemistry and Pharmacy, Friedrich-Alexander-University of Erlangen-Nürnberg, Egerlandstraße 1, 91058 Erlangen, Germany
| | | | - Stéphane Ménage
- Univ. Grenoble-Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France
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13
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Visser SP. Second‐Coordination Sphere Effects on Selectivity and Specificity of Heme and Nonheme Iron Enzymes. Chemistry 2020; 26:5308-5327. [DOI: 10.1002/chem.201905119] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/04/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Sam P. Visser
- The Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical ScienceThe University of Manchester 131 Princess Street Manchester M1 7DN UK
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14
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Mehmood R, Qi HW, Steeves AH, Kulik HJ. The Protein’s Role in Substrate Positioning and Reactivity for Biosynthetic Enzyme Complexes: The Case of SyrB2/SyrB1. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00865] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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15
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Timmins A, Fowler NJ, Warwicker J, Straganz GD, de Visser SP. Does Substrate Positioning Affect the Selectivity and Reactivity in the Hectochlorin Biosynthesis Halogenase? Front Chem 2018; 6:513. [PMID: 30425979 PMCID: PMC6218459 DOI: 10.3389/fchem.2018.00513] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 10/04/2018] [Indexed: 12/17/2022] Open
Abstract
In this work we present the first computational study on the hectochlorin biosynthesis enzyme HctB, which is a unique three-domain halogenase that activates non-amino acid moieties tethered to an acyl-carrier, and as such may have biotechnological relevance beyond other halogenases. We use a combination of small cluster models and full enzyme structures calculated with quantum mechanics/molecular mechanics methods. Our work reveals that the reaction is initiated with a rate-determining hydrogen atom abstraction from substrate by an iron (IV)-oxo species, which creates an iron (III)-hydroxo intermediate. In a subsequent step the reaction can bifurcate to either halogenation or hydroxylation of substrate, but substrate binding and positioning drives the reaction to optimal substrate halogenation. Furthermore, several key residues in the protein have been identified for their involvement in charge-dipole interactions and induced electric field effects. In particular, two charged second coordination sphere amino acid residues (Glu223 and Arg245) appear to influence the charge density on the Cl ligand and push the mechanism toward halogenation. Our studies, therefore, conclude that nonheme iron halogenases have a chemical structure that induces an electric field on the active site that affects the halide and iron charge distributions and enable efficient halogenation. As such, HctB is intricately designed for a substrate halogenation and operates distinctly different from other nonheme iron halogenases.
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Affiliation(s)
- Amy Timmins
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, University of Manchester, Manchester, United Kingdom
| | - Nicholas J. Fowler
- The Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Jim Warwicker
- The Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Grit D. Straganz
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
- Institute of Molecular Biosciences, Graz University, Graz, Austria
| | - Sam P. de Visser
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, University of Manchester, Manchester, United Kingdom
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16
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A Comparative Review on the Catalytic Mechanism of Nonheme Iron Hydroxylases and Halogenases. Catalysts 2018. [DOI: 10.3390/catal8080314] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Enzymatic halogenation and haloperoxidation are unusual processes in biology; however, a range of halogenases and haloperoxidases exist that are able to transfer an aliphatic or aromatic C–H bond into C–Cl/C–Br. Haloperoxidases utilize hydrogen peroxide, and in a reaction with halides (Cl−/Br−), they react to form hypohalides (OCl−/OBr−) that subsequently react with substrate by halide transfer. There are three types of haloperoxidases, namely the iron-heme, nonheme vanadium, and flavin-dependent haloperoxidases that are reviewed here. In addition, there are the nonheme iron halogenases that show structural and functional similarity to the nonheme iron hydroxylases and form an iron(IV)-oxo active species from a reaction of molecular oxygen with α-ketoglutarate on an iron(II) center. They subsequently transfer a halide (Cl−/Br−) to an aliphatic C–H bond. We review the mechanism and function of nonheme iron halogenases and hydroxylases and show recent computational modelling studies of our group on the hectochlorin biosynthesis enzyme and prolyl-4-hydroxylase as examples of nonheme iron halogenases and hydroxylases. These studies have established the catalytic mechanism of these enzymes and show the importance of substrate and oxidant positioning on the stereo-, chemo- and regioselectivity of the reaction that takes place.
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17
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Li J, Molenda MA, Biros SM, Staples RJ, Chavez FA. Assembly of a mononuclear ferrous site using a bulky aldehyde-imidazole ligand. Inorganica Chim Acta 2017; 464:152-156. [PMID: 29238096 PMCID: PMC5724793 DOI: 10.1016/j.ica.2017.05.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A new iron(II) complex has been prepared and characterized. [Fe(TrImA)2(OTf)2] (1, TrImA = 1-Tritylimidazole-4-carboxaldehyde). The solid state structure of 1 has been determined by X-ray crystallography. Compound 1 crystallizes in monoclinic space group P21/c, with a = 10.8323(18) Å, b = 8.1606(13) Å and c = 24.818(4) Å. The iron center is coordinated to two imidazole groups, two pendant aldehyde-derived carbonyl oxygens and two triflate oxygens. The complex is high spin between 300 and 20 K as indicated by variable field variable temperature magnetic measurements. A fit of the magnetic data yielded g = 2.17 and D = 4.05 cm-1. A large HOMO-LUMO gap energy (4.49 eV) exists for 1 indicating high stability.
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Affiliation(s)
- Jia Li
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA
| | - Monika A Molenda
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA
| | - Shannon M Biros
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Richard J Staples
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Ferman A Chavez
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA
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18
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Gomes CA, Lube LM, Fernandes C, Franco RWA, Resende JALC, Horn A. A new system for cyclohexane functionalization employing iron(iii) catalysts and trichloroisocyanuric acid. NEW J CHEM 2017. [DOI: 10.1039/c7nj01164d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, dinuclear and mononuclear iron complexes were investigated as catalysts in the reaction of cyclohexane chlorination employing trichloroisocyanuric acid as oxidant.
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Affiliation(s)
- Clicia A. Gomes
- Universidade Estadual do Norte Fluminense Darcy Ribeiro
- Laboratório de Ciências Químicas
- Campos dos Goytacazes
- Brazil
| | - Leonardo M. Lube
- Instituto Federal Fluminense
- Campus Centro
- Campos dos Goytacazes
- Brazil
| | - Christiane Fernandes
- Universidade Estadual do Norte Fluminense Darcy Ribeiro
- Laboratório de Ciências Químicas
- Campos dos Goytacazes
- Brazil
| | - Roberto W. A. Franco
- Universidade Estadual do Norte Fluminense Darcy Ribeiro
- Laboratório de Ciências Físicas
- Campos dos Goytacazes
- Brazil
| | - Jackson A. L. C. Resende
- Universidade Federal Fluminense
- Laboratório de Difração de Raios X
- 24020-150 Niterói/RJ
- Brazil
- Instituto de Ciências Exatas e da Terra
| | - Adolfo Horn
- Universidade Estadual do Norte Fluminense Darcy Ribeiro
- Laboratório de Ciências Químicas
- Campos dos Goytacazes
- Brazil
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19
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Saraf SL, Miłaczewska A, Borowski T, James CD, Tierney DL, Popova M, Arif AM, Berreau LM. Anion Effects in Oxidative Aliphatic Carbon-Carbon Bond Cleavage Reactions of Cu(II) Chlorodiketonate Complexes. Inorg Chem 2016; 55:6916-28. [PMID: 27377103 DOI: 10.1021/acs.inorgchem.6b00456] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Aliphatic oxidative carbon-carbon bond cleavage reactions involving Cu(II) catalysts and O2 as the terminal oxidant are of significant current interest. However, little is currently known regarding how the nature of the Cu(II) catalyst, including the anions present, influence the reaction with O2. In previous work, we found that exposure of the Cu(II) chlorodiketonate complex [(6-Ph2TPA)Cu(PhC(O)CClC(O)Ph)]ClO4 (1) to O2 results in oxidative aliphatic carbon-carbon bond cleavage within the diketonate unit, leading to the formation of benzoic acid, benzoic anhydride, benzil, and 1,3-diphenylpropanedione as organic products. Kinetic studies of this reaction revealed a slow induction phase followed by a rapid decay of the absorption features of 1. Notably, the induction phase is not present when the reaction is performed in the presence of a catalytic amount of chloride anion. In the studies presented herein, a combination of spectroscopic (UV-vis, EPR) and density functional theory (DFT) methods have been used to examine the chloride and benzoate ion binding properties of 1 under anaerobic conditions. These studies provide evidence that each anion coordinates in an axial position of the Cu(II) center. DFT studies reveal that the presence of the anion in the Cu(II) coordination sphere decreases the barrier for O2 activation and the formation of a Cu(II)-peroxo species. Notably, the chloride anion more effectively lowers the barrier associated with O-O bond cleavage. Thus, the nature of the anion plays an important role in determining the rate of reaction of the diketonate complex with O2. The same type of anion effects were observed in the O2 reactivity of the simple Cu(II)-bipyridine complex [(bpy)Cu(PhC(O)C(Cl)C(O)Ph)ClO4] (3).
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Affiliation(s)
- Sushma L Saraf
- Department of Chemistry & Biochemistry, Utah State University , Logan, Utah 84322-0300, United States
| | - Anna Miłaczewska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Science , Krakow 30-239, Poland
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Science , Krakow 30-239, Poland
| | - Christopher D James
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - David L Tierney
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Marina Popova
- Department of Chemistry & Biochemistry, Utah State University , Logan, Utah 84322-0300, United States
| | - Atta M Arif
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - Lisa M Berreau
- Department of Chemistry & Biochemistry, Utah State University , Logan, Utah 84322-0300, United States
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20
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Kleigrewe K, Gerwick L, Sherman DH, Gerwick WH. Unique marine derived cyanobacterial biosynthetic genes for chemical diversity. Nat Prod Rep 2016; 33:348-64. [PMID: 26758451 DOI: 10.1039/c5np00097a] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Cyanobacteria are a prolific source of structurally unique and biologically active natural products that derive from intriguing biochemical pathways. Advancements in genome sequencing have accelerated the identification of unique modular biosynthetic gene clusters in cyanobacteria and reveal a wealth of unusual enzymatic reactions involved in their construction. This article examines several interesting mechanistic transformations involved in cyanobacterial secondary metabolite biosynthesis with a particular focus on marine derived modular polyketide synthases (PKS), nonribosomal peptide synthetases (NRPS) and combinations thereof to form hybrid natural products. Further, we focus on the cyanobacterial genus Moorea and the co-evolution of its enzyme cassettes that create metabolic diversity. Progress in the development of heterologous expression systems for cyanobacterial gene clusters along with chemoenzymatic synthesis makes it possible to create new analogs. Additionally, phylum-wide genome sequencing projects have enhanced the discovery rate of new natural products and their distinctive enzymatic reactions. Summarizing, cyanobacterial biosynthetic gene clusters encode for a large toolbox of novel enzymes that catalyze unique chemical reactions, some of which may be useful in synthetic biology.
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Affiliation(s)
- Karin Kleigrewe
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, USA.
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, USA.
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, USA. and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, USA
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21
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Wu LF, Meng S, Tang GL. Ferrous iron and α-ketoglutarate-dependent dioxygenases in the biosynthesis of microbial natural products. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:453-70. [DOI: 10.1016/j.bbapap.2016.01.012] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/22/2016] [Accepted: 01/29/2016] [Indexed: 01/29/2023]
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22
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Huang J, Li C, Wang B, Sharon DA, Wu W, Shaik S. Selective Chlorination of Substrates by the Halogenase SyrB2 Is Controlled by the Protein According to a Combined Quantum Mechanics/Molecular Mechanics and Molecular Dynamics Study. ACS Catal 2016. [DOI: 10.1021/acscatal.5b02825] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jing Huang
- The
State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM,
Fujian Provincial Key Laboratory of Theoretical and Computational
Chemistry and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Chunsen Li
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
| | - Binju Wang
- Institute
of Chemistry and the Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, 91904, Israel
| | - Dina A. Sharon
- Institute
of Chemistry and the Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, 91904, Israel
| | - Wei Wu
- The
State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM,
Fujian Provincial Key Laboratory of Theoretical and Computational
Chemistry and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Sason Shaik
- Institute
of Chemistry and the Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, 91904, Israel
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23
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Abstract
Mononuclear non-heme Fe(II)- and 2-oxoglutarate (2OG)-dependent oxygenases comprise a large family of enzymes that utilize an Fe(IV)-oxo intermediate to initiate diverse oxidative transformations with important biological roles. Here, four of the major types of Fe(II)/2OG-dependent reactions are detailed: hydroxylation, halogenation, ring formation, and desaturation. In addition, an atypical epimerization reaction is described. Studies identifying several key intermediates in catalysis are concisely summarized, and the proposed mechanisms are explained. In addition, a variety of other transformations catalyzed by selected family members are briefly described to further highlight the chemical versatility of these enzymes.
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Affiliation(s)
- Salette Martinez
- Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
| | - Robert P Hausinger
- Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824; Departments of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824.
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24
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Enzymatic Halogenases and Haloperoxidases: Computational Studies on Mechanism and Function. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2015; 100:113-51. [PMID: 26415843 DOI: 10.1016/bs.apcsb.2015.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Despite the fact that halogenated compounds are rare in biology, a number of organisms have developed processes to utilize halogens and in recent years, a string of enzymes have been identified that selectively insert halogen atoms into, for instance, a CH aliphatic bond. Thus, a number of natural products, including antibiotics, contain halogenated functional groups. This unusual process has great relevance to the chemical industry for stereoselective and regiospecific synthesis of haloalkanes. Currently, however, industry utilizes few applications of biological haloperoxidases and halogenases, but efforts are being worked on to understand their catalytic mechanism, so that their catalytic function can be upscaled. In this review, we summarize experimental and computational studies on the catalytic mechanism of a range of haloperoxidases and halogenases with structurally very different catalytic features and cofactors. This chapter gives an overview of heme-dependent haloperoxidases, nonheme vanadium-dependent haloperoxidases, and flavin adenine dinucleotide-dependent haloperoxidases. In addition, we discuss the S-adenosyl-l-methionine fluoridase and nonheme iron/α-ketoglutarate-dependent halogenases. In particular, computational efforts have been applied extensively for several of these haloperoxidases and halogenases and have given insight into the essential structural features that enable these enzymes to perform the unusual halogen atom transfer to substrates.
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25
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Boaz NC, Bell SR, Groves JT. Ferryl protonation in oxoiron(IV) porphyrins and its role in oxygen transfer. J Am Chem Soc 2015; 137:2875-85. [PMID: 25651467 PMCID: PMC4363944 DOI: 10.1021/ja508759t] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Ferryl porphyrins, P-Fe(IV)═O, are central reactive intermediates in the catalytic cycles of numerous heme proteins and a variety of model systems. There has been considerable interest in elucidating factors, such as terminal oxo basicity, that may control ferryl reactivity. Here, the sulfonated, water-soluble ferryl porphyrin complexes tetramesitylporphyrin, oxoFe(IV)TMPS (FeTMPS-II), its 2,6-dichlorophenyl analogue, oxoFe(IV)TDClPS (FeTDClPS-II), and two other analogues are shown to be protonated under turnover conditions to produce the corresponding bis-aqua-iron(III) porphyrin cation radicals. The results reveal a novel internal electromeric equilibrium, P-Fe(IV)═O ⇆ P(+)-Fe(III)(OH2)2. Reversible pKa values in the range of 4-6.3 have been measured for this process by pH-jump, UV-vis spectroscopy. Ferryl protonation has important ramifications for C-H bond cleavage reactions mediated by oxoiron(IV) porphyrin cation radicals in protic media. Both solvent O-H and substrate C-H deuterium kinetic isotope effects are observed for these reactions, indicating that hydrocarbon oxidation by these oxoiron(IV) porphyrin cation radicals occurs via a solvent proton-coupled hydrogen atom transfer from the substrate that has not been previously described. The effective FeO-H bond dissociation energies for FeTMPS-II and FeTDClPS-II were estimated from similar kinetic reactivities of the corresponding oxoFe(IV)TMPS(+) and oxoFe(IV)TDClPS(+) species to be ∼92-94 kcal/mol. Similar values were calculated from the two-proton P(+)-Fe(III)(OH2)2 pKa(obs) and the porphyrin oxidation potentials, despite a 230 mV range for the iron porphyrins examined. Thus, the iron porphyrin with the lower ring oxidation potential has a compensating higher basicity of the ferryl oxygen. The solvent-derived proton adds significantly to the driving force for C-H bond scission.
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Affiliation(s)
- Nicholas C. Boaz
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Seth R. Bell
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - John T. Groves
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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