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Zheng Z, Xiong J, Bu J, Ren D, Lee YH, Yeh YC, Lin CI, Parry R, Guo Y, Liu HW. Reconstitution of the Final Steps in the Biosynthesis of Valanimycin Reveals the Origin of Its Characteristic Azoxy Moiety. Angew Chem Int Ed Engl 2024; 63:e202315844. [PMID: 37963815 PMCID: PMC10843709 DOI: 10.1002/anie.202315844] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/11/2023] [Accepted: 11/14/2023] [Indexed: 11/16/2023]
Abstract
Valanimycin is an azoxy-containing natural product isolated from the fermentation broth of Streptomyces viridifaciens MG456-hF10. While the biosynthesis of valanimycin has been partially characterized, how the azoxy group is constructed remains obscure. Herein, the membrane protein VlmO and the putative hydrazine synthetase ForJ from the formycin biosynthetic pathway are demonstrated to catalyze N-N bond formation converting O-(l-seryl)-isobutyl hydroxylamine into N-(isobutylamino)-l-serine. Subsequent installation of the azoxy group is shown to be catalyzed by the non-heme diiron enzyme VlmB in a reaction in which the N-N single bond in the VlmO/ForJ product is oxidized by four electrons to yield the azoxy group. The catalytic cycle of VlmB appears to begin with a resting μ-oxo diferric complex in VlmB, as supported by Mössbauer spectroscopy. This study also identifies N-(isobutylamino)-d-serine as an alternative substrate for VlmB leading to two azoxy regioisomers. The reactions catalyzed by the kinase VlmJ and the lyase VlmK during the final steps of valanimycin biosynthesis are established as well. The biosynthesis of valanimycin was thus fully reconstituted in vitro using the enzymes VlmO/ForJ, VlmB, VlmJ and VlmK. Importantly, the VlmB-catalyzed reaction represents the first example of enzyme-catalyzed azoxy formation and is expected to proceed by an atypical mechanism.
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Affiliation(s)
- Ziyang Zheng
- Department of Chemistry, University of Texas at Austin, Austin, TX-78712, USA
| | - Jin Xiong
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA-15213, USA
| | - Junling Bu
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX-78712, USA
| | - Daan Ren
- Department of Chemistry, University of Texas at Austin, Austin, TX-78712, USA
| | - Yu-Hsuan Lee
- Department of Chemistry, University of Texas at Austin, Austin, TX-78712, USA
| | - Yu-Cheng Yeh
- Department of Chemistry, University of Texas at Austin, Austin, TX-78712, USA
| | - Chia-I Lin
- Department of Chemistry, University of Texas at Austin, Austin, TX-78712, USA
| | - Ronald Parry
- Department of Chemistry, Rice University, Houston, TX-77005, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA-15213, USA
| | - Hung-Wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, TX-78712, USA
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX-78712, USA
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2
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Fan C, Zhou F, Huang W, Xue Y, Xu C, Zhang R, Xian M, Feng X. Characterization of an efficient N-oxygenase from Saccharothrix sp. and its application in the synthesis of azomycin. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:194. [PMID: 38104149 PMCID: PMC10724926 DOI: 10.1186/s13068-023-02446-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND The nitro group constitutes a significant functional moiety within numerous valuable substances, such as nitroimidazoles, a class of antimicrobial drugs exhibiting broad spectrum activity. Conventional chemical methods for synthesizing nitro compounds suffer from harsh conditions, multiple steps, and environmental issues. Biocatalysis has emerged as a promising alternative to overcome these drawbacks, with certain enzymes capable of catalyzing nitro group formation gradually being discovered in nature. Nevertheless, the practical application is hindered by the restricted diversity and low catalytic activity exhibited by the reported nitrifying enzymes. RESULTS A novel N-oxygenase SaRohS harboring higher catalytic capability of transformation 2-aminoimidazole to azomycin was characterized from Saccharothrix sp. Phylogenetic tree analysis revealed that SaRohS belongs to the heme-oxygenase-like diiron oxygenase (HDOs) family. SaRohS exhibited optimal activity at pH 5.5 and 25 ℃, respectively. The enzyme maintained relatively stable activity within the pH range of 4.5 to 6.5 and the temperature range of 20 ℃ to 35 ℃. Following sequence alignment and structural analysis, several promising amino acid residues were meticulously chosen for catalytic performance evaluation. Site-directed mutations showed that threonine 75 was essential for the catalytic activity. The dual mutant enzyme G95A/K115T exhibited the highest catalytic efficiency, which was approximately 5.8-fold higher than that of the wild-type and 22.3-fold higher than that of the reported N-oxygenase KaRohS from Kitasatospora azatica. The underlying catalytic mechanism was investigated through molecular docking and molecular dynamics. Finally, whole-cell biocatalysis was performed and 2-aminoimidazole could be effectively converted into azomycin with a reaction conversion rate of 42% within 14 h. CONCLUSIONS An efficient N-oxygenase that catalyzes 2-aminoimidazole to azomycin was screened form Saccharothrix sp., its phylogenetics and enzymatic properties were analyzed. Through site-directed mutation, enhancements in catalytic competence were achieved, and the molecular basis underlying the enhanced enzymatic activity of the mutants was revealed via molecular docking and dynamic simulation. Furthermore, the application potential of this enzyme was assessed through whole cell biocatalysis, demonstrating it as a promising alternative method for azomycin production.
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Affiliation(s)
- Chuanle Fan
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Fang Zhou
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Wei Huang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Yi Xue
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Chao Xu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Rubing Zhang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Shandong Energy Institute, Qingdao, 266101, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China.
| | - Xinjun Feng
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Shandong Energy Institute, Qingdao, 266101, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China.
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3
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Stierhof M, Myronovskyi M, Zapp J, Luzhetskyy A. Heterologous Production and Biosynthesis of Threonine-16:0dioic acids with a Hydroxamate Moiety. JOURNAL OF NATURAL PRODUCTS 2023; 86:2258-2269. [PMID: 37728876 PMCID: PMC10616846 DOI: 10.1021/acs.jnatprod.3c00097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Indexed: 09/21/2023]
Abstract
Dereplication and genome mining in Streptomyces aureus LU18118 combined with heterologous expression of selected biosynthetic gene clusters (BGCs) led to the discovery of various threonine-16:0dioic acids named lipothrenins. Lipothrenins consist of the core elements l-Thr, d-allo-Thr, or Dhb, which are linked to hexadecanedioic acid by an amide bond. The main compound lipothrenin A (1) carries the N-hydroxylated d-allo form of threonine and expresses a siderophore activity. The lipothrenin BGC was analyzed by a series of deletion experiments. As a result, a variety of interesting genes involved in the recruitment and selective activation of linear 16:0dioic acids, amide bond formation, and the epimerization of l-Thr were revealed. Furthermore, a diiron N-oxygenase was identified that may be directly involved in the monooxygenation of the amide bond. This is divergent from the usual hydroxamate formation mechanism in siderophores, which involves hydroxylation of the free amine prior to amide bond formation. Siderophore activity was observed for all N-hydroxylated lipothrenins by application of the CAS assay method.
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Affiliation(s)
- Marc Stierhof
- Department
of Pharmaceutical Biotechnology and Department of Pharmaceutical Biology, Saarland University, 66123 Saarbruecken, Germany
| | - Maksym Myronovskyi
- Department
of Pharmaceutical Biotechnology and Department of Pharmaceutical Biology, Saarland University, 66123 Saarbruecken, Germany
| | - Josef Zapp
- Department
of Pharmaceutical Biotechnology and Department of Pharmaceutical Biology, Saarland University, 66123 Saarbruecken, Germany
| | - Andriy Luzhetskyy
- Department
of Pharmaceutical Biotechnology and Department of Pharmaceutical Biology, Saarland University, 66123 Saarbruecken, Germany
- Helmholtz
Institute for Pharmaceutical Research Saarland, Saarland University, 66123 Saarbruecken, Germany
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Wu MR, Miao LL, Liu Y, Qian XX, Hou TT, Ai GM, Yu L, Ma L, Gao XY, Qin YL, Zhu HZ, Du L, Li SY, Tian CL, Li DF, Liu ZP, Liu SJ. Identification and characterization of a novel hydroxylamine oxidase, DnfA, that catalyzes the oxidation of hydroxylamine to N 2. J Biol Chem 2022; 298:102372. [PMID: 35970391 PMCID: PMC9478400 DOI: 10.1016/j.jbc.2022.102372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/30/2022] Open
Abstract
Nitrogen (N2) gas in the atmosphere is partially replenished by microbial denitrification of ammonia. Recent study has shown that Alcaligenes ammonioxydans oxidizes ammonia to dinitrogen via a process featuring the intermediate hydroxylamine, termed “Dirammox” (direct ammonia oxidation). However, the unique biochemistry of this process remains unknown. Here, we report an enzyme involved in Dirammox that catalyzes the conversion of hydroxylamine to N2. We tested previously annotated proteins involved in redox reactions, DnfA, DnfB, and DnfC, to determine their ability to catalyze the oxidation of ammonia or hydroxylamine. Our results showed that none of these proteins bound to ammonia or catalyzed its oxidation; however, we did find DnfA bound to hydroxylamine. Further experiments demonstrated that, in the presence of NADH and FAD, DnfA catalyzed the conversion of 15N-labeled hydroxylamine to 15N2. This conversion did not happen under oxygen (O2)-free conditions. Thus, we concluded that DnfA encodes a hydroxylamine oxidase. We demonstrate that DnfA is not homologous to any known hydroxylamine oxidoreductases and contains a diiron center, which was shown to be involved in catalysis via electron paramagnetic resonance experiments. Furthermore, enzyme kinetics of DnfA were assayed, revealing a Km of 92.9 ± 3.0 μM for hydroxylamine and a kcat of 0.028 ± 0.001 s−1. Finally, we show that DnfA was localized in the cytoplasm and periplasm as well as in tubular membrane invaginations in HO-1 cells. To the best of our knowledge, we conclude that DnfA is the first enzyme discovered that catalyzes oxidation of hydroxylamine to N2.
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Affiliation(s)
- Meng-Ru Wu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, China 100049
| | - Li-Li Miao
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ying Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xin-Xin Qian
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ting-Ting Hou
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, China 100049
| | - Guo-Min Ai
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lu Yu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 230031, Hefei, China
| | - Lan Ma
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, China 100049
| | - Xi-Yan Gao
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, China 100049
| | - Ya-Ling Qin
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, China 100049
| | - Hai-Zhen Zhu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lei Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266273, China
| | - Sheng-Ying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266273, China
| | - Chang-Lin Tian
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 230031, Hefei, China; The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, and Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, 230026, Hefei, Anhui, China
| | - De-Feng Li
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, China 100049.
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, China 100049.
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, China 100049; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266273, China.
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5
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Solomon EI, DeWeese DE, Babicz JT. Mechanisms of O 2 Activation by Mononuclear Non-Heme Iron Enzymes. Biochemistry 2021; 60:3497-3506. [PMID: 34266238 PMCID: PMC8768060 DOI: 10.1021/acs.biochem.1c00370] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Two major subclasses of mononuclear non-heme ferrous enzymes use two electron-donating organic cofactors (α-ketoglutarate or pterin) to activate O2 to form FeIV═O intermediates that further react with their substrates through hydrogen atom abstraction or electrophilic aromatic substitution. New spectroscopic methodologies have been developed, enabling the study of the active sites in these enzymes and their oxygen intermediates. Coupled to electronic structure calculations, the results of these spectroscopies provide fundamental insight into mechanism. This Perspective summarizes the results of these studies in elucidating the mechanism of dioxygen activation to form the FeIV═O intermediate and the geometric and electronic structure of this intermediate that enables its high reactivity and selectivity in product formation.
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Affiliation(s)
- Edward I. Solomon
- Department of Chemistry, Stanford University, 333 Campus Dr. Stanford, CA, 94305, United States,SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, United States
| | - Dory E. DeWeese
- Department of Chemistry, Stanford University, 333 Campus Dr. Stanford, CA, 94305, United States
| | - Jeffrey T. Babicz
- Department of Chemistry, Stanford University, 333 Campus Dr. Stanford, CA, 94305, United States
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6
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Chen L, Deng Z, Zhao C. Nitrogen-Nitrogen Bond Formation Reactions Involved in Natural Product Biosynthesis. ACS Chem Biol 2021; 16:559-570. [PMID: 33721494 DOI: 10.1021/acschembio.1c00052] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Construction of nitrogen-nitrogen bonds involves sophisticated biosynthetic mechanisms to overcome the difficulties inherent to the nucleophilic nitrogen atom of amine. Over the past decade, a multitude of reactions responsible for nitrogen-nitrogen bond formation in natural product biosynthesis have been uncovered. On the basis of the intrinsic properties of these reactions, this Review classifies these reactions into three categories: comproportionation, rearrangement, and radical recombination reactions. To expound the metallobiochemistry underlying nitrogen-nitrogen bond formation reactions, we discuss the enzymatic mechanisms in comparison to well characterized canonical heme-dependent enzymes, mononuclear nonheme iron-dependent enzymes, and nonheme di-iron enzymes. We also illuminate the intermediary properties of nitrogen oxide species NO2-, NO+, and N2O3 in nitrogen-nitrogen bond formation reactions with clues derived from inorganic nitrogen metabolism driven by anammox bacteria and nitrifying bacteria. These multidimentional discussions will provide further insights into the mechanistic proposals of nitrogen-nitrogen bond formation in natural product biosynthesis.
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Affiliation(s)
- Linyue Chen
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Zixin Deng
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Changming Zhao
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
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7
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Kisgeropoulos EC, Griese JJ, Smith ZR, Branca RMM, Schneider CR, Högbom M, Shafaat HS. Key Structural Motifs Balance Metal Binding and Oxidative Reactivity in a Heterobimetallic Mn/Fe Protein. J Am Chem Soc 2020; 142:5338-5354. [PMID: 32062969 DOI: 10.1021/jacs.0c00333] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Heterobimetallic Mn/Fe proteins represent a new cofactor paradigm in bioinorganic chemistry and pose countless outstanding questions. The assembly of the active site defies common chemical convention by contradicting the Irving-Williams series, while the scope of reactivity remains unexplored. In this work, the assembly and C-H bond activation process in the Mn/Fe R2-like ligand-binding oxidase (R2lox) protein is investigated using a suite of biophysical techniques, including time-resolved optical spectroscopy, global kinetic modeling, X-ray crystallography, electron paramagnetic resonance spectroscopy, protein electrochemistry, and mass spectrometry. Selective metal binding is found to be under thermodynamic control, with the binding sites within the apo-protein exhibiting greater MnII affinity than FeII affinity. The comprehensive analysis of structure and reactivity of wild-type R2lox and targeted primary and secondary sphere mutants indicate that the efficiency of C-H bond activation directly correlates with the Mn/Fe cofactor reduction potentials and is inversely related to divalent metal binding affinity. These findings suggest the R2lox active site is precisely tuned for achieving both selective heterobimetallic binding and high levels of reactivity and offer a mechanism to examine the means by which proteins achieve appropriate metal incorporation.
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Affiliation(s)
| | - Julia J Griese
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | | | - Rui M M Branca
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, SE-171 21 Solna, Sweden
| | | | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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8
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Wei W, Siegbahn PEM, Liao R. Mechanism of the Dinuclear Iron Enzymep‐Aminobenzoate N‐oxygenase from Density Functional Calculations. ChemCatChem 2018. [DOI: 10.1002/cctc.201801072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Wen‐Jie Wei
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica Hubei Key Laboratory of Materials Chemistry and Service Failure School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 P. R. China
| | - Per E. M. Siegbahn
- Department of Organic Chemistry, Arrhenius LaboratoryStockholm University Stockholm SE-10691 Sweden
| | - Rong‐Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica Hubei Key Laboratory of Materials Chemistry and Service Failure School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 P. R. China
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9
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Komor AJ, Jasniewski AJ, Que L, Lipscomb JD. Diiron monooxygenases in natural product biosynthesis. Nat Prod Rep 2018; 35:646-659. [PMID: 29552683 PMCID: PMC6051903 DOI: 10.1039/c7np00061h] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to 2017 The participation of non-heme dinuclear iron cluster-containing monooxygenases in natural product biosynthetic pathways has been recognized only recently. At present, two families have been discovered. The archetypal member of the first family, CmlA, catalyzes β-hydroxylation of l-p-aminophenylalanine (l-PAPA) covalently linked to the nonribosomal peptide synthetase (NRPS) CmlP, thereby effecting the first step in the biosynthesis of chloramphenicol by Streptomyces venezuelae. CmlA houses the diiron cluster in a metallo-β-lactamase protein fold instead of the 4-helix bundle fold of nearly every other diiron monooxygenase. CmlA couples O2 activation and substrate hydroxylation via a structural change caused by formation of the l-PAPA-loaded CmlP:CmlA complex. The other new diiron family is typified by two enzymes, AurF and CmlI, which catalyze conversion of aryl-amine substrates to aryl-nitro products with incorporation of oxygen from O2. AurF from Streptomyces thioluteus catalyzes the formation of p-nitrobenzoate from p-aminobenzoate as a precursor to the biostatic compound aureothin, whereas CmlI from S. venezuelae catalyzes the ultimate aryl-amine to aryl-nitro step in chloramphenicol biosynthesis. Both enzymes stabilize a novel type of peroxo-intermediate as the reactive species. The rare 6-electron N-oxygenation reactions of CmlI and AurF involve two progressively oxidized pathway intermediates. The enzymes optimize efficiency by utilizing one of the reaction pathway intermediates as an in situ reductant for the diiron cluster, while simultaneously generating the next pathway intermediate. For CmlI, this reduction allows mid-pathway regeneration of the peroxo intermediate required to complete the biosynthesis. CmlI ensures specificity by carrying out the multistep aryl-amine oxygenation without dissociating intermediate products.
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Affiliation(s)
- Anna J Komor
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
| | - Andrew J Jasniewski
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
| | - Lawrence Que
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
| | - John D Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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10
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Wolf F, Leipoldt F, Kulik A, Wibberg D, Kalinowski J, Kaysser L. Characterization of the Actinonin Biosynthetic Gene Cluster. Chembiochem 2018; 19:1189-1195. [PMID: 29600569 DOI: 10.1002/cbic.201800116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Indexed: 11/05/2022]
Abstract
The hydroxamate moiety of the natural product actinonin mediates inhibition of metalloproteinases because of its chelating properties towards divalent cations in the active site of those enzymes. Owing to its antimicrobial activity, actinonin has served as a lead compound for the development of new antibiotic drug candidates. Recently, we identified a putative gene cluster for the biosynthesis of actinonin. Here, we confirm and characterize this cluster by heterologous pathway expression and gene-deletion experiments. We assigned the biosynthetic gene cluster to actinonin production and determine the cluster boundaries. Furthermore, we establish that ActI, an AurF-like oxygenase, is responsible for the N-hydroxylation reaction that forms the hydroxamate warhead. Our findings provide the basis for more detailed investigations of actinonin biosynthesis.
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Affiliation(s)
- Felix Wolf
- Department of Pharmaceutical Biology, University of Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner site Tübingen
| | - Franziska Leipoldt
- Department of Pharmaceutical Biology, University of Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner site Tübingen
| | - Andreas Kulik
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33594, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33594, Bielefeld, Germany
| | - Leonard Kaysser
- Department of Pharmaceutical Biology, University of Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner site Tübingen
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11
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Zhang L, Xu Y, Makris TM, Wang Q. Enhanced Arylamine N-Oxygenase Activity of Polymer–Enzyme Assemblies by Facilitating Electron-Transferring Efficiency. Biomacromolecules 2018; 19:918-925. [DOI: 10.1021/acs.biomac.7b01706] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Libo Zhang
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, South Carolina 29208, United States
| | - Yanmei Xu
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, South Carolina 29208, United States
| | - Thomas M. Makris
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, South Carolina 29208, United States
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, South Carolina 29208, United States
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12
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Komor AJ, Rivard BS, Fan R, Guo Y, Que L, Lipscomb JD. CmlI N-Oxygenase Catalyzes the Final Three Steps in Chloramphenicol Biosynthesis without Dissociation of Intermediates. Biochemistry 2017; 56:4940-4950. [PMID: 28823151 PMCID: PMC5605456 DOI: 10.1021/acs.biochem.7b00695] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CmlI catalyzes the six-electron oxidation of an aryl-amine precursor (NH2-CAM) to the aryl-nitro group of chloramphenicol (CAM). The active site of CmlI contains a (hydr)oxo- and carboxylate-bridged dinuclear iron cluster. During catalysis, a novel diferric-peroxo intermediate P is formed and is thought to directly effect oxygenase chemistry. Peroxo intermediates can facilitate at most two-electron oxidations, so the biosynthetic pathway of CmlI must involve at least three steps. Here, kinetic techniques are used to characterize the rate and/or dissociation constants for each step by taking advantage of the remarkable stability of P in the absence of substrates (decay t1/2 = 3 h at 4 °C) and the visible chromophore of the diiron cluster. It is found that diferrous CmlI (CmlIred) can react with NH2-CAM and O2 in either order to form a P-NH2-CAM intermediate. P-NH2-CAM undergoes rapid oxygen transfer to form a diferric CmlI (CmlIox) complex with the aryl-hydroxylamine [NH(OH)-CAM] pathway intermediate. CmlIox-NH(OH)-CAM undergoes a rapid internal redox reaction to form a CmlIred-nitroso-CAM (NO-CAM) complex. O2 binding results in formation of P-NO-CAM that converts to CmlIox-CAM by enzyme-mediated oxygen atom transfer. The kinetic analysis indicates that there is little dissociation of pathway intermediates as the reaction progresses. Reactions initiated by adding pathway intermediates from solution occur much more slowly than those in which the intermediate is generated in the active site as part of the catalytic process. Thus, CmlI is able to preserve efficiency and specificity while avoiding adventitious chemistry by performing the entire six-electron oxidation in one active site.
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Affiliation(s)
- Anna J. Komor
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Brent S. Rivard
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Ruixi Fan
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Lawrence Que
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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13
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Wang C, Chen H. Convergent Theoretical Prediction of Reactive Oxidant Structures in Diiron Arylamine Oxygenases AurF and CmlI: Peroxo or Hydroperoxo? J Am Chem Soc 2017; 139:13038-13046. [DOI: 10.1021/jacs.7b06343] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chao Wang
- Beijing
National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory
of Photochemistry, CAS Research/Education Center for Excellence in
Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Hui Chen
- Beijing
National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory
of Photochemistry, CAS Research/Education Center for Excellence in
Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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14
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Waldman AJ, Ng TL, Wang P, Balskus EP. Heteroatom-Heteroatom Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5784-5863. [PMID: 28375000 PMCID: PMC5534343 DOI: 10.1021/acs.chemrev.6b00621] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Natural products that contain functional groups with heteroatom-heteroatom linkages (X-X, where X = N, O, S, and P) are a small yet intriguing group of metabolites. The reactivity and diversity of these structural motifs has captured the interest of synthetic and biological chemists alike. Functional groups containing X-X bonds are found in all major classes of natural products and often impart significant biological activity. This review presents our current understanding of the biosynthetic logic and enzymatic chemistry involved in the construction of X-X bond containing functional groups within natural products. Elucidating and characterizing biosynthetic pathways that generate X-X bonds could both provide tools for biocatalysis and synthetic biology, as well as guide efforts to uncover new natural products containing these structural features.
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Affiliation(s)
- Abraham J. Waldman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Tai L. Ng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Peng Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
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15
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Knoot CJ, Kovaleva EG, Lipscomb JD. Crystal structure of CmlI, the arylamine oxygenase from the chloramphenicol biosynthetic pathway. J Biol Inorg Chem 2016; 21:589-603. [PMID: 27229511 PMCID: PMC4994471 DOI: 10.1007/s00775-016-1363-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 05/16/2016] [Indexed: 11/28/2022]
Abstract
The diiron cluster-containing oxygenase CmlI catalyzes the conversion of the aromatic amine precursor of chloramphenicol to the nitroaromatic moiety of the active antibiotic. The X-ray crystal structures of the fully active, N-terminally truncated CmlIΔ33 in the chemically reduced Fe(2+)/Fe(2+) state and a cis μ-1,2(η (1):η (1))-peroxo complex are presented. These structures allow comparison with the homologous arylamine oxygenase AurF as well as other types of diiron cluster-containing oxygenases. The structural model of CmlIΔ33 crystallized at pH 6.8 lacks the oxo-bridge apparent from the enzyme optical spectrum in solution at higher pH. In its place, residue E236 forms a μ-1,3(η (1):η (2)) bridge between the irons in both models. This orientation of E236 stabilizes a helical region near the cluster which closes the active site to substrate binding in contrast to the open site found for AurF. A very similar closed structure was observed for the inactive dimanganese form of AurF. The observation of this same structure in different arylamine oxygenases may indicate that there are two structural states that are involved in regulation of the catalytic cycle. Both the structural studies and single crystal optical spectra indicate that the observed cis μ-1,2(η (1):η (1))-peroxo complex differs from the μ-η (1):η (2)-peroxo proposed from spectroscopic studies of a reactive intermediate formed in solution by addition of O2 to diferrous CmlI. It is proposed that the structural changes required to open the active site also drive conversion of the µ-1,2-peroxo species to the reactive form.
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Affiliation(s)
- Cory J Knoot
- Department of Biochemistry Molecular Biology and Biophysics and the Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Elena G Kovaleva
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - John D Lipscomb
- Department of Biochemistry Molecular Biology and Biophysics and the Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN, 55455, USA.
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16
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Komor AJ, Rivard BS, Fan R, Guo Y, Que L, Lipscomb JD. Mechanism for Six-Electron Aryl-N-Oxygenation by the Non-Heme Diiron Enzyme CmlI. J Am Chem Soc 2016; 138:7411-21. [PMID: 27203126 PMCID: PMC4914076 DOI: 10.1021/jacs.6b03341] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The ultimate step in chloramphenicol (CAM) biosynthesis is a six-electron oxidation of an aryl-amine precursor (NH2-CAM) to the aryl-nitro group of CAM catalyzed by the non-heme diiron cluster-containing oxygenase CmlI. Upon exposure of the diferrous cluster to O2, CmlI forms a long-lived peroxo intermediate, P, which reacts with NH2-CAM to form CAM. Since P is capable of at most a two-electron oxidation, the overall reaction must occur in several steps. It is unknown whether P is the oxidant in each step or whether another oxidizing species participates in the reaction. Mass spectrometry product analysis of reactions under (18)O2 show that both oxygen atoms in the nitro function of CAM derive from O2. However, when the single-turnover reaction between (18)O2-P and NH2-CAM is carried out in an (16)O2 atmosphere, CAM nitro groups contain both (18)O and (16)O, suggesting that P can be reformed during the reaction sequence. Such reformation would require reduction by a pathway intermediate, shown here to be NH(OH)-CAM. Accordingly, the aerobic reaction of NH(OH)-CAM with diferric CmlI yields P and then CAM without an external reductant. A catalytic cycle is proposed in which NH2-CAM reacts with P to form NH(OH)-CAM and diferric CmlI. Then the NH(OH)-CAM rereduces the enzyme diiron cluster, allowing P to reform upon O2 binding, while itself being oxidized to NO-CAM. Finally, the reformed P oxidizes NO-CAM to CAM with incorporation of a second O2-derived oxygen atom. The complete six-electron oxidation requires only two exogenous electrons and could occur in one active site.
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Affiliation(s)
- Anna J. Komor
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
| | - Brent S. Rivard
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Ruixi Fan
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, United States
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, United States
| | - Lawrence Que
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
| | - John D. Lipscomb
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
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17
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Ding XB, Brimble MA, Furkert DP. Nitropyrrole natural products: isolation, biosynthesis and total synthesis. Org Biomol Chem 2016; 14:5390-401. [DOI: 10.1039/c5ob02599k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A review of the isolation, biological activity, biosynthesis and chemical synthesis of nitropyrrole-containing natural products reported to date, including the pyrrolomycins, heronapyrroles and nitropyrrolins.
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Affiliation(s)
- Xiao-Bo Ding
- School of Chemical Sciences
- University of Auckland
- Auckland 1010
- New Zealand
| | - Margaret A. Brimble
- School of Chemical Sciences
- University of Auckland
- Auckland 1010
- New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery
| | - Daniel P. Furkert
- School of Chemical Sciences
- University of Auckland
- Auckland 1010
- New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery
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18
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Snyder RA, Butch SE, Reig AJ, DeGrado WF, Solomon EI. Molecular-Level Insight into the Differential Oxidase and Oxygenase Reactivities of de Novo Due Ferri Proteins. J Am Chem Soc 2015; 137:9302-14. [PMID: 26090726 DOI: 10.1021/jacs.5b03524] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using the single-chain due ferri (DFsc) peptide scaffold, the differential oxidase and oxygenase reactivities of two 4A→4G variants, one with two histidines at the diiron center (G4DFsc) and the other with three histidines (3His-G4DFsc(Mut3)), are explored. By controlling the reaction conditions, the active form responsible for 4-aminophenol (4-AP) oxidase activity in both G4DFsc and 3His-G4DFsc(Mut3) is determined to be the substrate-bound biferrous site. Using circular dichroism (CD), magnetic CD (MCD), and variable-temperature, variable-field (VTVH) MCD spectroscopies, 4-AP is found to bind directly to the biferrous sites of the DF proteins. In G4DFsc, 4-AP increases the coordination of the biferrous site, while in 3His-G4DFsc(Mut3), the coordination number remains the same and the substrate likely replaces the additional bound histidine. This substrate binding enables a two-electron process where 4-AP is oxidized to benzoquinone imine and O2 is reduced to H2O2. In contrast, only the biferrous 3His variant is found to be active in the oxygenation of p-anisidine to 4-nitroso-methoxybenzene. From CD, MCD, and VTVH MCD, p-anisidine addition is found to minimally perturb the biferrous centers of both G4DFsc and 3His-G4DFsc(Mut3), indicating that this substrate binds near the biferrous site. In 3His-G4DFsc(Mut3), the coordinative saturation of one iron leads to the two-electron reduction of O2 at the second iron to generate an end-on hydroperoxo-Fe(III) active oxygenating species.
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Affiliation(s)
- Rae Ana Snyder
- †Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Susan E Butch
- ‡Department of Chemistry, Ursinus College, Collegeville, Pennsylvania 19426, United States
| | - Amanda J Reig
- ‡Department of Chemistry, Ursinus College, Collegeville, Pennsylvania 19426, United States
| | - William F DeGrado
- ⊥Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
| | - Edward I Solomon
- †Department of Chemistry, Stanford University, Stanford, California 94305, United States.,§Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Menlo Park, California 94025, United States
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19
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Chino M, Maglio O, Nastri F, Pavone V, DeGrado WF, Lombardi A. Artificial Diiron Enzymes with a De Novo Designed Four-Helix Bundle Structure. Eur J Inorg Chem 2015; 2015:3371-3390. [PMID: 27630532 PMCID: PMC5019575 DOI: 10.1002/ejic.201500470] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Indexed: 12/26/2022]
Abstract
A single polypeptide chain may provide an astronomical number of conformers. Nature selected only a trivial number of them through evolution, composing an alphabet of scaffolds, that can afford the complete set of chemical reactions needed to support life. These structural templates are so stable that they allow several mutations without disruption of the global folding, even having the ability to bind several exogenous cofactors. With this perspective, metal cofactors play a crucial role in the regulation and catalysis of several processes. Nature is able to modulate the chemistry of metals, adopting only a few ligands and slightly different geometries. Several scaffolds and metal-binding motifs are representing the focus of intense interest in the literature. This review discusses the widespread four-helix bundle fold, adopted as a scaffold for metal binding sites in the context of de novo protein design to obtain basic biochemical components for biosensing or catalysis. In particular, we describe the rational refinement of structure/function in diiron-oxo protein models from the due ferri (DF) family. The DF proteins were developed by us through an iterative process of design and rigorous characterization, which has allowed a shift from structural to functional models. The examples reported herein demonstrate the importance of the synergic application of de novo design methods as well as spectroscopic and structural characterization to optimize the catalytic performance of artificial enzymes.
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Affiliation(s)
- Marco Chino
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
- IBB, CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - Vincenzo Pavone
- Department of Structural and Functional Biology, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco San Francisco, CA 94158, USA
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
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20
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Makris TM, Vu VV, Meier KK, Komor AJ, Rivard BS, Münck E, Que L, Lipscomb JD. An unusual peroxo intermediate of the arylamine oxygenase of the chloramphenicol biosynthetic pathway. J Am Chem Soc 2015; 137:1608-17. [PMID: 25564306 PMCID: PMC4318726 DOI: 10.1021/ja511649n] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Streptomyces venezuelae CmlI catalyzes the six-electron oxygenation of the arylamine precursor of chloramphenicol in a nonribosomal peptide synthetase (NRPS)-based pathway to yield the nitroaryl group of the antibiotic. Optical, EPR, and Mössbauer studies show that the enzyme contains a nonheme dinuclear iron cluster. Addition of O(2) to the diferrous state of the cluster results in an exceptionally long-lived intermediate (t(1/2) = 3 h at 4 °C) that is assigned as a peroxodiferric species (CmlI-peroxo) based upon the observation of an (18)O(2)-sensitive resonance Raman (rR) vibration. CmlI-peroxo is spectroscopically distinct from the well characterized and commonly observed cis-μ-1,2-peroxo (μ-η(1):η(1)) intermediates of nonheme diiron enzymes. Specifically, it exhibits a blue-shifted broad absorption band around 500 nm and a rR spectrum with a ν(O-O) that is at least 60 cm(-1) lower in energy. Mössbauer studies of the peroxo state reveal a diferric cluster having iron sites with small quadrupole splittings and distinct isomer shifts (0.54 and 0.62 mm/s). Taken together, the spectroscopic comparisons clearly indicate that CmlI-peroxo does not have a μ-η(1):η(1)-peroxo ligand; we propose that a μ-η(1):η(2)-peroxo ligand accounts for its distinct spectroscopic properties. CmlI-peroxo reacts with a range of arylamine substrates by an apparent second-order process, indicating that CmlI-peroxo is the reactive species of the catalytic cycle. Efficient production of chloramphenicol from the free arylamine precursor suggests that CmlI catalyzes the ultimate step in the biosynthetic pathway and that the precursor is not bound to the NRPS during this step.
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Affiliation(s)
- Thomas M. Makris
- Department of Biochemistry, Molecular Biology, and
Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of
Minnesota, Minneapolis, MN 55455
| | - Van V. Vu
- Center for Metals in Biocatalysis, University of
Minnesota, Minneapolis, MN 55455
- Department of Chemistry, University of Minnesota, Minneapolis,
Minnesota 55455, United States
| | - Katlyn K. Meier
- Department of Chemistry, Carnegie Mellon University,
Pittsburgh, PA 15213, United States
| | - Anna J. Komor
- Center for Metals in Biocatalysis, University of
Minnesota, Minneapolis, MN 55455
- Department of Chemistry, University of Minnesota, Minneapolis,
Minnesota 55455, United States
| | - Brent S. Rivard
- Department of Biochemistry, Molecular Biology, and
Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of
Minnesota, Minneapolis, MN 55455
| | - Eckard Münck
- Department of Chemistry, Carnegie Mellon University,
Pittsburgh, PA 15213, United States
| | - Lawrence Que
- Center for Metals in Biocatalysis, University of
Minnesota, Minneapolis, MN 55455
- Department of Chemistry, University of Minnesota, Minneapolis,
Minnesota 55455, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology, and
Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of
Minnesota, Minneapolis, MN 55455
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21
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Indest KJ, Eberly JO, Hancock DE. Expression and characterization of an N-oxygenase from Rhodococcus jostii RHAI. J GEN APPL MICROBIOL 2015; 61:217-23. [DOI: 10.2323/jgam.61.217] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Karl J. Indest
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
| | - Jed O. Eberly
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
| | - Dawn E. Hancock
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
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22
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Characterization of the N-oxygenase AurF from Streptomyces thioletus. Bioorg Med Chem 2014; 22:5569-77. [PMID: 24973817 DOI: 10.1016/j.bmc.2014.06.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 05/29/2014] [Accepted: 06/01/2014] [Indexed: 11/21/2022]
Abstract
AurF catalyzes the N-oxidation of p-aminobenzoic acid to p-nitrobenzoic acid in the biosynthesis of the antibiotic aureothin. Here we report the characterization of AurF under optimized conditions to explore its potential use in biocatalysis. The pH optimum of the enzyme was established to be 5.5 using phenazine methosulfate (PMS)/NADH as the enzyme mediator system, showing ~10-fold higher activity than previous reports in literature. Kinetic characterization at optimized conditions give a Km of 14.7 ± 1.1 μM, a kcat of 47.5 ± 5.4 min(-1) and a kcat/Km of 3.2 ± 0.4 μM(-1)min(-1). PMS/NADH and the native electron transfer proteins showed significant formation of the p-hydroxylaminobenzoic acid intermediate, however H2O2 produced mostly p-nitrobenzoic acid. Alanine scanning identified the role of important active site residues. The substrate specificity of AurF was examined and rationalized based on the protein crystal structure. Kinetic studies indicate that the Km is the main determinant of AurF activity toward alternative substrates.
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23
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Reig AJ, Pires MM, Snyder RA, Wu Y, Jo H, Kulp DW, Butch SE, Calhoun JR, Szyperski T, Szyperski TG, Solomon EI, DeGrado WF. Alteration of the oxygen-dependent reactivity of de novo Due Ferri proteins. Nat Chem 2012; 4:900-6. [PMID: 23089864 PMCID: PMC3568993 DOI: 10.1038/nchem.1454] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 08/09/2012] [Indexed: 12/18/2022]
Abstract
De novo proteins provide a unique opportunity for investigating the structure-function relationships of metalloproteins in a minimal, well-defined, and controlled scaffold. Herein, we describe the rational programming of function in a de novo designed di-iron carboxylate protein from the due ferri family. Originally created to catalyze O2-dependent, two-electron oxidation of hydroquinones, the protein was reprogrammed to catalyze the selective N-hydroxylation of arylamines by remodeling the substrate access cavity and introducing a critical third His ligand to the metal binding cavity. Additional second-and third-shell modifications were required to stabilize the His ligand in the core of the protein. These changes resulted in at least a 106 –fold increase in the relative rates of the two reactions. This result highlights the potential for using de novo proteins as scaffolds for future investigations of geometric and electronic factors that influence the catalytic tuning of di-iron active sites.
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Affiliation(s)
- Amanda J Reig
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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24
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Abstract
The N-oxygenation of an amine group is one of the steps in the biosynthesis of the antibiotic chloramphenicol. The non-heme di-iron enzyme CmlI was identified as the enzyme catalyzing this reaction through bioinformatics studies and reconstitution of enzymatic activity. In vitro reconstitution was achieved using phenazine methosulfate and NADH as electron mediators, while in vivo activity was demonstrated in Escherichia coli using two substrates. Kinetic analysis showed a biphasic behavior of the enzyme. Oxidized hydroxylamine and nitroso compounds in the reaction were detected both in vitro and in vivo based on LC-MS. The active site metal was confirmed to be iron based on a ferrozine assay. These findings provide new insights into the biosynthesis of chloramphenicol and could lead to further development of CmlI as a useful biocatalyst.
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Affiliation(s)
- Haige Lu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Emmanuel Chanco
- Department of Chemistry, University of Illinois at Urbana-Champaign, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA ; Department of Chemistry, University of Illinois at Urbana-Champaign, USA
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25
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Li F, Chakrabarti M, Dong Y, Kauffmann K, Bominaar EL, Münck E, Que L. Structural, EPR, and Mössbauer characterization of (μ-alkoxo)(μ-carboxylato)diiron(II,III) model complexes for the active sites of mixed-valent diiron enzymes. Inorg Chem 2012; 51:2917-29. [PMID: 22360600 PMCID: PMC3298377 DOI: 10.1021/ic2021726] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To obtain structural and spectroscopic models for the diiron(II,III) centers in the active sites of diiron enzymes, the (μ-alkoxo)(μ-carboxylato)diiron(II,III) complexes [Fe(II)Fe(III)(N-Et-HPTB)(O(2)CPh)(NCCH(3))(2)](ClO(4))(3) (1) and [Fe(II)Fe(III)(N-Et-HPTB)(O(2)CPh)(Cl)(HOCH(3))](ClO(4))(2) (2) (N-Et-HPTB = N,N,N',N'-tetrakis(2-(1-ethyl-benzimidazolylmethyl))-2-hydroxy-1,3-diaminopropane) have been prepared and characterized by X-ray crystallography, UV-visible absorption, EPR, and Mössbauer spectroscopies. Fe1-Fe2 separations are 3.60 and 3.63 Å, and Fe1-O1-Fe2 bond angles are 128.0° and 129.4° for 1 and 2, respectively. Mössbauer and EPR studies of 1 show that the Fe(III) (S(A) = 5/2) and Fe(II) (S(B) = 2) sites are antiferromagnetically coupled to yield a ground state with S = 1/2 (g= 1.75, 1.88, 1.96); Mössbauer analysis of solid 1 yields J = 22.5 ± 2 cm(-1) for the exchange coupling constant (H = JS(A)·S(B) convention). In addition to the S = 1/2 ground-state spectrum of 1, the EPR signal for the S = 3/2 excited state of the spin ladder can also be observed, the first time such a signal has been detected for an antiferromagnetically coupled diiron(II,III) complex. The anisotropy of the (57)Fe magnetic hyperfine interactions at the Fe(III) site is larger than normally observed in mononuclear complexes and arises from admixing S > 1/2 excited states into the S = 1/2 ground state by zero-field splittings at the two Fe sites. Analysis of the "D/J" mixing has allowed us to extract the zero-field splitting parameters, local g values, and magnetic hyperfine structural parameters for the individual Fe sites. The methodology developed and followed in this analysis is presented in detail. The spin Hamiltonian parameters of 1 are related to the molecular structure with the help of DFT calculations. Contrary to what was assumed in previous studies, our analysis demonstrates that the deviations of the g values from the free electron value (g = 2) for the antiferromagnetically coupled diiron(II,III) core in complex 1 are predominantly determined by the anisotropy of the effective g values of the ferrous ion and only to a lesser extent by the admixture of excited states into ground-state ZFS terms (D/J mixing). The results for 1 are discussed in the context of the data available for diiron(II,III) clusters in proteins and synthetic diiron(II,III) complexes.
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Affiliation(s)
- Feifei Li
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
| | | | - Yanhong Dong
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
| | - Karl Kauffmann
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Emile L. Bominaar
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Eckard Münck
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
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Jayapal P, Rajaraman G. On the controversy of metal ion composition on amine oxygenase (AurF): a computational investigation. Phys Chem Chem Phys 2012; 14:9050-3. [DOI: 10.1039/c2cp40874k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Platter E, Lawson M, Marsh C, Sazinsky MH. Characterization of a non-ribosomal peptide synthetase-associated diiron arylamine N-oxygenase from Pseudomonas syringae pv. phaseolicola. Arch Biochem Biophys 2011; 508:39-45. [DOI: 10.1016/j.abb.2011.01.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 01/10/2011] [Accepted: 01/12/2011] [Indexed: 11/16/2022]
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Vey JL, Al-Mestarihi A, Hu Y, Funk MA, Bachmann BO, Iverson TM. Structure and mechanism of ORF36, an amino sugar oxidizing enzyme in everninomicin biosynthesis . Biochemistry 2010; 49:9306-17. [PMID: 20866105 DOI: 10.1021/bi101336u] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Everninomicin is a highly modified octasaccharide that belongs to the orthosomycin family of antibiotics and possesses potent Gram-positive antibiotic activity, including broad-spectrum efficacy against multidrug resistant enterococci and Staphylococcus aureus. Among its distinctive structural features is a nitro sugar, l-evernitrose, analogues of which decorate a variety of natural products. Recently, we identified a nitrososynthase enzyme encoded by orf36 from Micromonospora carbonacea var. africana that mediates the flavin-dependent double oxidation of synthetically generated thymidine diphosphate (TDP)-l-epi-vancosamine to the corresponding nitroso sugar. Herein, we utilize a five-enzyme in vitro pathway both to verify that ORF36 catalyzes oxidation of biogenic TDP-l-epi-vancosamine and to determine whether ORF36 exhibits catalytic competence for any of its biosynthetic progenitors, which are candidate substrates for nitrososynthases in vivo. Progenitors solely undergo single-oxidation reactions and terminate in the hydroxylamine oxidation state. Performing the in vitro reactions in the presence of (18)O(2) establishes that molecular oxygen, rather than oxygen from water, is incorporated into ORF36-generated intermediates and products and identifies an off-pathway product that correlates with the oxidation product of a progenitor substrate. The 3.15 Å resolution X-ray crystal structure of ORF36 reveals a tetrameric enzyme that shares a fold with acyl-CoA dehydrogenases and class D flavin-containing monooxygenases, including the nitrososynthase KijD3. However, ORF36 and KijD3 have unusually open active sites in comparison to these related enzymes. Taken together, these studies map substrate determinants and allow the proposal of a minimal monooxygenase mechanism for amino sugar oxidation by ORF36.
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Affiliation(s)
- Jessica L Vey
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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Li N, Korboukh VK, Krebs C, Bollinger JM. Four-electron oxidation of p-hydroxylaminobenzoate to p-nitrobenzoate by a peroxodiferric complex in AurF from Streptomyces thioluteus. Proc Natl Acad Sci U S A 2010; 107:15722-7. [PMID: 20798054 PMCID: PMC2936605 DOI: 10.1073/pnas.1002785107] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The nonheme di-iron oxygenase, AurF, converts p-aminobenzoate (Ar-NH(2), where Ar = 4-carboxyphenyl) to p-nitrobenzoate (Ar-NO(2)) in the biosynthesis of the antibiotic, aureothin, by Streptomyces thioluteus. It has been reported that this net six-electron oxidation proceeds in three consecutive, two-electron steps, through p-hydroxylaminobenzoate (Ar-NHOH) and p-nitrosobenzoate (Ar-NO) intermediates, with each step requiring one equivalent of O(2) and two exogenous reducing equivalents. We recently demonstrated that a peroxodiiron(III/III) complex (peroxo- -AurF) formed by addition of O(2) to the diiron(II/II) enzyme ( -AurF) effects the initial oxidation of Ar-NH(2), generating a mu-(oxo)diiron(III/III) form of the enzyme (mu-oxo- -AurF) and (presumably) Ar-NHOH. Here we show that peroxo- -AurF also oxidizes Ar-NHOH. Unexpectedly, this reaction proceeds through to the Ar-NO(2) final product, a four-electron oxidation, and produces -AurF, with which O(2) can combine to regenerate peroxo- -AurF. Thus, conversion of Ar-NHOH to Ar-NO(2) requires only a single equivalent of O(2) and (starting from -AurF or peroxo- -AurF) is fully catalytic in the absence of exogenous reducing equivalents, by contrast to the published stoichiometry. This novel type of four-electron N-oxidation is likely also to occur in the reaction sequences of nitro-installing di-iron amine oxygenases in the biosyntheses of other natural products.
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Affiliation(s)
- Ning Li
- Departments of Biochemistry and Molecular Biology and
| | - Victoria Korneeva Korboukh
- Departments of Biochemistry and Molecular Biology and
- Chemistry, Pennsylvania State University, University Park, PA 16802
| | - Carsten Krebs
- Departments of Biochemistry and Molecular Biology and
- Chemistry, Pennsylvania State University, University Park, PA 16802
| | - J. Martin Bollinger
- Departments of Biochemistry and Molecular Biology and
- Chemistry, Pennsylvania State University, University Park, PA 16802
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Abstract
Nitroaromatic compounds are relatively rare in nature and have been introduced into the environment mainly by human activities. This important class of industrial chemicals is widely used in the synthesis of many diverse products, including dyes, polymers, pesticides, and explosives. Unfortunately, their extensive use has led to environmental contamination of soil and groundwater. The nitro group, which provides chemical and functional diversity in these molecules, also contributes to the recalcitrance of these compounds to biodegradation. The electron-withdrawing nature of the nitro group, in concert with the stability of the benzene ring, makes nitroaromatic compounds resistant to oxidative degradation. Recalcitrance is further compounded by their acute toxicity, mutagenicity, and easy reduction into carcinogenic aromatic amines. Nitroaromatic compounds are hazardous to human health and are registered on the U.S. Environmental Protection Agency's list of priority pollutants for environmental remediation. Although the majority of these compounds are synthetic in nature, microorganisms in contaminated environments have rapidly adapted to their presence by evolving new biodegradation pathways that take advantage of them as sources of carbon, nitrogen, and energy. This review provides an overview of the synthesis of both man-made and biogenic nitroaromatic compounds, the bacteria that have been identified to grow on and completely mineralize nitroaromatic compounds, and the pathways that are present in these strains. The possible evolutionary origins of the newly evolved pathways are also discussed.
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Affiliation(s)
- Kou-San Ju
- Department of Microbiology, University of California, Davis, California 95616
| | - Rebecca E. Parales
- Department of Microbiology, University of California, Davis, California 95616
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Korboukh VK, Li N, Barr EW, Bollinger JM, Krebs C. A long-lived, substrate-hydroxylating peroxodiiron(III/III) intermediate in the amine oxygenase, AurF, from Streptomyces thioluteus. J Am Chem Soc 2009; 131:13608-9. [PMID: 19731912 DOI: 10.1021/ja9064969] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The amine oxygenase AurF from Streptomyces thioluteus catalyzes the six-electron oxidation of p-aminobenzoate (pABA) to p-nitrobenzoate (pNBA). In this work, we have studied the reaction of its reduced Fe(2)(II/II) cofactor with O(2), which results in generation of a peroxo-Fe(2)(III/III) intermediate. In the absence of substrate, this intermediate is unusually stable (t(1/2) = 7 min at 20 degrees C), allowing for its accumulation to almost stoichiometric amounts. Its decay is accelerated approximately 10(5)-fold by the substrate, pABA, implying that it is the complex that effects the two-electron oxidation of the amine to the hydroxylamine. The nearly quantitative conversion of pABA to pNBA by solutions containing an excess of the intermediate suggests that it may also be competent for the two subsequent two-electron oxidations leading to the product.
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Busch B, Hertweck C. Evolution of metabolic diversity in polyketide-derived pyrones: using the non-colinear aureothin assembly line as a model system. PHYTOCHEMISTRY 2009; 70:1833-1840. [PMID: 19651421 DOI: 10.1016/j.phytochem.2009.05.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Revised: 05/26/2009] [Accepted: 05/27/2009] [Indexed: 05/28/2023]
Abstract
Polyketide-derived pyrones are structurally diverse secondary metabolites that are represented in all three kingdoms of life and are endowed with various biological functions. The aureothin family of Streptomyces metabolites was chosen as a model to study the factors governing structural diversity and the evolutionary processes involved. This review highlights recent insights into the non-colinear aureothin and neoaureothin modular type I polyketide synthase (PKS), aromatic starter unit biosynthesis, polyketide tailoring reactions, and a non-enzymatic polyene splicing cascade. Pyrone biosynthesis in bacteria, fungi, and plants is compared. Finally, various strategies to increase metabolic diversity of aureothin derivatives through mutasynthesis, pathway engineering, and biotransformation are presented. The unusual aureothin and neoaureothin assembly lines thus not only represent a model for PKS evolution, but provided important insights into non-canonical enzymatic processes that could be employed for the production of antitumor and antifungal agents.
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Affiliation(s)
- Benjamin Busch
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Department of Biomolecular Chemistry, Jena, Germany
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Roth A, Plass W. Carboxylate-Bridged Dinuclear Active Sites in Oxygenases: Diiron, Dimanganese, or is Heterodinuclear Better? Angew Chem Int Ed Engl 2008; 47:7588-91. [DOI: 10.1002/anie.200802366] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Roth A, Plass W. Carboxylatverbrückte Zweikernzentren in Oxygenasen: Dieisen, Dimangan oder doch besser heterozweikernig? Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200802366] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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In vitro reconstitution and crystal structure of p-aminobenzoate N-oxygenase (AurF) involved in aureothin biosynthesis. Proc Natl Acad Sci U S A 2008; 105:6858-63. [PMID: 18458342 DOI: 10.1073/pnas.0712073105] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
p-Aminobenzoate N-oxygenase (AurF) from Streptomyces thioluteus catalyzes the formation of unusual polyketide synthase starter unit p-nitrobenzoic acid (pNBA) from p-aminobenzoic acid (pABA) in the biosynthesis of antibiotic aureothin. AurF is a metalloenzyme, but its native enzymatic activity has not been demonstrated in vitro, and its catalytic mechanism is unclear. In addition, the nature of the cofactor remains a controversy. Here, we report the in vitro reconstitution of the AurF enzyme activity, the crystal structure of AurF in the oxidized state, and the cocrystal structure of AurF with its product pNBA. Our combined biochemical and structural analysis unequivocally indicates that AurF is a non-heme di-iron monooxygenase that catalyzes sequential oxidation of aminoarenes to nitroarenes via hydroxylamine and nitroso intermediates.
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Winkler R, Zocher G, Richter I, Friedrich T, Schulz G, Hertweck C. A Binuclear Manganese Cluster That Catalyzes Radical-Mediated N-Oxygenation. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200703089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Winkler R, Zocher G, Richter I, Friedrich T, Schulz G, Hertweck C. A Binuclear Manganese Cluster That Catalyzes Radical-Mediated N-Oxygenation. Angew Chem Int Ed Engl 2007; 46:8605-8. [DOI: 10.1002/anie.200703089] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Identification and characterization of the flavin:NADH reductase (PrnF) involved in a novel two-component arylamine oxygenase. J Bacteriol 2007; 189:8556-63. [PMID: 17921302 DOI: 10.1128/jb.01050-07] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two-component oxygenases catalyze a wide variety of important oxidation reactions. Recently we characterized a novel arylamine N-oxygenase (PrnD), a new member of the two-component oxygenase family (J. Lee et al., J. Biol. Chem. 280:36719-36728, 2005). Although arylamine N-oxygenases are widespread in nature, aminopyrrolnitrin N-oxygenase (PrnD) represents the only biochemically and mechanistically characterized arylamine N-oxygenase to date. Here we report the use of bioinformatic and biochemical tools to identify and characterize the reductase component (PrnF) involved in the PrnD-catalyzed unusual arylamine oxidation. The prnF gene was identified via sequence analysis of the whole genome of Pseudomonas fluorescens Pf-5 and subsequently cloned and overexpressed in Escherichia coli. The purified PrnF protein catalyzes reduction of flavin adenine dinucleotide (FAD) by NADH with a k(cat) of 65 s(-1) (K(m) = 3.2 muM for FAD and 43.1 muM for NADH) and supplies reduced FAD to the PrnD oxygenase component. Unlike other known reductases in two-component oxygenase systems, PrnF strictly requires NADH as an electron donor to reduce FAD and requires unusual protein-protein interaction with the PrnD component for the efficient transfer of reduced FAD. This PrnF enzyme represents the first cloned and characterized flavin reductase component in a novel two-component arylamine oxygenase system.
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Zocher G, Winkler R, Hertweck C, Schulz GE. Structure and Action of the N-oxygenase AurF from Streptomyces thioluteus. J Mol Biol 2007; 373:65-74. [PMID: 17765264 DOI: 10.1016/j.jmb.2007.06.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2007] [Revised: 06/05/2007] [Accepted: 06/06/2007] [Indexed: 11/16/2022]
Abstract
Nitro groups are found in a number of bioactive compounds. Most of them arise by a stepwise mono-oxygenation of amino groups. One of the involved enzymes is AurF participating in the biosynthesis of aureothin. Its structure was established at 2.1 A resolution showing a homodimer with a binuclear manganese cluster. The enzyme preparation, which yielded the analyzed crystals, showed activity using in vitro and in vivo assays. Chain fold and cluster are homologous with ribonucleotide reductase subunit R2 and related enzymes. The two manganese ions and an iron content of about 15% were established by anomalous X-ray diffraction. A comparison of the cluster with more common di-iron clusters suggested an additional histidine in the coordination sphere to cause the preference for manganese over iron. There is no oxo-bridge. The substrate p-amino-benzoate was modeled into the active center. The model is supported by mutant activity measurements. It shows the geometry of the reaction and explains the established substrate spectrum.
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Affiliation(s)
- Georg Zocher
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany
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Zhang X, Parry RJ. Cloning and characterization of the pyrrolomycin biosynthetic gene clusters from Actinosporangium vitaminophilum ATCC 31673 and Streptomyces sp. strain UC 11065. Antimicrob Agents Chemother 2006; 51:946-57. [PMID: 17158935 PMCID: PMC1803119 DOI: 10.1128/aac.01214-06] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The pyrrolomycins are a family of polyketide antibiotics, some of which contain a nitro group. To gain insight into the nitration mechanism associated with the formation of these antibiotics, the pyrrolomycin biosynthetic gene cluster from Actinosporangium vitaminophilum was cloned. Sequencing of ca. 56 kb of A. vitaminophilum DNA revealed 35 open reading frames (ORFs). Sequence analysis revealed a clear relationship between some of these ORFs and the biosynthetic gene cluster for pyoluteorin, a structurally related antibiotic. Since a gene transfer system could not be devised for A. vitaminophilum, additional proof for the identity of the cloned gene cluster was sought by cloning the pyrrolomycin gene cluster from Streptomyces sp. strain UC 11065, a transformable pyrrolomycin producer. Sequencing of ca. 26 kb of UC 11065 DNA revealed the presence of 17 ORFs, 15 of which exhibit strong similarity to ORFs in the A. vitaminophilum cluster as well as a nearly identical organization. Single-crossover disruption of two genes in the UC 11065 cluster abolished pyrrolomycin production in both cases. These results confirm that the genetic locus cloned from UC 11065 is essential for pyrrolomycin production, and they also confirm that the highly similar locus in A. vitaminophilum encodes pyrrolomycin biosynthetic genes. Sequence analysis revealed that both clusters contain genes encoding the two components of an assimilatory nitrate reductase. This finding suggests that nitrite is required for the formation of the nitrated pyrrolomycins. However, sequence analysis did not provide additional insights into the nitration process, suggesting the operation of a novel nitration mechanism.
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Affiliation(s)
- Xiujun Zhang
- Rice University, Department of Chemistry MS60, 6100 Main Street, Houston, TX 77005, USA
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