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Wu L, Wang Z, Cen Y, Wang B, Zhou J. Reply to Correspondence on "Structural Insight into the Catalytic Mechanism of the Endoperoxide Synthase FtmOx1''. Angew Chem Int Ed Engl 2023; 62:e202306059. [PMID: 37541667 DOI: 10.1002/anie.202306059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Indexed: 08/06/2023]
Abstract
The high-resolution X-ray crystal structure of the ternary complex FtmOx1 ⋅ 2OG ⋅ fumitremorgin B and the catalytic mechanism were recently reported by us (DOI 10.1002/anie.202112063). In their Correspondence, Zhang, Costello, Liu et al. criticize our work in several aspects. Herein, we address these questions one by one. These structural clarifications and new computational results further support the CarC-like mechanistic model.
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Affiliation(s)
- Lian Wu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Zhanfeng 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
| | - Yixin Cen
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine (IRI), Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, 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
| | - Jiahai Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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Mori T, Abe I. Structural basis for endoperoxide-forming oxygenases. Beilstein J Org Chem 2022; 18:707-721. [PMID: 35821691 PMCID: PMC9235837 DOI: 10.3762/bjoc.18.71] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/10/2022] [Indexed: 12/04/2022] Open
Abstract
Endoperoxide natural products are widely distributed in nature and exhibit various biological activities. Due to their chemical features, endoperoxide and endoperoxide-derived secondary metabolites have attracted keen attention in the field of natural products and organic synthesis. In this review, we summarize the structural analyses, mechanistic investigations, and proposed reaction mechanisms of endoperoxide-forming oxygenases, including cyclooxygenase, fumitremorgin B endoperoxidase (FtmOx1), and the asnovolin A endoperoxygenase NvfI.
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Affiliation(s)
- Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
- PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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3
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Lin CY, Muñoz AL, Laremore TN, Silakov A, Krebs C, Boal AK, Bollinger JM. Use of Noncanonical Tyrosine Analogues to Probe Control of Radical Intermediates during Endoperoxide Installation by Verruculogen Synthase (FtmOx1). ACS Catal 2022; 12:6968-6979. [PMID: 37744570 PMCID: PMC10516331 DOI: 10.1021/acscatal.2c01037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Important bioactive natural products, including prostaglandin H2 and artemisinin, contain reactive endoperoxides. Known enzymatic pathways for endoperoxide installation require multiple hydrogen-atom transfers (HATs). For example, iron(II)- and 2-oxoglutarate-dependent verruculogen synthase (FtmOx1; EC 1.14.11.38) mediates HAT from aliphatic C21 of fumitremorgin B, capture of O2 by the C21 radical (C21•), addition of the peroxyl radical (C21-O-O•) to olefinic C27, and HAT to the resultant C26•. Recent studies proposed conflicting roles for FtmOx1 tyrosine residues, Tyr224 and Tyr68, in the HATs from C21 and to C26•. Here, analysis of variant proteins bearing a ring-halogenated tyrosine or (amino)phenylalanine in place of either residue establishes that Tyr68 is the hydrogen donor to C26•, while Tyr224 has no essential role. The radicals that accumulate rapidly in FtmOx1 variants bearing a HAT-competent tyrosine analog at position 68 exhibit hypsochromically shifted absorption and, in cases of fluorine substitution, 19F-coupled electron-paramagnetic-resonance (EPR) spectra. By contrast, functional Tyr224-substituted variants generate radicals with unaltered light-absorption and EPR signatures as they produce verruculogen. The alternative major product of the Tyr68Phe variant, which forms competitively with verruculogen also in wild-type FtmOx1 in 2H2O and in the variant with the less readily oxidized 2,3-F2Tyr at position 68, is identified by mass spectrometry and isotopic labeling as the 26-hydroxy-21,27-endoperoxide compound formed after capture of another equivalent of O2 by the longer lived C26•. The results highlight the considerable chemical challenges the enzyme must navigate in averting both oxygen rebound and a second O2 coupling to obtain verruculogen selectively over other possible products.
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Affiliation(s)
- Chi-Yun Lin
- Department of Chemistry, The Pennsylvania State University; University Park, PA 16802, USA
| | - Angel L. Muñoz
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University; University Park, PA 16802, USA
| | - Tatiana N. Laremore
- Huck Institutes of the Life Sciences, The Pennsylvania State University; University Park, PA 16802, USA
| | - Alexey Silakov
- Department of Chemistry, The Pennsylvania State University; University Park, PA 16802, USA
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University; University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University; University Park, PA 16802, USA
| | - Amie K. Boal
- Department of Chemistry, The Pennsylvania State University; University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University; University Park, PA 16802, USA
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University; University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University; University Park, PA 16802, USA
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Wu L, Wang Z, Cen Y, Wang B, Zhou J. Structural Insight into the Catalytic Mechanism of the Endoperoxide Synthase FtmOx1. Angew Chem Int Ed Engl 2022; 61:e202112063. [PMID: 34796596 DOI: 10.1002/anie.202112063] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Indexed: 11/11/2022]
Abstract
The 2-oxoglutarate (2OG)-dependent non-heme enzyme FtmOx1 catalyzes the endoperoxide biosynthesis of verruculogen. Although several mechanistic studies have been carried out, the catalytic mechanism of FtmOx1 is not well determined owing to the lack of a reliable complex structure of FtmOx1 with fumitremorgin B. Herein we provide the X-ray crystal structure of the ternary complex FtmOx1⋅2OG⋅fumitremorgin B at a resolution of 1.22 Å. Our structures show that the binding of fumitremorgin B induces significant compression of the active pocket and that Y68 is in close proximity to C26 of the substrate. Further MD simulation and QM/MM calculations support a CarC-like mechanism, in which Y68 acts as the H atom donor for quenching the C26-centered substrate radical. Our results are consistent with all available experimental data and highlight the importance of accurate complex structures in the mechanistic study of enzymatic catalysis.
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Affiliation(s)
- Lian Wu
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine (IRI), Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhanfeng Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Yixin Cen
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine (IRI), Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Jiahai Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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Wu J, Chen SL. Key Piece in the Wolfe Cycle of Methanogenesis: The S–S Bond Dissociation Conducted by Noncubane [Fe4S4] Cluster-Dependent Heterodisulfide Reductase. ACS Catal 2022. [DOI: 10.1021/acscatal.1c06036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jue Wu
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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Wu L, Wang Z, Cen Y, Wang B, Zhou J. Structural Insight into the Catalytic Mechanism of the Endoperoxide Synthase FtmOx1. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Lian Wu
- The Research Center of Chiral Drugs Innovation Research Institute of Traditional Chinese Medicine (IRI) Shanghai University of Traditional Chinese Medicine Shanghai 201203 China
- Key Laboratory of Synthetic Biology CAS Center for Excellence in Molecular Plant Sciences University of Chinese Academy of Sciences Shanghai 200032 China
| | - Zhanfeng Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Yixin Cen
- The Research Center of Chiral Drugs Innovation Research Institute of Traditional Chinese Medicine (IRI) Shanghai University of Traditional Chinese Medicine Shanghai 201203 China
- Key Laboratory of Synthetic Biology CAS Center for Excellence in Molecular Plant Sciences University of Chinese Academy of Sciences Shanghai 200032 China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Jiahai Zhou
- CAS Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
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Enzymatic N N bond formation: Mechanism for the N-nitroso synthesis catalyzed by non-heme iron SznF enzyme. J Catal 2021. [DOI: 10.1016/j.jcat.2021.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Yan J, Chen S. How To Produce Methane Precursor in the Upper Ocean by An Untypical Non‐Heme Fe‐Dependent Methylphosphonate Synthase? Chemphyschem 2020; 21:385-396. [DOI: 10.1002/cphc.202000025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Ji‐Fan Yan
- Key Laboratory of Cluster Science of Ministry of Education School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 China
| | - Shi‐Lu Chen
- Key Laboratory of Cluster Science of Ministry of Education School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 China
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Song H, Naowarojna N, Cheng R, Lopez J, Liu P. Non-heme iron enzyme-catalyzed complex transformations: Endoperoxidation, cyclopropanation, orthoester, oxidative C-C and C-S bond formation reactions in natural product biosynthesis. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 117:1-61. [PMID: 31564305 DOI: 10.1016/bs.apcsb.2019.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Non-heme iron enzymes catalyze a wide range of chemical transformations, serving as one of the key types of tailoring enzymes in the biosynthesis of natural products. Hydroxylation reaction is the most common type of reactions catalyzed by these enzymes and hydroxylation reactions have been extensively investigated mechanistically. However, the mechanistic details for other types of transformations remain largely unknown or unexplored. In this paper, we present some of the most recently discovered transformations, including endoperoxidation, orthoester formation, cyclopropanation, oxidative C-C and C-S bond formation reactions. In addition, many of them are multi-functional enzymes, which further complicate their mechanistic investigations. In this work, we summarize their biosynthetic pathways, with special emphasis on the mechanistic details available for these newly discovered enzymes.
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Affiliation(s)
- Heng Song
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, People's Republic of China
| | | | - Ronghai Cheng
- Department of Chemistry, Boston University, Boston, MA, United States
| | - Juan Lopez
- Department of Chemistry, Boston University, Boston, MA, United States
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, MA, United States
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Yu MJ, Chen SL. From Alkane to Alkene: The Inert Aliphatic C–H Bond Activation Presented by Binuclear Iron Stearoyl-CoA Desaturase with a Long di-Fe Distance of 6 Å. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00456] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ming-Jia Yu
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People’s Republic of China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People’s Republic of China
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Abstract
C–H functionalization is a chemically challenging but highly desirable transformation. 2-oxoglutarate-dependent oxygenases (2OGXs) are remarkably versatile biocatalysts for the activation of C–H bonds. In nature, they have been shown to accept both small and large molecules carrying out a plethora of reactions, including hydroxylations, demethylations, ring formations, rearrangements, desaturations, and halogenations, making them promising candidates for industrial manufacture. In this review, we describe the current status of 2OGX use in biocatalytic applications concentrating on 2OGX-catalyzed oxyfunctionalization of amino acids and synthesis of antibiotics. Looking forward, continued bioinformatic sourcing will help identify additional, practical useful members of this intriguing enzyme family, while enzyme engineering will pave the way to enhance 2OGX reactivity for non-native substrates.
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