1
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Xu S, Zhao J, Liu X, Yang X, Xu Z, Gao Y, Ma Y, Yang H. Structures of SenB and SenA enzymes from Variovorax paradoxus provide insights into carbon-selenium bond formation in selenoneine biosynthesis. Heliyon 2024; 10:e32888. [PMID: 38994077 PMCID: PMC11237966 DOI: 10.1016/j.heliyon.2024.e32888] [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: 04/16/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 07/13/2024] Open
Abstract
Selenoneine, an ergothioneine analog, is important for antioxidation and detoxification. SenB and SenA are two crucial enzymes that form carbon-selenium bonds in the selenoneine biosynthetic pathway. To investigate their underlying catalytic mechanisms, we obtained complex structures of SenB with its substrate UDP-N-acetylglucosamine (UDP-GlcNAc) and SenA with N-α-trimethyl histidine (TMH). SenB adopts a type-B glycosyltransferase fold. Structural and functional analysis of the interaction network at the active center provide key information on substrate recognition and suggest a metal-ion-independent, inverting mechanism is utilized for SenB-mediated selenoglycoside formation. Moreover, the complex structure of SenA with TMH and enzymatic activity assays highlight vital residues that control substrate binding and specificity. Based on the conserved structure and substrate-binding pocket of the type I sulfoxide synthase EgtB in the ergothioneine biosynthetic pathway, a similar reaction mechanism was proposed for the formation of C-Se bonds by SenA. The structures provide knowledge on selenoneine synthesis and lay groundwork for further applications of this pathway.
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Affiliation(s)
- Sihan Xu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Jinyi Zhao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Xiang Liu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Response, College of Life Sciences, College of Pharmacy, Nankai University, Tianjin, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Zili Xu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yuanyuan Ma
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
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2
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Sun Y, Xu G, Wang Y, Song P, Zhang Y, Xia L. Surface plasmon-assisted catalytic reduction of p-nitrothiophenol for the detection of Fe 2+ by surface-enhanced Raman spectroscopy. Anal Biochem 2023; 680:115314. [PMID: 37678582 DOI: 10.1016/j.ab.2023.115314] [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: 05/01/2023] [Revised: 08/12/2023] [Accepted: 09/04/2023] [Indexed: 09/09/2023]
Abstract
Herein, we developed a concise, time-efficient, and high selective assay for detecting Fe2+ through its triggered surface plasmon-assisted reduction reaction of p-nitrothiophenol (PNTP) to p,p'-dimercaptoazobenzene (DMAB) on the surface of gold nanoparticles (AuNPs) based on surface-enhanced Raman scattering (SERS) spectroscopy. When Fe2+ was added to the PNTP-AuNPs system, the appearance of three characteristic peaks at 1142, 1392, and 1440 cm-1 attributed to DMAB demonstrated that Fe2+ induced the catalytic coupling reaction of PNTP. The Raman intensity ratio of the peak at 1142 cm-1 to the peak at 1336 cm-1 and the concentration of Fe2+ presented a good linear response from 10 to 100 μM with a limit of detection (LOD) of 0.35 μM. More importantly, the entire detection process can be completed within 2 min and further successfully used for the detection of Fe2+ in river water.
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Affiliation(s)
- Ye Sun
- College of Chemistry, Liaoning University, Shenyang, 110036, People's Republic of China
| | - Guangda Xu
- College of Chemistry, Liaoning University, Shenyang, 110036, People's Republic of China
| | - Yue Wang
- College of Chemistry, Liaoning University, Shenyang, 110036, People's Republic of China
| | - Peng Song
- College of Physics, Liaoning University, Shenyang, 110036, People's Republic of China
| | - Yao Zhang
- College of Chemistry, Liaoning University, Shenyang, 110036, People's Republic of China; Chemistry and Chemical Engineering Guangdong Laboratory, Shantou, 515031, People's Republic of China.
| | - Lixin Xia
- College of Chemistry, Liaoning University, Shenyang, 110036, People's Republic of China.
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3
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The functional importance of bacterial oxidative phosphonate pathways. Biochem Soc Trans 2023; 51:487-499. [PMID: 36892197 DOI: 10.1042/bst20220479] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/10/2023]
Abstract
Organophosphonates (Pns) are a unique class of natural products characterized by a highly stable C-P bond. Pns exhibit a wide array of interesting structures as well as useful bioactivities ranging from antibacterial to herbicidal. More structurally simple Pns are scavenged and catabolized by bacteria as a source of phosphorus. Despite their environmental and industrial importance, the pathways involved in the metabolism of Pns are far from being fully elucidated. Pathways that have been characterized often reveal unusual chemical transformations and new enzyme mechanisms. Among these, oxidative enzymes play an outstanding role during the biosynthesis and degradation of Pns. They are to a high extent responsible for the structural diversity of Pn secondary metabolites and for the break-down of both man-made and biogenic Pns. Here, we review our current understanding of the importance of oxidative enzymes for microbial Pn metabolism, discuss the underlying mechanistic principles, similarities, and differences between pathways. This review illustrates Pn biochemistry to involve a mix of classical redox biochemistry and unique oxidative reactions, including ring formations, rearrangements, and desaturations. Many of these reactions are mediated by specialized iron-dependent oxygenases and oxidases. Such enzymes are the key to both early pathway diversification and late-stage functionalization of complex Pns.
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4
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Gordon JB, Albert T, Yadav S, Thomas J, Siegler MA, Moënne-Loccoz P, Goldberg DP. Oxygen versus Sulfur Coordination in Cobalt Superoxo Complexes: Spectroscopic Properties, O 2 Binding, and H-Atom Abstraction Reactivity. Inorg Chem 2023; 62:392-400. [PMID: 36538786 PMCID: PMC10194424 DOI: 10.1021/acs.inorgchem.2c03484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A five-coordinate, disiloxide-ligated cobalt(II) (S = 3/2) complex (1) was prepared as an oxygen-ligated analogue to the previously reported silanedithiolate-ligated CoII(Me3TACN)(S2SiMe2) (J. Am. Chem. Soc., 2019, 141, 3641-3653). The structural and spectroscopic properties of 1 were analyzed by single-crystal X-ray diffraction, electron paramagnetic resonance (EPR), and NMR spectroscopies. The reactivity of 1 with dioxygen was examined, and it was shown to bind O2 reversibly in a range of solvents at low temperatures. A cobalt(III)-superoxo complex, CoIII(O2·-)(Me3TACN)((OSi2Ph)2O) (2), was generated, and was analyzed by UV-vis, EPR, and resonance Raman spectroscopies. Unlike its sulfur-ligated analogue, complex 2 can thermally release O2 to regenerate 1. Vibrational assignments for selective 18O isotopic labeling of both O2 and disiloxide ligands in 2 are consistent with a 6-coordinate, Co(η1-O2·-)("end-on") complex. Complex 2 reacts with the O-H bond of 4-methoxy-2,2,6,6-tetramethylpiperidin-1-ol (4-MeO-TEMPOH) via H-atom abstraction with a rate of 0.58(2) M-1 s-1 at -105 °C, but it is unable to oxidize phenol substrates. This bracketed reactivity suggests that the O-H bond being formed in the putative CoIII(OOH) product has a relatively weak O-H bond strength (BDFE ∼66-74 kcal mol-1). These thermodynamic and kinetic parameters are similar to those seen for the sulfur-ligated Co(O2)(Me3TACN)(S2SiMe2), indicating that the differences in the electronic structure for O versus S ligation do not have a large impact on H-atom abstraction reactivity.
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Affiliation(s)
- Jesse B Gordon
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Therese Albert
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Sudha Yadav
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Jithin Thomas
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Maxime A Siegler
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Pierre Moënne-Loccoz
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
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5
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Bopp CE, Bernet NM, Kohler HPE, Hofstetter TB. Elucidating the Role of O 2 Uncoupling in the Oxidative Biodegradation of Organic Contaminants by Rieske Non-heme Iron Dioxygenases. ACS ENVIRONMENTAL AU 2022; 2:428-440. [PMID: 36164353 PMCID: PMC9502038 DOI: 10.1021/acsenvironau.2c00023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Oxygenations of aromatic
soil and water contaminants with molecular
O2 catalyzed by Rieske dioxygenases are frequent initial
steps of biodegradation in natural and engineered environments. Many
of these non-heme ferrous iron enzymes are known to be involved in
contaminant metabolism, but the understanding of enzyme–substrate
interactions that lead to successful biodegradation is still elusive.
Here, we studied the mechanisms of O2 activation and substrate
hydroxylation of two nitroarene dioxygenases to evaluate enzyme- and
substrate-specific factors that determine the efficiency of oxygenated
product formation. Experiments in enzyme assays of 2-nitrotoluene
dioxygenase (2NTDO) and nitrobenzene dioxygenase (NBDO) with methyl-,
fluoro-, chloro-, and hydroxy-substituted nitroaromatic substrates
reveal that typically 20–100% of the enzyme’s activity
involves unproductive paths of O2 activation with generation
of reactive oxygen species through so-called O2 uncoupling.
The 18O and 13C kinetic isotope effects of O2 activation and nitroaromatic substrate hydroxylation, respectively,
suggest that O2 uncoupling occurs after generation of FeIII-(hydro)peroxo species in the catalytic cycle. While 2NTDO
hydroxylates ortho-substituted nitroaromatic substrates
more efficiently, NBDO favors meta-substituted, presumably
due to distinct active site residues of the two enzymes. Our data
implies, however, that the O2 uncoupling and hydroxylation
activity cannot be assessed from simple structure–reactivity
relationships. By quantifying O2 uncoupling by Rieske dioxygenases,
our work provides a mechanistic link between contaminant biodegradation,
the generation of reactive oxygen species, and possible adaptation
strategies of microorganisms to the exposure of new contaminants.
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Affiliation(s)
- Charlotte E. Bopp
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Nora M. Bernet
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Hans-Peter E. Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Thomas B. Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
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6
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Pati SG, Bopp CE, Kohler HPE, Hofstetter TB. Substrate-Specific Coupling of O 2 Activation to Hydroxylations of Aromatic Compounds by Rieske Non-heme Iron Dioxygenases. ACS Catal 2022; 12:6444-6456. [PMID: 35692249 PMCID: PMC9171724 DOI: 10.1021/acscatal.2c00383] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/09/2022] [Indexed: 02/07/2023]
Abstract
![]()
Rieske dioxygenases
catalyze the initial steps in the hydroxylation
of aromatic compounds and are critical for the metabolism of xenobiotic
substances. Because substrates do not bind to the mononuclear non-heme
FeII center, elementary steps leading to O2 activation
and substrate hydroxylation are difficult to delineate, thus making
it challenging to rationalize divergent observations on enzyme mechanisms,
reactivity, and substrate specificity. Here, we show for nitrobenzene
dioxygenase, a Rieske dioxygenase capable of transforming nitroarenes
to nitrite and substituted catechols, that unproductive O2 activation with the release of the unreacted substrate and reactive
oxygen species represents an important path in the catalytic cycle.
Through correlation of O2 uncoupling for a series of substituted
nitroaromatic compounds with 18O and 13C kinetic
isotope effects of dissolved O2 and aromatic substrates,
respectively, we show that O2 uncoupling occurs after the
rate-limiting formation of FeIII-(hydro)peroxo species
from which substrates are hydroxylated. Substituent effects on the
extent of O2 uncoupling suggest that the positioning of
the substrate in the active site rather than the susceptibility of
the substrate for attack by electrophilic oxygen species is responsible
for unproductive O2 uncoupling. The proposed catalytic
cycle provides a mechanistic basis for assessing the very different
efficiencies of substrate hydroxylation vs unproductive O2 activation and generation of reactive oxygen species in reactions
catalyzed by Rieske dioxygenases.
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Affiliation(s)
- Sarah G. Pati
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Charlotte E. Bopp
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Hans-Peter E. Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Thomas B. Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
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7
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Loya M, Dolai B, Atta AK. Solvent Controlled Colorimetric and Fluorometric Detection of Fe2+ and Cu2+ Ions by Naphthaldimine-Glucofuranose Conjugate. J Fluoresc 2022; 32:745-758. [DOI: 10.1007/s10895-021-02854-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/22/2021] [Indexed: 10/19/2022]
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8
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Song X, Liu J, Wang B. Emergence of Function from Nonheme Diiron Oxygenases: A Quantum Mechanical/Molecular Mechanical Study of Oxygen Activation and Organophosphonate Catabolism Mechanisms by PhnZ. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xitong Song
- 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, People’s Republic of China
| | - Jia Liu
- 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, People’s Republic of 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, People’s Republic of China
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9
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Mingroni MA, Knapp MJ. Kinetic Studies of the Hydrogen Atom Transfer in a Hypoxia-Sensing Enzyme, FIH-1: KIE and O 2 Reactivity. Biochemistry 2021; 60:3315-3322. [PMID: 34714626 DOI: 10.1021/acs.biochem.1c00476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cellular hypoxia plays a crucial role in tissue development and adaptation to pO2. Central to cellular oxygen sensing is factor-inhibiting HIF-1α (FIH), an α-ketoglutarate (αKG)/non-heme iron(II)-dependent dioxygenase that hydroxylates a specific asparagine residue of hypoxia inducible factor-1α (HIF-1α). The high KM(O2) and rate-limiting decarboxylation step upon O2 activation are key features of the enzyme that classify it as an oxygen sensor and set it apart from other αKG/Fe(II)-dependent dioxygenases. Although the chemical intermediates following decarboxylation are presumed to follow the consensus mechanism of other αKG/Fe(II)-dependent dioxygenases, experiments have not previously demonstrated these canonical steps in FIH. In this work, a deuterated peptide substrate was used as a mechanistic probe for the canonical hydrogen atom transfer (HAT). Our data show a large kinetic isotope effect (KIE) in steady-state kinetics (Dkcat = 10 ± 1), revealing that the HAT occurs and is partially rate limiting on kcat. Kinetic studies showed that the deuterated peptide led FIH to uncouple O2 activation and provided the opportunity to spectroscopically observe the ferryl intermediate. This enzyme uncoupling was used as an internal competition with respect to the fate of the ferryl intermediate, demonstrating a large observed KIE on the uncoupling (Dk5 = 1.147 ± 0.005) and an intrinsic KIE on the HAT step (Dk > 15). The close energy barrier between αKG decarboxylation and HAT distinguishes FIH as an O2-sensing enzyme and is crucial for ensuring substrate specificity in the regulation of cellular O2 homeostasis.
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Affiliation(s)
- Michael A Mingroni
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Michael J Knapp
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
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10
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Liu J, Wu P, Yan S, Li Y, Cao Z, Wang B. Spin-Regulated Inner-Sphere Electron Transfer Enables Efficient O—O Bond Activation in Nonheme Diiron Monooxygenase MIOX. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jia Liu
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Peng Wu
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Shengheng Yan
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Yuanyuan Li
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, China
| | - Zexing Cao
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Binju Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
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11
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Abstract
This first serious attempt at an autobiographical accounting has forced me to sit still long enough to compile my thoughts about a long personal and scientific journey. I especially hope that my trajectory will be of interest and perhaps beneficial to much younger women who are just getting started in their careers. To paraphrase from Virginia Woolf's writings in A Room of One's Own at the beginning of the 20th century, "for most of history Anonymous was a Woman." However, Ms. Woolf is also quoted as saying "nothing has really happened until it has been described," a harbinger of the enormous historical changes that were about to be enacted and recorded by women in the sciences and other disciplines. The progress in my chosen field of study-the chemical basis of enzyme action-has also been remarkable, from the first description of an enzyme's 3D structure to a growing and deep understanding of the origins of enzyme catalysis.
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Affiliation(s)
- Judith P Klinman
- Department of Chemistry, Department of Molecular and Cell Biology, and California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, USA;
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12
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Zhou C, Luo X, Chen N, Zhang L, Gao J. C-P Natural Products as Next-Generation Herbicides: Chemistry and Biology of Glufosinate. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:3344-3353. [PMID: 32125843 DOI: 10.1021/acs.jafc.0c00052] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In modern agriculture and weed management practices, herbicides have been widely used to control weeds effectively and represent more than 50% of commercial pesticides applied in the world. Herbicides with unique mechanisms of actions (MOA) have historically been discovered and commercialized every two or three years from the 1950s to the 1980s. However, this trend lowered dramatically as no herbicide with a novel MOA has been marketed for more than 30 years. The fast-growing resistance to commercial herbicides has reignited the agricultural chemical industry interest in new structural scaffolds targeting novel sites in plants. Carbon-phosphorus bonds (C-P) containing natural products (NPs) have played an essential role in herbicide discovery as the chemical diversity, and the promising bioactivity of natural C-P phytotoxins can provide exciting opportunities for the discovery of both natural and semisynthetic herbicides with novel targets. Among commercial herbicides, glyphosate (Roundup), a famous C-P containing herbicide, is by far the most universally used herbicide worldwide. Furthermore, glufosinate is one of the most widely used natural herbicides in the world. Therefore, C-P NPs are a treasure for discovering new herbicides with novel mechanisms of actions (MOAs). Here, we present an overview of the chemistry and biology of glufosinate including isolation and characterization, mode of action, herbicidal use, biosynthesis, and chemical synthesis since its discovery in order to not only help scientists reassess the role of this famous herbicide in the field of agrichemical chemistry but also build a new stage for discovering novel C-P herbicides with new MOAs.
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Affiliation(s)
- Chengzeng Zhou
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaoxia Luo
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, College of Life Science, Tarim University, Alar 843300, China
| | - Nengyi Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lili Zhang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, College of Life Science, Tarim University, Alar 843300, China
| | - Jiangtao Gao
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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13
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Zhang QP, Wei TB, An JN, Chen YY, Gong GF, Zhou Q, Yang HL, Yao H, Zhang YM, Lin Q. A simple chemosensor for ultrasensitive fluorescent “turn-on” detection of Fe3+ and alternant detection of CN-. Supramol Chem 2019. [DOI: 10.1080/10610278.2019.1690655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Qin-Peng Zhang
- Key Laboratory of Eco-Environment-Related Polymer Materials, Ministry of Education of China; Research Center of Gansu Military and Civilian Integration Advanced Structural Materials; College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, P. R. China
| | - Tai-Bao Wei
- Key Laboratory of Eco-Environment-Related Polymer Materials, Ministry of Education of China; Research Center of Gansu Military and Civilian Integration Advanced Structural Materials; College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, P. R. China
| | - Jun-Nian An
- Key Laboratory of Eco-Environment-Related Polymer Materials, Ministry of Education of China; Research Center of Gansu Military and Civilian Integration Advanced Structural Materials; College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, P. R. China
| | - Yan-Yan Chen
- Key Laboratory of Eco-Environment-Related Polymer Materials, Ministry of Education of China; Research Center of Gansu Military and Civilian Integration Advanced Structural Materials; College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, P. R. China
| | - Guan-Fei Gong
- Key Laboratory of Eco-Environment-Related Polymer Materials, Ministry of Education of China; Research Center of Gansu Military and Civilian Integration Advanced Structural Materials; College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, P. R. China
| | - Qi Zhou
- Key Laboratory of Eco-Environment-Related Polymer Materials, Ministry of Education of China; Research Center of Gansu Military and Civilian Integration Advanced Structural Materials; College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, P. R. China
| | - Hai-Long Yang
- Key Laboratory of Eco-Environment-Related Polymer Materials, Ministry of Education of China; Research Center of Gansu Military and Civilian Integration Advanced Structural Materials; College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, P. R. China
| | - Hong Yao
- Key Laboratory of Eco-Environment-Related Polymer Materials, Ministry of Education of China; Research Center of Gansu Military and Civilian Integration Advanced Structural Materials; College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, P. R. China
| | - You-Ming Zhang
- Key Laboratory of Eco-Environment-Related Polymer Materials, Ministry of Education of China; Research Center of Gansu Military and Civilian Integration Advanced Structural Materials; College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, P. R. China
- College of Chemistry and Chemical Engineering, Lanzhou City University, Lanzhou, Gansu, P. R. China
| | - Qi Lin
- Key Laboratory of Eco-Environment-Related Polymer Materials, Ministry of Education of China; Research Center of Gansu Military and Civilian Integration Advanced Structural Materials; College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, P. R. China
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14
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Wang B, Cao Z, Rovira C, Song J, Shaik S. Fenton-Derived OH Radicals Enable the MPnS Enzyme to Convert 2-Hydroxyethylphosphonate to Methylphosphonate: Insights from Ab Initio QM/MM MD Simulations. J Am Chem Soc 2019; 141:9284-9291. [PMID: 31132257 DOI: 10.1021/jacs.9b02659] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The mechanism for dioxygen activation represents one of the core issues in metalloenzymes. In most cases, the activation of the O2 molecule requires additional electrons from an external reducant. However, nonheme hydroxyethylphosphonate dioxygenase (HEPD) and methylphosphonate synthase (MPnS) are exceptional C-H oxygenases. Both enzymes do not utilize reductants, rather they employ directly iron(III)-superoxide species to initiate H-abstraction reactions and lead thereby to catalysis of the C-C cleavage in 2-hydroxyethylphosphonate (2-HEP). Using the recently characterized MPnS structure and QM(B3LYP)/MM-based metadynamics simulations, we deciphered the chemical mechanism for MPnS. Our simulations demonstrate O2 activation in MPnS is mediated by an adjacent Lysine residue (Lys28) in the active site, leading to an unusual H 2 O 2 intermediate in the reductant-independent nonheme MPnS enzyme. Furthermore, the so-generated H 2 O 2 intermediate is subsequently employed in a Fenton-type reaction, leading to a locked •OH radical that spontaneously attaches to the substrate carbonyl group. Meanwhile, the proton from the Fe(III)-OH is shuttled back to the deprotonated Lys28, affording the Fe(IV)-oxo species that is identified by experiment in HEPD. Thus, our calculations demonstrate an unusual proton-shuttle mechanism for O 2 activation in metalloenzymes.
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Affiliation(s)
- 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 360015 , P. R. China
| | - Zexing Cao
- 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 360015 , P. R. China
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & IQTCUB , Universitat de Barcelona , Martí i Franquès 1 , 08028 Barcelona , Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA) , Passeig Lluís Companys, 23 , 08020 Barcelona , Spain
| | - Jinshuai Song
- College of Chemistry and Molecular Engineering , Zhengzhou University , Zhengzhou 450001 , P. R. China
| | - Sason Shaik
- Institute of Chemistry , The Hebrew University of Jerusalem , 9190407 Jerusalem , Israel
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15
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Gama SR, Lo BSY, Séguin J, Pallitsch K, Hammerschmidt F, Zechel DL. C-H Bond Cleavage Is Rate-Limiting for Oxidative C-P Bond Cleavage by the Mixed Valence Diiron-Dependent Oxygenase PhnZ. Biochemistry 2019; 58:5271-5280. [PMID: 31046250 DOI: 10.1021/acs.biochem.9b00145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PhnZ utilizes a mixed valence diiron(II/III) cofactor and O2 to oxidatively cleave the carbon-phosphorus bond of (R)-2-amino-1-hydroxyethylphosphonic acid to form glycine and orthophosphate. The active site residues Y24 and E27 are proposed to mediate induced-fit recognition of the substrate and access of O2 to one of the active site Fe ions. H62 is proposed to deprotonate the C1-hydroxyl of the substrate during catalysis. Kinetic isotope effects (KIEs), pH-rate dependence, and site-directed mutagenesis were used to probe the rate-determining transition state and the roles of these three active site residues. Primary deuterium KIE values of 5.5 ± 0.3 for D(V) and 2.2 ± 0.4 for D(V/K) were measured with (R)-2-amino[1-2H1]-1-hydroxyethylphosphonic acid, indicating that cleavage of the C1-H bond of the substrate is rate-limiting. This step is also rate-limiting for PhnZ Y24F, as shown by a significant deuterium KIE value of 2.3 ± 0.1 for D(V). In contrast, a different reaction step appears to be rate-limiting for the PhnZ E27A and H62A variants, which exhibited D(V) values near unity. A solvent KIE of 2.2 ± 0.3 for D2O(V) is observed for PhnZ. Significant solvent KIE values are also observed for the PhnZ Y24F and E27A variants. In contrast, the PhnZ H62A variant does not show a significant solvent KIE, suggesting that H62 is mediating proton transfer in the transition state. A proton inventory study with PhnZ indicates that 1.5 ± 0.6 protons are in flight in the rate-determining step. Overall, the rate-determining transition state for oxidative C-P bond cleavage by PhnZ is proposed to involve C-H bond cleavage that is coupled to deprotonation of the substrate C1-hydroxyl by H62.
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Affiliation(s)
- Simanga R Gama
- Department of Chemistry , Queen's University , Kingston , Ontario , Canada K7L 3N6
| | - Becky Suet Yan Lo
- Department of Chemistry , Queen's University , Kingston , Ontario , Canada K7L 3N6
| | - Jacqueline Séguin
- Department of Chemistry , Queen's University , Kingston , Ontario , Canada K7L 3N6
| | - Katharina Pallitsch
- Institute of Organic Chemistry , University of Vienna , 1090 Vienna , Austria
| | | | - David L Zechel
- Department of Chemistry , Queen's University , Kingston , Ontario , Canada K7L 3N6
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16
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Stampfli AR, Goncharenko KV, Meury M, Dubey BN, Schirmer T, Seebeck FP. An Alternative Active Site Architecture for O 2 Activation in the Ergothioneine Biosynthetic EgtB from Chloracidobacterium thermophilum. J Am Chem Soc 2019; 141:5275-5285. [PMID: 30883103 DOI: 10.1021/jacs.8b13023] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Sulfoxide synthases are nonheme iron enzymes that catalyze oxidative carbon-sulfur bond formation between cysteine derivatives and N-α-trimethylhistidine as a key step in the biosynthesis of thiohistidines. The complex catalytic mechanism of this enzyme reaction has emerged as the controversial subject of several biochemical and computational studies. These studies all used the structure of the γ-glutamyl cysteine utilizing sulfoxide synthase, MthEgtB from Mycobacterium thermophilum (EC 1.14.99.50), as a structural basis. To provide an alternative model system, we have solved the crystal structure of CthEgtB from Chloracidobacterium thermophilum (EC 1.14.99.51) that utilizes cysteine as a sulfur donor. This structure reveals a completely different configuration of active site residues that are involved in oxygen binding and activation. Furthermore, comparison of the two EgtB structures enables a classification of all ergothioneine biosynthetic EgtBs into five subtypes, each characterized by unique active-site features. This active site diversity provides an excellent platform to examine the catalytic mechanism of sulfoxide synthases by comparative enzymology, but also raises the question as to why so many different solutions to the same biosynthetic problem have emerged.
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Affiliation(s)
- Anja R Stampfli
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland.,Focal Area Structural Biology and Biophysics, Biozentrum , University of Basel , Basel 4056 , Switzerland
| | - Kristina V Goncharenko
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland
| | - Marcel Meury
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland
| | - Badri N Dubey
- Focal Area Structural Biology and Biophysics, Biozentrum , University of Basel , Basel 4056 , Switzerland
| | - Tilman Schirmer
- Focal Area Structural Biology and Biophysics, Biozentrum , University of Basel , Basel 4056 , Switzerland
| | - Florian P Seebeck
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland
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17
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Luo K, Zhao Y, Zhang J, He J, Huang R, Yan S, Lin J, Jin Y. Enantioselective Epoxypyrrolidines via a Tandem Cycloaddition/Autoxidation in Air and Mechanistic Studies. Org Lett 2018; 21:423-427. [PMID: 30588819 DOI: 10.1021/acs.orglett.8b03605] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A tandem cycloaddition/autoxidation reaction between heterocyclic ketene aminals and diazoester in air is described for the enantioselective preparation of epoxypyrrolidines. Notably, the results of mechanistic studies suggest that epoxide was oxidized from an sp3 C-C single bond, which is of mechanistic and practical interest as this protocol may be suitable for constructing other bioactive heterocyclic epoxides.
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Affiliation(s)
- Kaixiu Luo
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology , Yunnan University , Kunming 650091 , P. R. China
| | - Yongqiang Zhao
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology , Yunnan University , Kunming 650091 , P. R. China
| | - Jiawei Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology , Yunnan University , Kunming 650091 , P. R. China
| | - Jia He
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology , Yunnan University , Kunming 650091 , P. R. China
| | - Rong Huang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology , Yunnan University , Kunming 650091 , P. R. China
| | - Shengjiao Yan
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology , Yunnan University , Kunming 650091 , P. R. China
| | - Jun Lin
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology , Yunnan University , Kunming 650091 , P. R. China
| | - Yi Jin
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology , Yunnan University , Kunming 650091 , P. R. China
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18
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Haschke S, Mader M, Schlicht S, Roberts AM, Angeles-Boza AM, Barth JAC, Bachmann J. Direct oxygen isotope effect identifies the rate-determining step of electrocatalytic OER at an oxidic surface. Nat Commun 2018; 9:4565. [PMID: 30385759 PMCID: PMC6212532 DOI: 10.1038/s41467-018-07031-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/09/2018] [Indexed: 11/22/2022] Open
Abstract
Understanding the mechanism of water oxidation to dioxygen represents the bottleneck towards the design of efficient energy storage schemes based on water splitting. The investigation of kinetic isotope effects has long been established for mechanistic studies of various such reactions. However, so far natural isotope abundance determination of O2 produced at solid electrode surfaces has not been applied. Here, we demonstrate that such measurements are possible. Moreover, they are experimentally simple and sufficiently accurate to observe significant effects. Our measured kinetic isotope effects depend strongly on the electrode material and on the applied electrode potential. They suggest that in the case of iron oxide as the electrode material, the oxygen evolution reaction occurs via a rate-determining O−O bond formation via nucleophilic water attack on a ferryl unit. Understanding reaction mechanisms is crucial for catalyst design. Here, natural-abundance isotope quantifications of O2 yield mechanistically significant reaction kinetic isotope effects for water oxidation over metal oxide electrodes, the bottleneck step of water electrolysis.
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Affiliation(s)
- Sandra Haschke
- Department of Chemistry and Pharmacy, Chemistry of Thin Film Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstr. 4, 91058, Erlangen, Germany
| | - Michael Mader
- Department für Geographie und Geowissenschaften, GeoZentrum NordBayern, Applied Geology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schlossgarten 5, 91054, Erlangen, Germany
| | - Stefanie Schlicht
- Department of Chemistry and Pharmacy, Chemistry of Thin Film Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstr. 4, 91058, Erlangen, Germany
| | - André M Roberts
- Department für Geographie und Geowissenschaften, GeoZentrum NordBayern, Applied Geology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schlossgarten 5, 91054, Erlangen, Germany
| | - Alfredo M Angeles-Boza
- Department of Chemistry and Institute of Materials Science, University of Connecticut, 55 North Eagleville Rd., Storrs, CT, 06269, USA.
| | - Johannes A C Barth
- Department für Geographie und Geowissenschaften, GeoZentrum NordBayern, Applied Geology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schlossgarten 5, 91054, Erlangen, Germany.
| | - Julien Bachmann
- Department of Chemistry and Pharmacy, Chemistry of Thin Film Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstr. 4, 91058, Erlangen, Germany. .,Institute of Chemistry, Saint Petersburg State University, Universitetskii pr. 26, Saint Petersburg, Russian Federation, 198504.
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19
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Abeyawardhane DL, Fernández RD, Murgas CJ, Heitger DR, Forney AK, Crozier MK, Lucas HR. Iron Redox Chemistry Promotes Antiparallel Oligomerization of α-Synuclein. J Am Chem Soc 2018; 140:5028-5032. [PMID: 29608844 DOI: 10.1021/jacs.8b02013] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Brain metal dyshomeostasis and altered structural dynamics of the presynaptic protein α-synuclein (αS) are both implicated in the pathology of Parkinson's disease (PD), yet a mechanistic understanding of disease progression in the context of αS structure and metal interactions remains elusive. In this Communication, we detail the influence of iron, a prevalent redox-active brain biometal, on the aggregation propensity and secondary structure of N-terminally acetylated αS (NAcαS), the physiologically relevant form in humans. We demonstrate that under aerobic conditions, Fe(II) commits NAcαS to a PD-relevant oligomeric assembly, verified by the oligomer-selective A11 antibody, that does not have any parallel β-sheet character but contains a substantial right-twisted antiparallel β-sheet component based on CD analyses and descriptive deconvolution of the secondary structure. This NAcαS-FeII oligomer does not develop into the β-sheet fibrils that have become hallmarks of PD, even after extended incubation, as verified by TEM imaging and the fibril-specific OC antibody. Thioflavin T (ThT), a fluorescent probe for β-sheet fibril formation, also lacks coordination to this antiparallel conformer. We further show that this oligomeric state is not observed when O2 is excluded, indicating a role for iron(II)-mediated O2 chemistry in locking this dynamic protein into a conformation that may have physiological or pathological implications.
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Affiliation(s)
- Dinendra L Abeyawardhane
- Department of Chemistry , Virginia Commonwealth University , Richmond , Virginia 23284 , United States
| | - Ricardo D Fernández
- Department of Chemistry , Virginia Commonwealth University , Richmond , Virginia 23284 , United States
| | - Cody J Murgas
- Department of Chemistry , Virginia Commonwealth University , Richmond , Virginia 23284 , United States
| | - Denver R Heitger
- Department of Chemistry , Virginia Commonwealth University , Richmond , Virginia 23284 , United States
| | - Ashley K Forney
- Department of Chemistry , Virginia Commonwealth University , Richmond , Virginia 23284 , United States
| | - Madeleine K Crozier
- Department of Chemistry , Virginia Commonwealth University , Richmond , Virginia 23284 , United States
| | - Heather R Lucas
- Department of Chemistry , Virginia Commonwealth University , Richmond , Virginia 23284 , United States
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20
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Ulrich EC, Kamat SS, Hove-Jensen B, Zechel DL. Methylphosphonic Acid Biosynthesis and Catabolism in Pelagic Archaea and Bacteria. Methods Enzymol 2018; 605:351-426. [DOI: 10.1016/bs.mie.2018.01.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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21
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Peck SC, Wang C, Dassama LMK, Zhang B, Guo Y, Rajakovich LJ, Bollinger JM, Krebs C, van der Donk WA. O-H Activation by an Unexpected Ferryl Intermediate during Catalysis by 2-Hydroxyethylphosphonate Dioxygenase. J Am Chem Soc 2017; 139:2045-2052. [PMID: 28092705 PMCID: PMC5302023 DOI: 10.1021/jacs.6b12147] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Activation
of O–H bonds by inorganic metal-oxo complexes
has been documented, but no cognate enzymatic process is known. Our
mechanistic analysis of 2-hydroxyethylphosphonate dioxygenase
(HEPD), which cleaves the C1–C2 bond of its substrate to afford
hydroxymethylphosphonate on the biosynthetic pathway to
the commercial herbicide phosphinothricin, uncovered an example
of such an O–H-bond-cleavage event. Stopped-flow UV–visible
absorption and freeze-quench Mössbauer experiments identified
a transient iron(IV)-oxo (ferryl) complex. Maximal accumulation of
the intermediate required both the presence of deuterium in the substrate
and, importantly, the use of 2H2O as solvent.
The ferryl complex forms and decays rapidly enough to be on the catalytic
pathway. To account for these unanticipated results, a new mechanism
that involves activation of an O–H bond by the ferryl complex
is proposed. This mechanism accommodates all available data on the
HEPD reaction.
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Affiliation(s)
- Spencer C Peck
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States.,Institute for Genomic Biology, University of Illinois at Urbana-Champaign , 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| | - Chen Wang
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Laura M K Dassama
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Bo Zhang
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Yisong Guo
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Lauren J Rajakovich
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - J Martin Bollinger
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States.,Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States.,Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States.,Institute for Genomic Biology, University of Illinois at Urbana-Champaign , 1206 West Gregory Drive, Urbana, Illinois 61801, United States
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22
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Abstract
Organophosphonic acids are unique as natural products in terms of stability and mimicry. The C-P bond that defines these compounds resists hydrolytic cleavage, while the phosphonyl group is a versatile mimic of transition-states, intermediates, and primary metabolites. This versatility may explain why a variety of organisms have extensively explored the use organophosphonic acids as bioactive secondary metabolites. Several of these compounds, such as fosfomycin and bialaphos, figure prominently in human health and agriculture. The enzyme reactions that create these molecules are an interesting mix of chemistry that has been adopted from primary metabolism as well as those with no chemical precedent. Additionally, the phosphonate moiety represents a source of inorganic phosphate to microorganisms that live in environments that lack this nutrient; thus, unusual enzyme reactions have also evolved to cleave the C-P bond. This review is a comprehensive summary of the occurrence and function of organophosphonic acids natural products along with the mechanisms of the enzymes that synthesize and catabolize these molecules.
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Affiliation(s)
- Geoff P Horsman
- Department of Chemistry and Biochemistry, Wilfrid Laurier University , Waterloo, Ontario N2L 3C5, Canada
| | - David L Zechel
- Department of Chemistry, Queen's University , Kingston, Ontario K7L 3N6, Canada
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23
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Peck SC, van der Donk WA. Go it alone: four-electron oxidations by mononuclear non-heme iron enzymes. J Biol Inorg Chem 2016; 22:381-394. [PMID: 27783267 DOI: 10.1007/s00775-016-1399-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 10/11/2016] [Indexed: 10/20/2022]
Abstract
This review discusses the current mechanistic understanding of a group of mononuclear non-heme iron-dependent enzymes that catalyze four-electron oxidation of their organic substrates without the use of any cofactors or cosubstrates. One set of enzymes acts on α-ketoacid-containing substrates, coupling decarboxylation to oxygen activation. This group includes 4-hydroxyphenylpyruvate dioxygenase, 4-hydroxymandelate synthase, and CloR involved in clorobiocin biosynthesis. A second set of enzymes acts on substrates containing a thiol group that coordinates to the iron. This group is comprised of isopenicillin N synthase, thiol dioxygenases, and enzymes involved in the biosynthesis of ergothioneine and ovothiol. The final group of enzymes includes HEPD and MPnS that both carry out the oxidative cleavage of the carbon-carbon bond of 2-hydroxyethylphosphonate but generate different products. Commonalities amongst many of these enzymes are discussed and include the initial substrate oxidation by a ferric-superoxo-intermediate and a second oxidation by a ferryl species.
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Affiliation(s)
- Spencer C Peck
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL, 61801, USA.,Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL, 61801, USA. .,Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA.
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24
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Chang WC, Li J, Lee JL, Cronican AA, Guo Y. Mechanistic Investigation of a Non-Heme Iron Enzyme Catalyzed Epoxidation in (-)-4'-Methoxycyclopenin Biosynthesis. J Am Chem Soc 2016; 138:10390-3. [PMID: 27442345 DOI: 10.1021/jacs.6b05400] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mechanisms have been proposed for α-KG-dependent non-heme iron enzyme catalyzed oxygen atom insertion into an olefinic moiety in various natural products, but they have not been examined in detail. Using a combination of methods including transient kinetics, Mössbauer spectroscopy, and mass spectrometry, we demonstrate that AsqJ-catalyzed (-)-4'-methoxycyclopenin formation uses a high-spin Fe(IV)-oxo intermediate to carry out epoxidation. Furthermore, product analysis on (16)O/(18)O isotope incorporation from the reactions using the native substrate, 4'-methoxydehydrocyclopeptin, and a mechanistic probe, dehydrocyclopeptin, reveals evidence supporting oxo↔hydroxo tautomerism of the Fe(IV)-oxo species in the non-heme iron enzyme catalysis.
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Affiliation(s)
- Wei-Chen Chang
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Jikun Li
- Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Justin L Lee
- Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Andrea A Cronican
- Department of Environmental and Occupational Health, University of Pittsburgh , Pittsburgh, Pennsylvania 15219, United States
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
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25
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Mono- and binuclear non-heme iron chemistry from a theoretical perspective. J Biol Inorg Chem 2016; 21:619-44. [DOI: 10.1007/s00775-016-1357-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/29/2016] [Indexed: 10/21/2022]
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26
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Catalytic strategies of the non-heme iron dependent oxygenases and their roles in plant biology. Curr Opin Chem Biol 2016; 31:126-35. [PMID: 27015291 PMCID: PMC4879150 DOI: 10.1016/j.cbpa.2016.02.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/25/2016] [Accepted: 02/26/2016] [Indexed: 12/18/2022]
Abstract
Current evidence for iron-oxo reactive intermediates is reviewed. In crystallo intermediates detected in a native extradiol dioxygenase reaction. Carotenoid cleavage dioxygenases catalyse strigolactone biosynthesis. Identification of plant cysteine oxidases involved in the plant hypoxic response. Applications of enzyme manipulation to plant biology and agriculture are discussed.
Non-heme iron-dependent oxygenases catalyse the incorporation of O2 into a wide range of biological molecules and use diverse strategies to activate their substrates. Recent kinetic studies, including in crystallo, have provided experimental support for some of the intermediates used by different subclasses of this enzyme family. Plant non-heme iron-dependent oxygenases have diverse and important biological roles, including in growth signalling, stress responses and secondary metabolism. Recently identified roles include in strigolactone biosynthesis, O-demethylation in morphine biosynthesis and regulating the stability of hypoxia-responsive transcription factors. We discuss current structural and mechanistic understanding of plant non-heme iron oxygenases, and how their chemical/genetic manipulation could have agricultural benefit, for example, for improved yield, stress tolerance or herbicide development.
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