1
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Bopp C, Bernet NM, Meyer F, Khan R, Robinson SL, Kohler HPE, Buller R, Hofstetter TB. Elucidating the Role of O 2 Uncoupling for the Adaptation of Bacterial Biodegradation Reactions Catalyzed by Rieske Oxygenases. ACS ENVIRONMENTAL AU 2024; 4:204-218. [PMID: 39035869 PMCID: PMC11258757 DOI: 10.1021/acsenvironau.4c00016] [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: 03/04/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 07/23/2024]
Abstract
Oxygenation of aromatic and aliphatic hydrocarbons by Rieske oxygenases is the initial step of various biodegradation pathways for environmental organic contaminants. Microorganisms carrying Rieske oxygenases are able to quickly adapt their substrate spectra to alternative carbon and energy sources that are structurally related to the original target substrate, yet the molecular events responsible for this rapid adaptation are not well understood. Here, we evaluated the hypothesis that reactive oxygen species (ROS) generated by unproductive activation of O2, the so-called O2 uncoupling, in the presence of the alternative substrate exert a selective pressure on the bacterium for increasing the oxygenation efficiency of Rieske oxygenases. To that end, we studied wild-type 2-nitrotoluene dioxygenase from Acidovorax sp. strain JS42 and five enzyme variants that have evolved from adaptive laboratory evolution experiments with 3- and 4-nitrotoluene as alternative growth substrates. The enzyme variants showed a substantially increased oxygenation efficiency toward the new target substrates concomitant with a reduction of ROS production, while mechanisms and kinetics of enzymatic O2 activation remained unchanged. Structural analyses and docking studies suggest that amino acid substitutions in enzyme variants occurred at residues lining both substrate and O2 transport tunnels, enabling tighter binding of the target substrates in the active site. Increased oxygenation efficiencies measured in vitro for the various enzyme (variant)-substrate combinations correlated linearly with in vivo changes in growth rates for evolved Acidovorax strains expressing the variants. Our data suggest that the selective pressure from oxidative stress toward more efficient oxygenation by Rieske oxygenases was most notable when O2 uncoupling exceeded 60%.
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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
- Institute
of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Fabian Meyer
- Competence
Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland
| | - Riyaz Khan
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Serina L. Robinson
- 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
| | - Rebecca Buller
- Competence
Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zürich University of Applied Sciences, 8820 Wädenswil, 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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2
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Krishnan A, Waheed SO, Melayikandy S, LaRouche C, Paik M, Schofield CJ, Karabencheva-Christova TG. Effects of Clinical Mutations in the Second Coordination Sphere and Remote Regions on the Catalytic Mechanism of Non-Heme Fe(II)/2-Oxoglutarate-Dependent Aspartyl Hydroxylase AspH. Chemphyschem 2024:e202400303. [PMID: 38839574 DOI: 10.1002/cphc.202400303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/07/2024]
Abstract
Aspartyl/asparaginyl hydroxylase (AspH) catalyzes the post-translational hydroxylations of vital human proteins, playing an essential role in maintaining their biological functions. Single-point mutations in the Second Coordination Sphere (SCS) and long-range (LR) residues of AspH have been linked to pathological conditions such as the ophthalmologic condition Traboulsi syndrome and chronic kidney disease (CKD). Although the clinical impacts of these mutations are established, there is a critical knowledge gap regarding their specific atomistic effects on the catalytic mechanism of AspH. In this study, we report integrated computational investigations on the potential mechanistic implications of four mutant forms of human AspH with clinical importance: R735W, R735Q, R688Q, and G434V. All the mutant forms exhibited altered binding interactions with the co-substrate 2-oxoglutarate (2OG) and the main substrate in the ferric-superoxo and ferryl complexes, which are critical for catalysis, compared to the wild-type (WT). Importantly, the mutations strongly influence the energetics of the frontier molecular orbitals (FMOs) and, thereby, the activation energies for the hydrogen atom transfer (HAT) step compared to the WT AspH. Insights from our study can contribute to enzyme engineering and the development of selective modulators for WT and mutants of AspH, ultimately aiding in treating cancers, Traboulsi syndrome and, CKD.
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Affiliation(s)
- Anandhu Krishnan
- Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Sodiq O Waheed
- Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Sreerag Melayikandy
- Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Ciara LaRouche
- Department of Chemical Engineering, Michigan Techno, Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Meredith Paik
- Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, OX1 3TA, United Kingdom
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3
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Krishnan A, Waheed SO, Varghese A, Cherilakkudy FH, Schofield CJ, Karabencheva-Christova TG. Unusual catalytic strategy by non-heme Fe(ii)/2-oxoglutarate-dependent aspartyl hydroxylase AspH. Chem Sci 2024; 15:3466-3484. [PMID: 38455014 PMCID: PMC10915816 DOI: 10.1039/d3sc05974j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/02/2024] [Indexed: 03/09/2024] Open
Abstract
Biocatalytic C-H oxidation reactions are of important synthetic utility, provide a sustainable route for selective synthesis of important organic molecules, and are an integral part of fundamental cell processes. The multidomain non-heme Fe(ii)/2-oxoglutarate (2OG) dependent oxygenase AspH catalyzes stereoselective (3R)-hydroxylation of aspartyl- and asparaginyl-residues. Unusually, compared to other 2OG hydroxylases, crystallography has shown that AspH lacks the carboxylate residue of the characteristic two-His-one-Asp/Glu Fe-binding triad. Instead, AspH has a water molecule that coordinates Fe(ii) in the coordination position usually occupied by the Asp/Glu carboxylate. Molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) studies reveal that the iron coordinating water is stabilized by hydrogen bonding with a second coordination sphere (SCS) carboxylate residue Asp721, an arrangement that helps maintain the six coordinated Fe(ii) distorted octahedral coordination geometry and enable catalysis. AspH catalysis follows a dioxygen activation-hydrogen atom transfer (HAT)-rebound hydroxylation mechanism, unusually exhibiting higher activation energy for rebound hydroxylation than for HAT, indicating that the rebound step may be rate-limiting. The HAT step, along with substrate positioning modulated by the non-covalent interactions with SCS residues (Arg688, Arg686, Lys666, Asp721, and Gln664), are essential in determining stereoselectivity, which likely proceeds with retention of configuration. The tetratricopeptide repeat (TPR) domain of AspH influences substrate binding and manifests dynamic motions during catalysis, an observation of interest with respect to other 2OG oxygenases with TPR domains. The results provide unique insights into how non-heme Fe(ii) oxygenases can effectively catalyze stereoselective hydroxylation using only two enzyme-derived Fe-ligating residues, potentially guiding enzyme engineering for stereoselective biocatalysis, thus advancing the development of non-heme Fe(ii) based biomimetic C-H oxidation catalysts, and supporting the proposal that the 2OG oxygenase superfamily may be larger than once perceived.
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Affiliation(s)
- Anandhu Krishnan
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | - Sodiq O Waheed
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | - Ann Varghese
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | | | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford OX1 3TA Oxford UK
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4
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Rogers MS, Gordon AM, Rappe TM, Goodpaster JD, Lipscomb JD. Contrasting Mechanisms of Aromatic and Aryl-Methyl Substituent Hydroxylation by the Rieske Monooxygenase Salicylate 5-Hydroxylase. Biochemistry 2023; 62:507-523. [PMID: 36583545 PMCID: PMC9854337 DOI: 10.1021/acs.biochem.2c00610] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The hydroxylase component (S5HH) of salicylate-5-hydroxylase catalyzes C5 ring hydroxylation of salicylate but switches to methyl hydroxylation when a C5 methyl substituent is present. The use of 18O2 reveals that both aromatic and aryl-methyl hydroxylations result from monooxygenase chemistry. The functional unit of S5HH comprises a nonheme Fe(II) site located 12 Å across a subunit boundary from a one-electron reduced Rieske-type iron-sulfur cluster. Past studies determined that substrates bind near the Fe(II), followed by O2 binding to the iron to initiate catalysis. Stopped-flow-single-turnover reactions (STOs) demonstrated that the Rieske cluster transfers an electron to the iron site during catalysis. It is shown here that fluorine ring substituents decrease the rate constant for Rieske electron transfer, implying a prior reaction of an Fe(III)-superoxo intermediate with a substrate. We propose that the iron becomes fully oxidized in the resulting Fe(III)-peroxo-substrate-radical intermediate, allowing Rieske electron transfer to occur. STO using 5-CD3-salicylate-d8 occurs with an inverse kinetic isotope effect (KIE). In contrast, STO of a 1:1 mixture of unlabeled and 5-CD3-salicylate-d8 yields a normal product isotope effect. It is proposed that aromatic and aryl-methyl hydroxylation reactions both begin with the Fe(III)-superoxo reaction with a ring carbon, yielding the inverse KIE due to sp2 → sp3 carbon hybridization. After Rieske electron transfer, the resulting Fe(III)-peroxo-salicylate intermediate can continue to aromatic hydroxylation, whereas the equivalent aryl-methyl intermediate formation must be reversible to allow the substrate exchange necessary to yield a normal product isotope effect. The resulting Fe(III)-(hydro)peroxo intermediate may be reactive or evolve through a high-valent iron intermediate to complete the aryl-methyl hydroxylation.
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Affiliation(s)
- Melanie S. Rogers
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Adrian M. Gordon
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Todd M. Rappe
- Minnesota NMR Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jason D. Goodpaster
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, 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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Managing argon interference during measurements of 18O/ 16O ratios in O 2 by continuous-flow isotope ratio mass spectrometry. Anal Bioanal Chem 2022; 414:6177-6186. [PMID: 35841416 PMCID: PMC9314310 DOI: 10.1007/s00216-022-04184-3] [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: 04/08/2022] [Revised: 06/08/2022] [Accepted: 06/17/2022] [Indexed: 11/08/2022]
Abstract
Abstract Monitoring changes in stable oxygen isotope ratios in molecular oxygen allows for studying many fundamental processes in bio(geo)chemistry and environmental sciences. While the measurement of \documentclass[12pt]{minimal}
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\begin{document}$$\mathrm {O}_{2}$$\end{document}O2 in gaseous samples can be carried out conveniently and from extracting moderately small aqueous samples for analyses by continuous-flow isotope ratio mass spectrometry (CF-IRMS), oxygen isotope signatures, \documentclass[12pt]{minimal}
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\begin{document}$$\permille$$\end{document}‱ because of interferences from argon in air. Here, we systematically evaluated the extent of such Ar interferences on \documentclass[12pt]{minimal}
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\begin{document}$$^{16}$$\end{document}16O ratios of \documentclass[12pt]{minimal}
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\begin{document}$$\mathrm {O}_{2}$$\end{document}O2 for measurements by gas chromatography/IRMS and GasBench/IRMS and propose simple instrumental modifications for improved Ar and \documentclass[12pt]{minimal}
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\begin{document}$$\mathrm {O}_{2}$$\end{document}O2 separation as well as post-measurement correction procedures for obtaining accurate \documentclass[12pt]{minimal}
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\begin{document}$$\updelta ^{18}$$\end{document}δ18O. We subsequently evaluated the consequences of Ar interferences for the quantification of O isotope fractionation in terms of isotope enrichment factors, \documentclass[12pt]{minimal}
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\begin{document}$$\upepsilon _{\mathrm {O}}$$\end{document}ϵO, and \documentclass[12pt]{minimal}
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\begin{document}$$^{18}$$\end{document}18O kinetic isotope effects (\documentclass[12pt]{minimal}
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\begin{document}$$^{18}$$\end{document}18O KIEs) in samples where \documentclass[12pt]{minimal}
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\begin{document}$$\mathrm {O}_{2}$$\end{document}O2 is consumed and Ar:\documentclass[12pt]{minimal}
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\begin{document}$$\mathrm {O}_{2}$$\end{document}O2 ratios increase steadily and substantially over the course of a reaction. We show that the extent of O isotope fractionation is overestimated only slightly and that this effect is typically smaller than uncertainties originating from the precision of \documentclass[12pt]{minimal}
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\begin{document}$$\updelta ^{18}$$\end{document}δ18O measurements and experimental variability. Ar interferences can become more relevant and bias \documentclass[12pt]{minimal}
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\begin{document}$$\mathrm {O}_{2}$$\end{document}O2 conversion exceeds 90%. Practically, however, such samples would typically contain less than 25 \documentclass[12pt]{minimal}
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\begin{document}$$\mathrm {O}_{2}$$\end{document}O2 at ambient temperature, an amount that is close to the method detection limit of \documentclass[12pt]{minimal}
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\begin{document}$$^{16}$$\end{document}16O ratio measurement by CF-IRMS. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s00216-022-04184-3.
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7
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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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8
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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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9
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Xu J, Martien J, Gilbertson C, Ma J, Amador-Noguez D, Park JO. Metabolic flux analysis and fluxomics-driven determination of reaction free energy using multiple isotopes. Curr Opin Biotechnol 2020; 64:151-160. [PMID: 32304936 DOI: 10.1016/j.copbio.2020.02.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 02/08/2020] [Accepted: 02/25/2020] [Indexed: 10/24/2022]
Abstract
Metabolite concentrations, fluxes, and free energies constitute the basis for understanding and controlling metabolism. Mass spectrometry and stable isotopes are integral tools in quantifying these metabolic features. For absolute metabolite concentration and flux measurement, 13C internal standards and tracers have been the gold standard. In contrast, no established methods exist for comprehensive thermodynamic quantitation under physiological environments. Recently, using high-resolution mass spectrometry and multi-isotope tracing, flux quantitation has been increasingly adopted in broader metabolism. The improved flux quantitation led to determination of Gibbs free energy of reaction (ΔG) in central carbon metabolism using a relationship between reaction reversibility and thermodynamic driving force. Here we highlight recent advances in multi-isotope tracing for metabolic flux and free energy analysis.
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Affiliation(s)
- Jimmy Xu
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Julia Martien
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Cole Gilbertson
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Junyu Ma
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Junyoung O Park
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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10
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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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11
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Ruszczycky MW, Liu HW. Measurement of Net Rate Constants from Enzyme Progress Curves without Curve Fitting. Biochemistry 2019; 58:4950-4956. [PMID: 31710808 DOI: 10.1021/acs.biochem.9b00762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A method is described whereby net rate constants can be directly inferred from the progress curves of enzyme intermediates without the need for model specification, numerical analysis, curve fitting, or the steady-state approximation. Specifically, if an enzyme intermediate in an ultimately irreversible serial subsequence is perturbed from and returns back to its equilibrium state as the substrate is consumed, then its net rate constant is given by the ratio of the total substrate consumed and the area under the progress curve for the enzyme intermediate. A rigorous analysis demonstrates this result to hold independent of the complete enzymatic reaction in which the subsequence is embedded, making it broadly applicable to a very wide range of kinetic mechanisms, including those complicated by inhibition. As a theoretical consequence, it is shown that traditionally steady-state parameters such as kcat, kcat/KM, and net rate constants can be expressed as limiting ratios of averages without requiring the steady-state hypothesis. Finally, a mock data set is generated for a system of contemporary interest that can serve as both an example of how the methodology would be used in practice and a proof of concept.
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Affiliation(s)
- Mark W Ruszczycky
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Hung-Wen Liu
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy , The University of Texas at Austin , Austin , Texas 78712 , United States.,Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
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12
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Xu C, Pan Y, Wan G, Liu H, Wang L, Zhou H, Yu SH, Jiang HL. Turning on Visible-Light Photocatalytic C-H Oxidation over Metal-Organic Frameworks by Introducing Metal-to-Cluster Charge Transfer. J Am Chem Soc 2019; 141:19110-19117. [PMID: 31707780 DOI: 10.1021/jacs.9b09954] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The tailorable structure and electronic structure of metal-organic frameworks (MOFs) greatly facilitate their modulated light harvesting, redox power, and consequently photocatalysis. Herein, a representative MOF, UiO-66, was furnished by installing Fe3+ onto the Zr-oxo clusters, to give Fe-UiO-66, which features extended visible light harvesting, based on metal-to-cluster charge transfer (MCCT). The Fe-UiO-66 with unique electronic structure and strong oxidizing power exhibits visible light-driven water oxidation, which is impossible for pristine UiO-66. More strikingly, under visible irradiation, the generated holes over Fe-UiO-66 are able to exclusively convert H2O to hydroxide radicals, initiating and driving the activation of stubborn C-H bond, such as toluene oxidation. The electrons reduce O2 to O2•- radicals that further promote the oxidation reaction. The related catalytic mechanism and the structure-activity relationship have been investigated in detail. As far as we know, this is not only an unprecedented report on activating "inert" MOFs for photocatalytic C-H activation but also the first work on extended light harvesting and enhanced photocatalysis for MOFs by introducing an MCCT process.
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Affiliation(s)
- Caiyun Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Suzhou Nano Science and Technology, Department of Chemistry , University of Science and Technology of China , Hefei , Anhui 230026 , P.R. China
| | - Yating Pan
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Suzhou Nano Science and Technology, Department of Chemistry , University of Science and Technology of China , Hefei , Anhui 230026 , P.R. China
| | - Gang Wan
- SLAC National Accelerator Laboratory , 2575 Sand Hill Rd , Menlo Park , California 94025 , United States
| | - Hang Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Suzhou Nano Science and Technology, Department of Chemistry , University of Science and Technology of China , Hefei , Anhui 230026 , P.R. China
| | - Liang Wang
- X-ray Science Division, Advanced Photon Source , Argonne National Laboratory , Lemont , Illinois 60439 , United States
| | - Hua Zhou
- X-ray Science Division, Advanced Photon Source , Argonne National Laboratory , Lemont , Illinois 60439 , United States
| | - Shu-Hong Yu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Suzhou Nano Science and Technology, Department of Chemistry , University of Science and Technology of China , Hefei , Anhui 230026 , P.R. China
| | - Hai-Long Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Suzhou Nano Science and Technology, Department of Chemistry , University of Science and Technology of China , Hefei , Anhui 230026 , P.R. China
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13
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Nesterova OV, Nesterov DS, Vranovičová B, Boča R, Pombeiro AJL. Heterometallic Cu IIFe III and Cu IIMn III alkoxo-bridged complexes revealing a rare hexanuclear M 6(μ-X) 7(μ 3-X) 2 molecular core. Dalton Trans 2018; 47:10941-10952. [PMID: 30019733 DOI: 10.1039/c8dt02290a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The novel hexanuclear complexes [Cu4Fe2(OH)(Piv)4(tBuDea)4Cl]·0.5CH3CN (1) and [Cu4Mn2(OH)(Piv)4(tBuDea)4Cl] (2) were prepared through one-pot self-assembly reactions of copper powder and iron(ii) or manganese(ii) chloride with N-tert-butyldiethanolamine (H2tBuDea) and pivalic acid (HPiv) in acetonitrile. Crystallographic studies revealed the uncommon molecular core type M6(μ-X)7(μ3-X)2 in 1 and 2, which can be viewed as a combination of two trimetallic M3(μ-X)2(μ3-X) fragments joined by three bridging atoms. The analysis and classification of the hexanuclear complexes having a M3(μ-X)2(μ3-X) moiety as a core forming fragment using data from the Cambridge Structural Database (CSD) were performed. Variable-temperature (1.8-300 K) magnetic susceptibility measurements of 1 showed a decrease of the effective magnetic moment value at low temperature, indicative of antiferromagnetic coupling between the magnetic centres (JFe-Cu/hc = -6.9 cm-1, JCu-Cu/hc = -4.1 cm-1, JFe-Fe/hc = -24.2 cm-1). Complex 1 acts as a catalyst in the reaction of mild oxidation of cyclohexane with H2O2, showing the yields of products, cyclohexanol and cyclohexanone, up to 17% using pyrazinecarboxylic acid as a promoter. In the oxidation of cis-1,2-dimethylcyclohexane with m-chloroperoxybenzoic acid (m-CPBA), 70% of retention of stereoconfiguration was observed for tertiary alcohols. Compound 1 also catalyses the amidation of cyclohexane with benzamide. In all three catalytic reactions the by-products were investigated in detail and discussed.
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Affiliation(s)
- Oksana V Nesterova
- Centro de Química Estrutural, Complexo I, Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, 1049-001 Lisboa, Portugal.
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14
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Olivares P, Ulrich EC, Chekan JR, van der Donk WA, Nair SK. Characterization of Two Late-Stage Enzymes Involved in Fosfomycin Biosynthesis in Pseudomonads. ACS Chem Biol 2017; 12:456-463. [PMID: 27977135 DOI: 10.1021/acschembio.6b00939] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The broad-spectrum phosphonate antibiotic fosfomycin is currently in use for clinical treatment of infections caused by both Gram-positive and Gram-negative uropathogens. The antibiotic is biosynthesized by various streptomycetes, as well as by pseudomonads. Notably, the biosynthetic strategies used by the two genera share only two steps: the first step in which primary metabolite phosphoenolpyruvate (PEP) is converted to phosphonopyruvate (PnPy) and the terminal step in which 2-hydroxypropylphosphonate (2-HPP) is converted to fosfomycin. Otherwise, distinct enzymatic paths are employed. Here, we biochemically confirm the last two steps in the fosfomycin biosynthetic pathway of Pseudomonas syringae PB-5123, showing that Psf3 performs the reduction of 2-oxopropylphosphonate (2-OPP) to (S)-2-HPP, followed by the Psf4-catalyzed epoxidation of (S)-2-HPP to fosfomycin. Psf4 can also accept (R)-2-HPP as a substrate but instead performs an oxidation to make 2-OPP. We show that the combined activities of Psf3 and Psf4 can be used to convert racemic 2-HPP to fosfomycin in an enantioconvergent process. X-ray structures of each enzyme with bound substrates provide insights into the stereospecificity of each conversion. These studies shed light on the reaction mechanisms of the two terminal enzymes in a distinct pathway employed by pseudomonads for the production of a potent antimicrobial agent.
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Affiliation(s)
- Philip Olivares
- Department
of Biochemistry, ‡Department of Chemistry, §Carl R. Woese Institute for Genomic
Biology, ∥Howard Hughes Medical Institute, and ⊥Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Emily C. Ulrich
- Department
of Biochemistry, ‡Department of Chemistry, §Carl R. Woese Institute for Genomic
Biology, ∥Howard Hughes Medical Institute, and ⊥Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jonathan R. Chekan
- Department
of Biochemistry, ‡Department of Chemistry, §Carl R. Woese Institute for Genomic
Biology, ∥Howard Hughes Medical Institute, and ⊥Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Biochemistry, ‡Department of Chemistry, §Carl R. Woese Institute for Genomic
Biology, ∥Howard Hughes Medical Institute, and ⊥Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Satish K. Nair
- Department
of Biochemistry, ‡Department of Chemistry, §Carl R. Woese Institute for Genomic
Biology, ∥Howard Hughes Medical Institute, and ⊥Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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15
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Kal S, Que L. Dioxygen activation by nonheme iron enzymes with the 2-His-1-carboxylate facial triad that generate high-valent oxoiron oxidants. J Biol Inorg Chem 2017; 22:339-365. [PMID: 28074299 DOI: 10.1007/s00775-016-1431-2] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/13/2016] [Indexed: 11/24/2022]
Abstract
The 2-His-1-carboxylate facial triad is a widely used scaffold to bind the iron center in mononuclear nonheme iron enzymes for activating dioxygen in a variety of oxidative transformations of metabolic significance. Since the 1990s, over a hundred different iron enzymes have been identified to use this platform. This structural motif consists of two histidines and the side chain carboxylate of an aspartate or a glutamate arranged in a facial array that binds iron(II) at the active site. This triad occupies one face of an iron-centered octahedron and makes the opposite face available for the coordination of O2 and, in many cases, substrate, allowing the tailoring of the iron-dioxygen chemistry to carry out a plethora of diverse reactions. Activated dioxygen-derived species involved in the enzyme mechanisms include iron(III)-superoxo, iron(III)-peroxo, and high-valent iron(IV)-oxo intermediates. In this article, we highlight the major crystallographic, spectroscopic, and mechanistic advances of the past 20 years that have significantly enhanced our understanding of the mechanisms of O2 activation and the key roles played by iron-based oxidants.
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Affiliation(s)
- Subhasree Kal
- Department of Chemistry, Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Lawrence Que
- Department of Chemistry, Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN, 55455, USA.
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16
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Spahr S, Cirpka OA, von Gunten U, Hofstetter TB. Formation of N-Nitrosodimethylamine during Chloramination of Secondary and Tertiary Amines: Role of Molecular Oxygen and Radical Intermediates. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:280-290. [PMID: 27958701 DOI: 10.1021/acs.est.6b04780] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
N-Nitrosodimethylamine (NDMA) is a carcinogenic disinfection byproduct from water chloramination. Despite the identification of numerous NDMA precursors, essential parts of the reaction mechanism such as the incorporation of molecular O2 are poorly understood. In laboratory model systems for the chloramination of secondary and tertiary amines, we investigated the kinetics of precursor disappearance and NDMA formation, quantified the stoichiometries of monochloramine (NH2Cl) and aqueous O2 consumption, derived 18O-kinetic isotope effects (18O-KIE) for the reactions of aqueous O2, and studied the impact of radical scavengers on NDMA formation. Although the molar NDMA yields from five N,N-dimethylamine-containing precursors varied between 1.4% and 90%, we observed the stoichiometric removal of one O2 per N,N-dimethylamine group of the precursor indicating that the oxygenation of N atoms did not determine the molar NDMA yield. Small 18O-KIEs between 1.0026 ± 0.0003 and 1.0092 ± 0.0009 found for all precursors as well as completely inhibited NDMA formation in the presence of radical scavengers (ABTS and trolox) imply that O2 reacted with radical species. Our study suggests that aminyl radicals from the oxidation of organic amines by NH2Cl and N-peroxyl radicals from the reaction of aminyl radicals with aqueous O2 are part of the NDMA formation mechanism.
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Affiliation(s)
- Stephanie Spahr
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , CH-8600 Dübendorf, Switzerland
- School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Federale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Olaf A Cirpka
- Center for Applied Geoscience, University of Tübingen , D-72074 Tübingen, Germany
| | - Urs von Gunten
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , CH-8600 Dübendorf, Switzerland
- School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Federale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich , CH-8092 Zürich, Switzerland
| | - Thomas B Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , CH-8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich , CH-8092 Zürich, Switzerland
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17
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Hangasky JA, Taabazuing CY, Martin CB, Eron SJ, Knapp MJ. The facial triad in the α-ketoglutarate dependent oxygenase FIH: A role for sterics in linking substrate binding to O 2 activation. J Inorg Biochem 2017; 166:26-33. [PMID: 27815979 PMCID: PMC5161613 DOI: 10.1016/j.jinorgbio.2016.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/07/2016] [Accepted: 10/13/2016] [Indexed: 02/06/2023]
Abstract
The factor inhibiting hypoxia inducible factor-1α (FIH) is a nonheme Fe(II)/αKG oxygenase using a 2-His-1-Asp facial triad. FIH activates O2 via oxidative decarboxylation of α-ketoglutarate (αKG) to generate an enzyme-based oxidant which hydroxylates the Asn803 residue within the C-terminal transactivation domain (CTAD) of HIF-1α. Tight coupling of these two sequential reactions requires a structural linkage between the Fe(II) and the substrate binding site to ensure that O2 activation occurs after substrate binds. We tested the hypothesis that the facial triad carboxylate (Asp201) of FIH linked substrate binding and O2 binding sites. Asp201 variants of FIH were constructed and thoroughly characterized in vitro using steady-state kinetics, crystallography, autohydroxylation, and coupling measurements. Our studies revealed each variant activated O2 with a catalytic efficiency similar to that of wild-type (WT) FIH (kcataKM(O2)=0.17μM-1min-1), but led to defects in the coupling of O2 activation to substrate hydroxylation. Steady-state kinetics showed similar catalytic efficiencies for hydroxylation by WT-FIH (kcat/KM(CTAD)=0.42μM-1min-1) and D201G (kcat/KM(CTAD)=0.34μM-1min-1); hydroxylation by D201E was greatly impaired, while hydroxylation by D201A was undetectable. Analysis of the crystal structure of the D201E variant revealed steric crowding near the diffusible ligand site supporting a role for sterics from the facial triad carboxylate in the O2 binding order. Our data support a model in which the facial triad carboxylate Asp201 provides both steric and polar contacts to favor O2 access to the Fe(II) only after substrate binds, leading to coupled turnover in FIH and other αKG oxygenases.
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Affiliation(s)
- John A Hangasky
- Department of Chemistry, University of Massachusetts, Amherst, United States
| | | | - Cristina B Martin
- Department of Chemistry, University of Massachusetts, Amherst, United States
| | - Scott J Eron
- Department of Chemistry, University of Massachusetts, Amherst, United States
| | - Michael J Knapp
- Department of Chemistry, University of Massachusetts, Amherst, United States.
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18
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Alberro N, Torrent-Sucarrat M, Arrastia I, Arrieta A, Cossío FP. Two-State Reactivity of Histone Demethylases Containing Jumonji-C Active Sites: Different Mechanisms for Different Methylation Degrees. Chemistry 2016; 23:137-148. [DOI: 10.1002/chem.201604219] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Nerea Alberro
- Department of Organic Chemistry I; Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU); Centro de Innovación en Química Avanzada (ORFEO-CINQA); Manuel Lardizabal Ibilbidea 3 20018 San Sebastián/Donostia Spain
| | - Miquel Torrent-Sucarrat
- Department of Organic Chemistry I; Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU); Centro de Innovación en Química Avanzada (ORFEO-CINQA); Manuel Lardizabal Ibilbidea 3 20018 San Sebastián/Donostia Spain
- Donostia International Physics Center (DIPC); Manuel Lardizabal Ibilbidea 4 20018 San Sebastián/Donostia Spain
- Ikerbasque; Basque Foundation for Science; María Díaz de Haro 3, 6 floor 48013 Bilbao Spain
| | - Iosune Arrastia
- Donostia International Physics Center (DIPC); Manuel Lardizabal Ibilbidea 4 20018 San Sebastián/Donostia Spain
| | - Ana Arrieta
- Department of Organic Chemistry I; Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU); Centro de Innovación en Química Avanzada (ORFEO-CINQA); Manuel Lardizabal Ibilbidea 3 20018 San Sebastián/Donostia Spain
| | - Fernando P. Cossío
- Department of Organic Chemistry I; Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU); Centro de Innovación en Química Avanzada (ORFEO-CINQA); Manuel Lardizabal Ibilbidea 3 20018 San Sebastián/Donostia Spain
- Donostia International Physics Center (DIPC); Manuel Lardizabal Ibilbidea 4 20018 San Sebastián/Donostia Spain
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19
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Proshlyakov DA, McCracken J, Hausinger RP. Spectroscopic analyses of 2-oxoglutarate-dependent oxygenases: TauD as a case study. J Biol Inorg Chem 2016; 22:367-379. [PMID: 27812832 DOI: 10.1007/s00775-016-1406-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/25/2016] [Indexed: 11/28/2022]
Abstract
A wide range of spectroscopic approaches have been used to interrogate the mononuclear iron metallocenter in 2-oxoglutarate (2OG)-dependent oxygenases. The results from these spectroscopic studies have provided valuable insights into the structural changes at the active site during substrate binding and catalysis, thus providing critical information that complements investigations of these enzymes by X-ray crystallography, biochemical, and computational approaches. This mini-review highlights taurine hydroxylase (taurine:2OG dioxygenase, TauD) as a case study to illustrate the wealth of knowledge that can be generated by applying a diverse array of spectroscopic investigations to a single enzyme. In particular, electronic absorption, circular dichroism, magnetic circular dichroism, conventional and pulse electron paramagnetic, Mössbauer, X-ray absorption, and resonance Raman methods have been exploited to uncover the properties of the metal site in TauD.
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Affiliation(s)
- Denis A Proshlyakov
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - John McCracken
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Robert P Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA. .,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
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20
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Pati SG, Bolotin J, Brennwald MS, Kohler HPE, Werner RA, Hofstetter TB. Measurement of oxygen isotope ratios ((18)O/(16)O) of aqueous O2 in small samples by gas chromatography/isotope ratio mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:684-690. [PMID: 26864520 DOI: 10.1002/rcm.7481] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/11/2015] [Accepted: 12/12/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE Oxygen isotope fractionation of molecular O2 is an important process for the study of aerobic metabolism, photosynthesis, and formation of reactive oxygen species. The latter is of particular interest for investigating the mechanism of enzyme-catalyzed reactions, such as the oxygenation of organic pollutants, which is an important detoxification mechanism. METHODS We developed a simple method to measure the δ(18) O values of dissolved O2 in small samples using automated split injection for gas chromatography coupled to isotope ratio mass spectrometry (GC/IRMS). After creating a N2 headspace, the dissolved O2 partitions from aqueous solution to the headspace, from which it can be injected into the gas chromatograph. RESULTS In aqueous samples of 10 mL and in diluted air samples, we quantified the δ(18) O values at O2 concentrations of 16 μM and 86 μM, respectively. The chromatographic separation of O2 and N2 with a molecular sieve column made it possible to use N2 as the headspace gas for the extraction of dissolved O2 from water. We were therefore able to apply a rigorous δ(18) O blank correction for the quantification of (18) O/(16) O ratios in 20 nmol of injected O2 . CONCLUSIONS The successful quantification of (18) O-kinetic isotope effects associated with enzymatic and chemical reduction of dissolved O2 illustrates how the proposed method can be applied for studying enzymatic O2 activation mechanisms in a variety of (bio)chemical processes.
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Affiliation(s)
- Sarah G Pati
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600, Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, CH-8092, Zürich, Switzerland
| | - Jakov Bolotin
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600, Dübendorf, Switzerland
| | - Matthias S Brennwald
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600, Dübendorf, Switzerland
| | - Hans-Peter E Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600, Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, CH-8092, Zürich, Switzerland
| | - Roland A Werner
- Institute of Agricultural Sciences, ETH Zürich, CH-8092, Zürich, Switzerland
| | - Thomas B Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600, Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, CH-8092, Zürich, Switzerland
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21
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Watson AJB, Frost JR. Highlights from the 51st EUCHEM conference on stereochemistry, Bürgenstock, Switzerland, May 2016. Chem Commun (Camb) 2016; 52:9173-7. [DOI: 10.1039/c6cc90302a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
On Sunday 1st May 2016, 104 chemists made their way to the picturesque town of Brunnen, located on the banks of the Vierwalstättersee (Lake Lucerne) to participate in the 51st EUCHEM conference on stereochemistry.
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Affiliation(s)
- Allan J. B. Watson
- Department of Pure and Applied Chemistry
- WestCHEM
- University of Strathclyde
- Glasgow
- UK
| | - James R. Frost
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- UK
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22
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Zhu H, Peck SC, Bonnot F, van der Donk WA, Klinman JP. Oxygen-18 Kinetic Isotope Effects of Nonheme Iron Enzymes HEPD and MPnS Support Iron(III) Superoxide as the Hydrogen Abstraction Species. J Am Chem Soc 2015; 137:10448-51. [PMID: 26267117 PMCID: PMC4970508 DOI: 10.1021/jacs.5b03907] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Nonheme
iron oxygenases that carry out four-electron oxidations
of substrate have been proposed to employ iron(III) superoxide species
to initiate this reaction [Paria, S.; Que, L.; Paine, T. K. Angew. Chem. Int. Ed.2011, 50, 11129]. Here we report experimental evidence in support of this
proposal. 18O KIEs were measured for two recently discovered
mononuclear nonheme iron oxygenases: hydroxyethylphosphonate dioxygenase
(HEPD) and methylphosphonate synthase (MPnS). Competitive 18O KIEs measured with deuterated substrates are larger than those
measured with unlabeled substrates, which indicates that C–H
cleavage must occur before an irreversible reductive step at molecular
oxygen. A similar observation was previously used to implicate copper(II)
superoxide in the H-abstraction reactions catalyzed by dopamine β-monooxygenase
[Tian, G. C.; Klinman, J. P. J. Am. Chem. Soc.1993, 115, 8891] and peptidylglycine α-hydroxylating
monooxygenase [Francisco, W. A.; Blackburn, N. J.; Klinman, J. P. Biochemistry2003, 42, 1813].
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Affiliation(s)
| | - Spencer C Peck
- Howard Hughes Medical Institute and Department of Chemistry, 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
| | | | - Wilfred A van der Donk
- Howard Hughes Medical Institute and Department of Chemistry, 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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23
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Hangasky JA, Gandhi H, Valliere MA, Ostrom NE, Knapp MJ. The rate-limiting step of O2 activation in the α-ketoglutarate oxygenase factor inhibiting hypoxia inducible factor. Biochemistry 2014; 53:8077-84. [PMID: 25423620 PMCID: PMC4283935 DOI: 10.1021/bi501246v] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
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Factor
inhibiting HIF (FIH) is a cellular O2-sensing enzyme, which
hydroxylates the hypoxia inducible factor-1α. Previously reported
inverse solvent kinetic isotope effects indicated that FIH limits
its overall turnover through an O2 activation step (HangaskyJ. A., SabanE.,
and KnappM. J. (2013) Biochemistry52, 1594−160223351038). Here we characterize the rate-limiting step for O2 activation by FIH using a suite of mechanistic probes on
the second order rate constant kcat/KM(O2). Steady-state kinetics showed
that the rate constant for O2 activation was slow (kcat/KM(O2)app = 3500 M–1 s–1) compared with other non-heme iron oxygenases,
and solvent viscosity assays further excluded diffusional encounter
with O2 from being rate limiting on kcat/KM(O2). Competitive
oxygen-18 kinetic isotope effect measurements (18kcat/KM(O2) = 1.0114(5)) indicated that the transition state for O2 activation resembled a cyclic peroxohemiketal, which precedes the
formation of the ferryl intermediate observed in related enzymes.
We interpret this data to indicate that FIH limits its overall activity
at the point of the nucleophilic attack of Fe-bound O2— on the C-2 carbon of αKG. Overall, these results
show that FIH follows the consensus mechanism for αKG oxygenases,
suggesting that FIH may be an ideal enzyme to directly access steps
involved in O2 activation among the broad family of αKG
oxygenases.
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Affiliation(s)
- John A Hangasky
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
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24
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Microbial biosynthesis of medium-chain 1-alkenes by a nonheme iron oxidase. Proc Natl Acad Sci U S A 2014; 111:18237-42. [PMID: 25489112 DOI: 10.1073/pnas.1419701112] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Aliphatic medium-chain 1-alkenes (MCAEs, ∼10 carbons) are "drop-in" compatible next-generation fuels and precursors to commodity chemicals. Mass production of MCAEs from renewable resources holds promise for mitigating dependence on fossil hydrocarbons. An MCAE, such as 1-undecene, is naturally produced by Pseudomonas as a semivolatile metabolite through an unknown biosynthetic pathway. We describe here the discovery of a single gene conserved in Pseudomonas responsible for 1-undecene biosynthesis. The encoded enzyme is able to convert medium-chain fatty acids (C10-C14) into their corresponding terminal olefins using an oxygen-activating, nonheme iron-dependent mechanism. Both biochemical and X-ray crystal structural analyses suggest an unusual mechanism of β-hydrogen abstraction during fatty acid substrate activation. Our discovery unveils previously unidentified chemistry in the nonheme Fe(II) enzyme family, provides an opportunity to explore the biology of 1-undecene in Pseudomonas, and paves the way for tailored bioconversion of renewable raw materials to MCAE-based biofuels and chemical commodities.
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25
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Hangasky JA, Ivison GT, Knapp MJ. Substrate positioning by Gln(239) stimulates turnover in factor inhibiting HIF, an αKG-dependent hydroxylase. Biochemistry 2014; 53:5750-8. [PMID: 25119663 PMCID: PMC4165446 DOI: 10.1021/bi500703s] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Nonheme Fe(II)/αKG-dependent
oxygenases catalyze diverse
reactions, typically inserting an O atom from O2 into a
C–H bond. Although the key to their catalytic cycle is the
fact that binding and positioning of primary substrate precede O2 activation, the means by which substrate binding stimulates
turnover is not well understood. Factor Inhibiting HIF (FIH) is a
Fe(II)/αKG-dependent oxygenase that acts as a cellular oxygen
sensor in humans by hydroxylating the target residue Asn803, found in the C-terminal transactivation domain (CTAD) of hypoxia
inducible factor-1. FIH-Gln239 makes two hydrogen bonds
with CTAD-Asn803, positioning this target residue over
the Fe(II). We hypothesized the positioning of the side chain of CTAD-Asn803 by FIH-Gln239 was critical for stimulating O2 activation and subsequent substrate hydroxylation. The steady-state
characterization of five FIH-Gln239 variants (Ala, Asn,
Glu, His, and Leu) tested the role of hydrogen bonding potential and
sterics near the target residue. Each variant exhibited a 20–1200-fold
decrease in kcat and kcat/KM(CTAD), but no change
in KM(CTAD), indicating that the step
after CTAD binding was affected by point mutation. Uncoupled O2 activation was prominent in these variants, as shown by large
coupling ratios (C = [succinate]/[CTAD-OH] = 3–5)
for each of the FIH-Gln239 → X variants. The coupling
ratios decreased in D2O, indicating an isotope-sensitive
inactivation for variants, not observed in the wild type. The data
presented indicate that the proper positioning of CTAD-Asn803 by FIH-Gln239 is necessary to suppress uncoupled turnover
and to support substrate hydroxylation, suggesting substrate positioning
may be crucial for directing O2 reactivity within the broader
class of αKG hydroxylases.
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Affiliation(s)
- John A Hangasky
- Department of Chemistry, University of Massachusetts at Amherst , Amherst, Massachusetts 01003, United States
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26
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Cheah MH, Millar AH, Myers RC, Day DA, Roth J, Hillier W, Badger MR. Online oxygen kinetic isotope effects using membrane inlet mass spectrometry can differentiate between oxidases for mechanistic studies and calculation of their contributions to oxygen consumption in whole tissues. Anal Chem 2014; 86:5171-8. [PMID: 24786640 DOI: 10.1021/ac501086n] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The reduction chemistry of molecular oxygen underpins the energy metabolism of multicellular organisms, liberating free energy needed to catalyze a plethora of enzymatic reactions. Measuring the isotope signatures of (16)O and (18)O during O2 reduction can provide insights into both kinetic and equilibrium isotope effects. However, current methods to measure O2 isotope signatures are time-consuming and disruptive. This paper describes the application of membrane inlet mass spectrometry to determine the oxygen isotope discrimination of a range of O2-consuming reactions, providing a rapid and convenient method for determining these values. A survey of oxygenase and oxidase reactions provides new insights into previously uncharacterized amino acid oxidase enzymes. Liquid and gas phase measurements show the ease of assays using this approach for purified enzymes, biological extracts and intact tissues.
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Affiliation(s)
- Mun Hon Cheah
- Division of Plant Science, Research School of Biology, the Australian National University , Canberra ACT 0200, Australia
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27
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Klinman JP. The power of integrating kinetic isotope effects into the formalism of the Michaelis-Menten equation. FEBS J 2013; 281:489-97. [PMID: 23937475 DOI: 10.1111/febs.12477] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 07/25/2013] [Accepted: 07/29/2013] [Indexed: 11/29/2022]
Abstract
The final arbiter of enzyme mechanism is the ability to establish and test a kinetic mechanism. Isotope effects play a major role in expanding the scope and insight derived from the Michaelis-Menten equation. The integration of isotope effects into the formalism of the Michaelis-Menten equation began in the 1970s and has continued until the present. This review discusses a family of eukaryotic copper proteins, including dopamine β-monooxygenase, tyramine β-monooxygenase and peptidylglycine α-amidating enzyme, which are responsible for the synthesis of neuroactive compounds, norepinephrine, octopamine and C-terminally carboxamidated peptides, respectively. The review highlights the results of studies showing how combining kinetic isotope effects with initial rate parameters permits the evaluation of: (a) the order of substrate binding to multisubstrate enzymes; (b) the magnitude of individual rate constants in complex, multistep reactions; (c) the identification of chemical intermediates; and (d) the role of nonclassical (tunnelling) behaviour in C-H activation.
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Affiliation(s)
- Judith P Klinman
- Departments of Chemistry and Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
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28
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Affiliation(s)
- Katarzyna Swiderek
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology , Zeromskiego 116, 90-924 Lodz, Poland
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29
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Chang WC, Mansoorabadi SO, Liu HW. Reaction of HppE with substrate analogues: evidence for carbon-phosphorus bond cleavage by a carbocation rearrangement. J Am Chem Soc 2013; 135:8153-6. [PMID: 23672451 DOI: 10.1021/ja403441x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
(S)-2-hydroxypropylphosphonic acid ((S)-2-HPP) epoxidase (HppE) is an unusual mononuclear non-heme iron enzyme that catalyzes the oxidative epoxidation of (S)-2-HPP in the biosynthesis of the antibiotic fosfomycin. Recently, HppE has been shown to accept (R)-1-hydroxypropylphosphonic acid as a substrate and convert it to an aldehyde product in a reaction involving a biologically unprecedented 1,2-phosphono migration. In this study, a series of substrate analogues were designed, synthesized, and used as mechanistic probes to study this novel enzymatic transformation. The resulting data, together with insights obtained from density functional theory calculations, are consistent with a mechanism of HppE-catalyzed phosphono group migration that involves the formation of a carbocation intermediate. As such, this reaction represents a new paradigm for biological C-P bond cleavage.
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Affiliation(s)
- Wei-chen Chang
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin , Austin, Texas 78712, United States
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30
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Mechanistic studies of an unprecedented enzyme-catalysed 1,2-phosphono-migration reaction. Nature 2013; 496:114-8. [PMID: 23552950 PMCID: PMC3725809 DOI: 10.1038/nature11998] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 02/08/2013] [Indexed: 01/10/2023]
Abstract
(S)-2-Hydroxypropylphosphonate ((S)-2-HPP) epoxidase (HppE) is a mononuclear non-heme iron-dependent enzyme1,2,3 responsible for the last step in the biosynthesis of the clinically useful antibiotic fosfomycin4. Enzymes of this class typically catalyze oxygenation reactions that proceed via the formation of substrate radical intermediates. In contrast, HppE catalyzes an unusual dehydrogenation reaction while converting the secondary alcohol of (S)-2-HPP to the epoxide ring of fosfomycin1,5. HppE is shown here to also catalyze a biologically unprecedented 1,2-phosphono migration with the alternative substrate (R)-1-HPP. This transformation likely involves an intermediary carbocation based on observations with additional substrate analogues, such as (1R)-1-hydroxy-2-aminopropylphosphonate, and model reactions for both radical- and carbocation-mediated migration. The ability of HppE to catalyze distinct reactions depending on the regio- and stereochemical properties of the substrate is given a structural basis using X-ray crystallography. These results provide compelling evidence for the formation of a substrate-derived cation intermediate in the catalytic cycle of a mononuclear non-heme iron-dependent enzyme. The underlying chemistry of this unusual phosphono migration may represent a new paradigm for the in vivo construction of phosphonate-containing natural products that can be exploited for the preparation of novel phosphonate derivatives.
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31
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Liu Y, Mukherjee A, Nahumi N, Ozbil M, Brown D, Angeles-Boza AM, Dooley DM, Prabhakar R, Roth JP. Experimental and Computational Evidence of Metal-O2 Activation and Rate-Limiting Proton-Coupled Electron Transfer in a Copper Amine Oxidase. J Phys Chem B 2012; 117:218-29. [DOI: 10.1021/jp3121484] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yi Liu
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
| | - Arnab Mukherjee
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
| | - Nadav Nahumi
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
| | - Mehmet Ozbil
- Department of Chemistry, University of Miami, 1301 Memorial Drive,
Coral Gables, Florida 33146, United States
| | - Doreen Brown
- Department of Chemistry
and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Alfredo M. Angeles-Boza
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
| | - David M. Dooley
- Department of Chemistry
and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, 1301 Memorial Drive,
Coral Gables, Florida 33146, United States
| | - Justine P. Roth
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
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32
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Miłaczewska A, Broclawik E, Borowski T. On the Catalytic Mechanism of (S)-2-Hydroxypropylphosphonic Acid Epoxidase (HppE): A Hybrid DFT Study. Chemistry 2012; 19:771-81. [DOI: 10.1002/chem.201202825] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Indexed: 11/10/2022]
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33
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Huang H, Chang WC, Pai PJ, Romo A, Mansoorabadi SO, Russell DH, Liu HW. Evidence for radical-mediated catalysis by HppE: a study using cyclopropyl and methylenecyclopropyl substrate analogues. J Am Chem Soc 2012; 134:16171-4. [PMID: 23006053 PMCID: PMC3463719 DOI: 10.1021/ja3078126] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
(S)-2-Hydroxypropylphosphonic acid epoxidase (HppE) is an unusual mononuclear iron enzyme that catalyzes the oxidative epoxidation of (S)-2-hydroxypropylphosphonic acid ((S)-HPP) in the biosynthesis of the antibiotic fosfomycin. HppE also recognizes (R)-2-hydroxypropylphosphonic acid ((R)-HPP) as a substrate and converts it to 2-oxo-propylphosphonic acid. To probe the mechanisms of these HppE-catalyzed oxidations, cyclopropyl- and methylenecyclopropyl-containing compounds were synthesized and studied as radical clock substrate analogues. Enzymatic assays indicated that the (S)- and (R)-isomers of the cyclopropyl-containing analogues were efficiently converted to epoxide and ketone products by HppE, respectively. In contrast, the ultrafast methylenecyclopropyl-containing probe inactivated HppE, consistent with a rapid radical-triggered ring-opening process that leads to enzyme inactivation. Taken together, these findings provide, for the first time, experimental evidence for the involvement of a C2-centered radical intermediate with a lifetime on the order of nanoseconds in the HppE-catalyzed oxidation of (R)-HPP.
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Affiliation(s)
- Hui Huang
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Wei-chen Chang
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Pei-Jing Pai
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Anthony Romo
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Steven O. Mansoorabadi
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Hung-wen Liu
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
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34
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Cooke HA, Peck SC, Evans BS, van der Donk WA. Mechanistic investigation of methylphosphonate synthase, a non-heme iron-dependent oxygenase. J Am Chem Soc 2012; 134:15660-3. [PMID: 22957470 PMCID: PMC3458437 DOI: 10.1021/ja306777w] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Methylphosphonate synthase is a non-heme iron-dependent
oxygenase
that converts 2-hydroxyethylphosphonate (2-HEP) to methylphosphonate.
On the basis of experiments with two enantiomers of a substrate analog,
2-hydroxypropylphosphonate, catalysis is proposed to commence with
stereospecific abstraction of the pro-S hydrogen
on C2 of the substrate. Experiments with isotopologues of 2-HEP indicate
stereospecific hydrogen transfer of the pro-R hydrogen
at C2 of the substrate to the methyl group of methylphosphonate. Kinetic
studies with these substrate isotopologues reveal that neither hydrogen
transfer is rate limiting under saturating substrate conditions. A
mechanism is proposed that is consistent with the available data.
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Affiliation(s)
- Heather A Cooke
- Howard Hughes Medical Institute and Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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35
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Ye S, Riplinger C, Hansen A, Krebs C, Bollinger JM, Neese F. Electronic structure analysis of the oxygen-activation mechanism by Fe(II)- and α-ketoglutarate (αKG)-dependent dioxygenases. Chemistry 2012; 18:6555-67. [PMID: 22511515 PMCID: PMC3955955 DOI: 10.1002/chem.201102829] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Indexed: 11/09/2022]
Abstract
α-Ketoglutarate (αKG)-dependent nonheme iron enzymes utilize a high-spin (HS) ferrous center to couple the activation of oxygen to the decarboxylation of the cosubstrate αKG to yield succinate and CO(2), and to generate a high-valent ferryl species that then acts as an oxidant to functionalize the target C-H bond. Herein a detailed analysis of the electronic-structure changes that occur in the oxygen activation by this enzyme was performed. The rate-limiting step, which is identical on the septet and quintet surfaces, is the nucleophilic attack of the distal O atom of the O(2) adduct on the carbonyl group in αKG through a bicyclic transition state ((5, 7) TS1). Due to the different electronic structures in (5, 7) TS1, the decay of (7)TS1 leads to a ferric oxyl species, which undergoes a rapid intersystem crossing to form the ferryl intermediate. By contrast, a HS ferrous center ligated by a peroxosuccinate is obtained on the quintet surface following (5)TS1. Thus, additional two single-electron transfer steps are required to afford the same Fe(IV)-oxo species. However, the triplet reaction channel is catalytically irrelevant. The biological role of αKG played in the oxygen-activation reaction is dual. The αKG LUMO (C=O π*) serves as an electron acceptor for the nucleophilic attack of the superoxide monoanion. On the other hand, the αKG HOMO (C1-C2 σ) provides the second and third electrons for the further reduction of the superoxide. In addition to density functional theory, high-level ab initio calculations have been used to calculate the accurate energies of the critical points on the alternative potential-energy surfaces. Overall, the results delivered by the ab initio calculations are largely parallel to those obtained with the B3LYP density functional, thus lending credence to our conclusions.
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Affiliation(s)
- Shengfa Ye
- Max-Plank Institute for Bioinorganic Chemistry Stiftstrasse 34–36 45470 Mülheim an der Ruhr (Germany)
| | - Christoph Riplinger
- Max-Plank Institute for Bioinorganic Chemistry Stiftstrasse 34–36 45470 Mülheim an der Ruhr (Germany)
| | - Andreas Hansen
- Max-Plank Institute for Bioinorganic Chemistry Stiftstrasse 34–36 45470 Mülheim an der Ruhr (Germany)
| | - Carsten Krebs
- Department of Chemistry Department of Biochemistry and Molecular Biology The Pennsylvania State University University Park, Pennsylvania 16802 (USA)
| | - J. Martin Bollinger
- Department of Chemistry Department of Biochemistry and Molecular Biology The Pennsylvania State University University Park, Pennsylvania 16802 (USA)
| | - Frank Neese
- Max-Plank Institute for Bioinorganic Chemistry Stiftstrasse 34–36 45470 Mülheim an der Ruhr (Germany)
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36
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Thibodeaux CJ, Chang WC, Liu HW. Enzymatic chemistry of cyclopropane, epoxide, and aziridine biosynthesis. Chem Rev 2012; 112:1681-709. [PMID: 22017381 PMCID: PMC3288687 DOI: 10.1021/cr200073d] [Citation(s) in RCA: 204] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Wei-chen Chang
- College of Pharmacy and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
| | - Hung-wen Liu
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
- College of Pharmacy and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
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37
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Chen H, Cho KB, Lai W, Nam W, Shaik S. Dioxygen Activation by a Non-Heme Iron(II) Complex: Theoretical Study toward Understanding Ferric–Superoxo Complexes. J Chem Theory Comput 2012; 8:915-26. [DOI: 10.1021/ct300015y] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Hui Chen
- Beijing National Laboratory for Molecular
Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute
of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
| | - Kyung-Bin Cho
- Department of Bioinspired Science, Department of Chemistry
and Nano Science, Ewha Womans University, Seoul, 120-750, Korea
| | - Wenzhen Lai
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
- Department of Chemistry, Renmin University of China, Beijing, 100872, China
| | - Wonwoo Nam
- Department of Bioinspired Science, Department of Chemistry
and Nano Science, Ewha Womans University, Seoul, 120-750, Korea
| | - Sason Shaik
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
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38
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Huff GS, Doncheva IS, Brinkley DW, Angeles-Boza AM, Mukherjee A, Cramer CJ, Roth JP. Experimental and Computational Investigations of Oxygen Reactivity in a Heme and Tyrosyl Radical-Containing Fatty Acid α-(Di)oxygenase. Biochemistry 2011; 50:7375-89. [DOI: 10.1021/bi201016h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Gregory S. Huff
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - Irina S. Doncheva
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - David W. Brinkley
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - Alfredo M. Angeles-Boza
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - Arnab Mukherjee
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
| | - Christopher J. Cramer
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis,
Minnesota 55455, United States
| | - Justine P. Roth
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street
Baltimore, Maryland 21218, United States
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Yun D, Dey M, Higgins LJ, Yan F, Liu HW, Drennan CL. Structural basis of regiospecificity of a mononuclear iron enzyme in antibiotic fosfomycin biosynthesis. J Am Chem Soc 2011; 133:11262-9. [PMID: 21682308 PMCID: PMC3140168 DOI: 10.1021/ja2025728] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydroxypropylphosphonic acid epoxidase (HppE) is an unusual mononuclear iron enzyme that uses dioxygen to catalyze the oxidative epoxidation of (S)-2-hydroxypropylphosphonic acid (S-HPP) in the biosynthesis of the antibiotic fosfomycin. Additionally, the enzyme converts the R-enantiomer of the substrate (R-HPP) to 2-oxo-propylphosphonic acid. To probe the mechanism of HppE regiospecificity, we determined three X-ray structures: R-HPP with inert cobalt-containing enzyme (Co(II)-HppE) at 2.1 Å resolution; R-HPP with active iron-containing enzyme (Fe(II)-HppE) at 3.0 Å resolution; and S-HPP-Fe(II)-HppE in complex with dioxygen mimic NO at 2.9 Å resolution. These structures, along with previously determined structures of S-HPP-HppE, identify the dioxygen binding site on iron and elegantly illustrate how HppE is able to recognize both substrate enantiomers to catalyze two completely distinct reactions.
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Affiliation(s)
- Danny Yun
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Sydor PK, Barry SM, Odulate OM, Barona-Gomez F, Haynes SW, Corre C, Song L, Challis GL. Regio- and stereodivergent antibiotic oxidative carbocyclizations catalysed by Rieske oxygenase-like enzymes. Nat Chem 2011; 3:388-92. [PMID: 21505498 PMCID: PMC3085852 DOI: 10.1038/nchem.1024] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 03/07/2011] [Indexed: 11/16/2022]
Abstract
Oxidative cyclizations, exemplified by the biosynthetic assembly of the penicillin nucleus from a tripeptide precursor, are arguably the most synthetically-powerful implementation of C-H activation reactions in Nature. Here we show that Rieske oxygenase-like enzymes mediate regio and stereodivergent oxidative cyclizations to form 10- and 12-membered carbocyclic rings in the key steps of the biosynthesis of the antibiotics streptorubin B and metacycloprodigiosin, respectively. These reactions represent the first examples of oxidative carbocyclizations catalyzed by non-heme iron-dependent oxidases and define a novel type of catalytic activity for Rieske enzymes. A better understanding of how these enzymes achieve such remarkable regio and stereocontrol in the functionalization of unactivated hydrocarbon chains will greatly facilitate the development of selective manmade C-H activation catalysts.
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Affiliation(s)
- Paulina K Sydor
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
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41
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Rose NR, McDonough MA, King ONF, Kawamura A, Schofield CJ. Inhibition of 2-oxoglutarate dependent oxygenases. Chem Soc Rev 2011; 40:4364-97. [PMID: 21390379 DOI: 10.1039/c0cs00203h] [Citation(s) in RCA: 307] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
2-Oxoglutarate (2OG) dependent oxygenases are ubiquitous iron enzymes that couple substrate oxidation to the conversion of 2OG to succinate and carbon dioxide. In humans their roles include collagen biosynthesis, fatty acid metabolism, DNA repair, RNA and chromatin modifications, and hypoxic sensing. Commercial applications of 2OG oxygenase inhibitors began with plant growth retardants, and now extend to a clinically used pharmaceutical compound for cardioprotection. Several 2OG oxygenases are now being targeted for therapeutic intervention for diseases including anaemia, inflammation and cancer. In this critical review, we describe studies on the inhibition of 2OG oxygenases, focusing on small molecules, and discuss the potential of 2OG oxygenases as therapeutic targets (295 references).
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Affiliation(s)
- Nathan R Rose
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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Nair SK, van der Donk WA. Structure and mechanism of enzymes involved in biosynthesis and breakdown of the phosphonates fosfomycin, dehydrophos, and phosphinothricin. Arch Biochem Biophys 2011; 505:13-21. [PMID: 20854789 PMCID: PMC3040005 DOI: 10.1016/j.abb.2010.09.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 09/11/2010] [Accepted: 09/14/2010] [Indexed: 11/28/2022]
Abstract
Recent years have seen a rapid increase in the mechanistic and structural information on enzymes that are involved in the biosynthesis and breakdown of naturally occurring phosphonates. This review focuses on these recent developments with an emphasis on those enzymes that have been characterized crystallographically in the past five years, including proteins involved in the biosynthesis of phosphinothricin, fosfomycin, and dehydrophos and proteins involved in resistance mechanisms.
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Affiliation(s)
- Satish K Nair
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
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van der Donk WA, Krebs C, Bollinger JM. Substrate activation by iron superoxo intermediates. Curr Opin Struct Biol 2010; 20:673-83. [PMID: 20951572 PMCID: PMC3030196 DOI: 10.1016/j.sbi.2010.08.005] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 08/21/2010] [Indexed: 11/17/2022]
Abstract
A growing number of non-heme-iron oxygenases and oxidases catalyze reactions for which the well-established mechanistic paradigm involving a single C-H-bond-cleaving intermediate of the Fe(IV)-oxo (ferryl) type [1(•)] is insufficient to explain the chemistry. It is becoming clear that, in several of these cases, Fe(III)-superoxide complexes formed by simple addition of O(2) to the reduced [Fe(II)] cofactor initiate substrate oxidation by abstracting hydrogen [2,3(•)]. This substrate-oxidizing entry route into high-valent-iron intermediates makes possible an array of complex and elegant oxidation reactions without the consumption of valuable reducing equivalents. Examples of this novel mechanistic strategy are discussed with the goal of bringing forth unifying principles.
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Affiliation(s)
- Wilfred A. van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, USA,
| | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Penn State University, 332 Chemistry Building, University Park, PA, 16802, USA,
| | - J. Martin Bollinger
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Penn State University, 336 Chemistry Building, University Park, PA, 16802, USA,
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Hirao H, Morokuma K. Ferric Superoxide and Ferric Hydroxide Are Used in the Catalytic Mechanism of Hydroxyethylphosphonate Dioxygenase: A Density Functional Theory Investigation. J Am Chem Soc 2010; 132:17901-9. [DOI: 10.1021/ja108174d] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hajime Hirao
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan, and Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan, and Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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Ashley DC, Brinkley DW, Roth JP. Oxygen Isotope Effects as Structural and Mechanistic Probes in Inorganic Oxidation Chemistry. Inorg Chem 2010; 49:3661-75. [DOI: 10.1021/ic901778g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Daniel C. Ashley
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
| | - David W. Brinkley
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
| | - Justine P. Roth
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
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Modular behavior of tauD provides insight into the origin of specificity in alpha-ketoglutarate-dependent nonheme iron oxygenases. Proc Natl Acad Sci U S A 2009; 106:19791-5. [PMID: 19892731 DOI: 10.1073/pnas.0910660106] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Taurine alpha-ketoglutarate dioxygenase (tauD) is one of the best-studied alpha-ketoglutarate (alphaKG)-dependent nonheme iron oxygenases. As with all oxygenases, a fine balance must be struck between generating a species sufficiently reactive for the required chemistry and controlling that species to prevent undesirable side reactions [Klinman JP (2007) Accts Chem Res 40:325-333]. In the case of tauD, the substrate oxidizing species has been shown to be a ferryl-oxo, and the introduction of deuterium at the reactive position of substrate results in an enormous kinetic isotope effect together with a partial uncoupling of oxygen activation from substrate oxidation [Price JC, Barr EW, Glass TE, Krebs C, Bollinger JM (2003) J Am Chem Soc 125:13008-13009]. We have generated a series of site-specific variants at a position that resides directly behind bound substrate (F159 to L, V, A, and G). Decreasing side-chain bulk diminishes the coupling of oxygen activation to C-H cleavage, which is further reduced by substrate deuteration. Despite this impact, oxygen activation remains completely coupled to the oxidative decarboxylation of alphaKG. The concentration of bis-Tris buffer impacts the extent of coupling of oxygen activation to C-H cleavage, implicating the buffer in the uncoupling pathway. These data indicate a critical role for residue 159 in substrate positioning and reaction in tauD and show that minor active-site perturbations in these enzymes could allow for changes in substrate reactivity while maintaining substrate triggering and oxygen binding/activation.
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Roth JP. Oxygen isotope effects as probes of electron transfer mechanisms and structures of activated O2. Acc Chem Res 2009; 42:399-408. [PMID: 19195996 DOI: 10.1021/ar800169z] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Competitively determined oxygen ((18)O) isotope effects can be powerful probes of chemical and biological transformations involving molecular oxygen as well as superoxide and hydrogen peroxide. They play a complementary role to crystallography and spectroscopy in the study of activated oxygen intermediates by forging a link between electronic/vibrational structure and the bonding that occurs within ground and transition states along the reaction coordinate. Such analyses can be used to assess the plausibility of intermediates and their catalytic relevance in oxidative processes. This Account describes efforts to advance oxygen kinetic isotope effects ((18)O KIEs) and equilibrium isotope effects ((18)O EIEs) as mechanistic probes of reactive, oxygen-derived species. We focus primarily on transition metal mediated oxidations, outlining both advances over the past five years and current limitations of this approach. Computational methods are now being developed to probe transition states and the accompanying kinetic isotope effects. In particular, we describe the importance of using a full-frequency model to accurately predict the magnitudes as well as the temperature dependence of the isotope effects. Earlier studies have used a "cut-off model," which employs only a few isotopic vibrational modes, and such models tend to overestimate (18)O EIEs. Researchers in mechanistic biological inorganic chemistry would like to differentiate "inner-sphere" from "outer-sphere" reactivity of O(2), a designation that describes the extent of the bonding interaction between metal and oxygen in the transition state. Though this problem remains unsolved, we expect that this isotopic approach will help differentiate these processes. For example, comparisons of (18)O KIEs to (18)O EIEs provide benchmarks that allow us to calibrate computationally derived reaction coordinates. Once the physical origins of heavy atom isotope effects are better understood, researchers will be able to apply the competitive isotope fractionation technique to a wide range of pressing problems in small molecule chemistry and biochemistry.
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Affiliation(s)
- Justine P. Roth
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
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49
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Smirnov VV, Lanci MP, Roth JP. Computational Modeling of Oxygen Isotope Effects on Metal-Mediated O2 Activation at Varying Temperatures. J Phys Chem A 2009; 113:1934-45. [DOI: 10.1021/jp807796c] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Valeriy V. Smirnov
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
| | - Michael P. Lanci
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
| | - Justine P. Roth
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
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