1
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Smith-Díaz C, Das AB, Jurkowski TP, Hore TA, Vissers MCM. Exploring the Ascorbate Requirement of the 2-Oxoglutarate-Dependent Dioxygenases. J Med Chem 2025; 68:2219-2237. [PMID: 39883951 PMCID: PMC11831678 DOI: 10.1021/acs.jmedchem.4c02342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2024] [Revised: 11/20/2024] [Accepted: 01/16/2025] [Indexed: 02/01/2025]
Abstract
In humans, the 2-oxoglutarate-dependent dioxygenases (2-OGDDs) catalyze hydroxylation reactions involved in cell metabolism, the biosynthesis of small molecules, DNA and RNA demethylation, the hypoxic response and the formation of collagen. The reaction is catalyzed by a highly oxidizing ferryl-oxo species produced when the active site non-heme iron engages molecular oxygen. Enzyme activity is specifically stimulated by l-ascorbic acid (ascorbate, vitamin C), an effect not well mimicked by other reducing agents. In this perspective article we discuss the reliance of the 2-OGDDs on ascorbate availability. We draw upon findings from studies with different 2-OGDDs to piece together a comprehensive theory for the specific role of ascorbate in supporting enzyme activity. Our discussion centers on the capacity for ascorbate to act as an efficient radical scavenger and its propensity to reduce and chelate transition metals. In addition, we consider the evidence supporting stereospecific binding of ascorbate in the enzyme active site.
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Affiliation(s)
- Carlos
C. Smith-Díaz
- Ma̅tai
Ha̅ora − Centre for Redox Biology and Medicine, Department
of Biomedical Science and Pathology, University
of Otago, Christchurch, Christchurch 8140, New Zealand
| | - Andrew B. Das
- Ma̅tai
Ha̅ora − Centre for Redox Biology and Medicine, Department
of Biomedical Science and Pathology, University
of Otago, Christchurch, Christchurch 8140, New Zealand
| | - Tomasz P. Jurkowski
- Cardiff
University, School of Biosciences, Museum Avenue, CF10 3AX Cardiff, Wales, U.K.
| | - Timothy A. Hore
- Department
of Anatomy, University of Otago, Dunedin 9016, New Zealand
| | - Margreet C. M. Vissers
- Ma̅tai
Ha̅ora − Centre for Redox Biology and Medicine, Department
of Biomedical Science and Pathology, University
of Otago, Christchurch, Christchurch 8140, New Zealand
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2
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Thomas M, Jaber Sathik Rifayee SB, Christov CZ. How Do Variants of Residues in the First Coordination Sphere, Second Coordination Sphere, and Remote Areas Influence the Catalytic Mechanism of Non-Heme Fe(II)/2-Oxoglutarate Dependent Ethylene-Forming Enzyme? ACS Catal 2024; 14:18550-18569. [PMID: 39722885 PMCID: PMC11668244 DOI: 10.1021/acscatal.4c04010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 11/22/2024] [Accepted: 11/25/2024] [Indexed: 12/28/2024]
Abstract
The ethylene-forming enzyme (EFE) is a Fe(II)/2-oxoglutarate (2OG) and l-arginine (l-Arg)-dependent oxygenase that primarily decomposes 2OG into ethylene while also catalyzing l-Arg hydroxylation. While the hydroxylation mechanism in EFE is similar to other Fe(II)/2OG-dependent oxygenases, the formation of ethylene is unique. Various redesign strategies have aimed to increase ethylene production in EFE, but success has been limited, highlighting the need for alternate approaches. It is crucial to incorporate an accurate and comprehensive description of the integrative and multidimensional effects of the protein environment to enhance the redesign strategy in metalloenzymes, particularly in EFE. This involves understanding the role of the second coordination sphere (SCS) and long-range (LR) interacting residues, correlated motions, electronic structure, intrinsic electric field (IntEF), as well as the stabilization of transition states and reaction intermediates. In this study, we employ a molecular dynamics-based quantum mechanics/molecular mechanics approach to examine the integrative effects of the protein environment on reactions catalyzed by EFE variants from the first coordination sphere (FCS, D191E), SCS (A198V and R171A) and LR (E215A). The study uncovers how substitutions at different positions in EFE similarly impact the ethylene-forming reaction while posing distinct effects on the hydroxylation reaction. Results predict the effect of the variants in controlling the 2OG coordination mode in the Fe(II) center. Specifically, the study suggests that D191E uniquely prefers transitioning from an off-line to an in-line 2OG coordination mode before dioxygen binding. However, studies on the 2OG flip in the presence of off-line approaching dioxygen and dioxygen binding in the D191E variant indicate that the 2OG flip might not be feasible in the 5C Fe(II) state. Calculations show the possibility of a hydrogen atom transfer (HAT)-assisted oxygen flip in EFE and its variants (other than D191E). MD simulations elucidate the characteristic dynamic change in the α7 region in the D191E variant that might contribute to its increased hydroxylation reaction. Results indicate the possibility of forming an in-line ferryl from the IM2 (Fe(III)-partial bond intermediate) in the D191E variant. This alternative pathway from IM2 may also exist in WT EFE and other variants, which are yet to be explored. The study also delineates the impact of substitutions on the electronic structure and IntEF. Overall, the calculations support the idea that understanding the integrative and multidimensional effects of the protein environment on the reactions catalyzed by EFE variants provides the basics for improved enzyme redesign protocols of EFE to increase ethylene production. The results of this study will also contribute to the development of alternate redesign strategies for other metalloenzymes.
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Affiliation(s)
- Midhun
George Thomas
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | | | - Christo Z. Christov
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
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3
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Paris JC, Cheung YH, Zhang T, Chang WC, Liu P, Guo Y. New Frontiers in Nonheme Enzymatic Oxyferryl Species. Chembiochem 2024; 25:e202400307. [PMID: 38900645 PMCID: PMC11983317 DOI: 10.1002/cbic.202400307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/13/2024] [Accepted: 06/20/2024] [Indexed: 06/22/2024]
Abstract
Non-heme mononuclear iron dependent (NHM-Fe) enzymes exhibit exceedingly diverse catalytic reactivities. Despite their catalytic versatilities, the mononuclear iron centers in these enzymes show a relatively simple architecture, in which an iron atom is ligated with 2-4 amino acid residues, including histidine, aspartic or glutamic acid. In the past two decades, a common high-valent reactive iron intermediate, the S=2 oxyferryl (Fe(IV)-oxo or Fe(IV)=O) species, has been repeatedly discovered in NHM-Fe enzymes containing a 2-His-Fe or 2-His-1-carboxylate-Fe center. However, for 3-His/4-His-Fe enzymes, no common reactive intermediate has been identified. Recently, we have spectroscopically characterized the first S=1 Fe(IV) intermediate in a 3-His-Fe containing enzyme, OvoA, which catalyzes a novel oxidative carbon-sulfur bond formation. In this review, we summarize the broad reactivities demonstrated by S=2 Fe(IV)-oxo intermediates, the discovery of the first S=1 Fe(IV) intermediate in OvoA and the mechanistic implication of such a discovery, and the intrinsic reactivity differences of the S=2 and the S=1 Fe(IV)-oxo species. Finally, we postulate the possible reasons to utilize an S=1 Fe(IV) species in OvoA and their implications to other 3-His/4-His-Fe enzymes.
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Affiliation(s)
- Jared C. Paris
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA 15213
| | - Yuk Hei Cheung
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215
| | - Tao Zhang
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215
| | - Wei-chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695
| | - Pinghua Liu
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA 15213
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4
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Lindahl PA, Vali SW. Mössbauer-based molecular-level decomposition of the Saccharomyces cerevisiae ironome, and preliminary characterization of isolated nuclei. Metallomics 2022; 14:mfac080. [PMID: 36214417 PMCID: PMC9624242 DOI: 10.1093/mtomcs/mfac080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/23/2022] [Indexed: 11/25/2022]
Abstract
One hundred proteins in Saccharomyces cerevisiae are known to contain iron. These proteins are found mainly in mitochondria, cytosol, nuclei, endoplasmic reticula, and vacuoles. Cells also contain non-proteinaceous low-molecular-mass labile iron pools (LFePs). How each molecular iron species interacts on the cellular or systems' level is underdeveloped as doing so would require considering the entire iron content of the cell-the ironome. In this paper, Mössbauer (MB) spectroscopy was used to probe the ironome of yeast. MB spectra of whole cells and isolated organelles were predicted by summing the spectral contribution of each iron-containing species in the cell. Simulations required input from published proteomics and microscopy data, as well as from previous spectroscopic and redox characterization of individual iron-containing proteins. Composite simulations were compared to experimentally determined spectra. Simulated MB spectra of non-proteinaceous iron pools in the cell were assumed to account for major differences between simulated and experimental spectra of whole cells and isolated mitochondria and vacuoles. Nuclei were predicted to contain ∼30 μM iron, mostly in the form of [Fe4S4] clusters. This was experimentally confirmed by isolating nuclei from 57Fe-enriched cells and obtaining the first MB spectra of the organelle. This study provides the first semi-quantitative estimate of all concentrations of iron-containing proteins and non-proteinaceous species in yeast, as well as a novel approach to spectroscopically characterizing LFePs.
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Affiliation(s)
- Paul A Lindahl
- Department of Chemistry, Texas A&M University, College Station, TX, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station TX, USA
| | - Shaik Waseem Vali
- Department of Chemistry, Texas A&M University, College Station, TX, USA
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5
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Parkinson EI, Lakkis HG, Alwali AA, Metcalf MEM, Modi R, Metcalf WW. An Unusual Oxidative Rearrangement Catalyzed by a Divergent Member of the 2-Oxoglutarate-Dependent Dioxygenase Superfamily during Biosynthesis of Dehydrofosmidomycin. Angew Chem Int Ed Engl 2022; 61:e202206173. [PMID: 35588368 PMCID: PMC9296572 DOI: 10.1002/anie.202206173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Indexed: 12/20/2022]
Abstract
The biosynthesis of the natural product dehydrofosmidomycin involves an unusual transformation in which 2-(trimethylamino)ethylphosphonate is rearranged, desaturated and demethylated by the enzyme DfmD, a divergent member of the 2-oxoglutarate-dependent dioxygenase superfamily. Although other members of this enzyme family catalyze superficially similar transformations, the combination of all three reactions in a single enzyme has not previously been observed. By characterizing the products of in vitro reactions with labeled and unlabeled substrates, we show that DfmD performs this transformation in two steps, with the first involving desaturation of the substrate to form 2-(trimethylamino)vinylphosphonate, and the second involving rearrangement and demethylation to form methyldehydrofosmidomycin. These data reveal significant differences from the desaturation and rearrangement reactions catalyzed by other family members.
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Affiliation(s)
- Elizabeth I. Parkinson
- Institute for Genomic BiologyUniversity of Illinois at Urbana-Champaign1206 W. Gregory Dr.UrbanaIL 61801USA
- Department of ChemistryPurdue UniversityHerbert C. Brown Laboratory of Chemistry, Room 4103E560 Oval Drive, Box 59West LafayetteIN 47907USA
- Department of Medicinal Chemistry and Molecular PharmacologyPurdue UniversityHerbert C. Brown Laboratory of Chemistry, Room 4103E560 Oval Drive, Box 59West LafayetteIN 47907USA
| | - Hani G. Lakkis
- Department of ChemistryPurdue UniversityHerbert C. Brown Laboratory of Chemistry, Room 4103E560 Oval Drive, Box 59West LafayetteIN 47907USA
| | - Amir A. Alwali
- Department of ChemistryPurdue UniversityHerbert C. Brown Laboratory of Chemistry, Room 4103E560 Oval Drive, Box 59West LafayetteIN 47907USA
| | - Mary Elizabeth M. Metcalf
- Institute for Genomic BiologyUniversity of Illinois at Urbana-Champaign1206 W. Gregory Dr.UrbanaIL 61801USA
- Department of MicrobiologyUniversity of Illinois at Urbana-Champaign, B103C&LSL601 S. GoodwinUrbanaIL 61801USA
| | - Ramya Modi
- Department of ChemistryPurdue UniversityHerbert C. Brown Laboratory of Chemistry, Room 4103E560 Oval Drive, Box 59West LafayetteIN 47907USA
| | - William W. Metcalf
- Institute for Genomic BiologyUniversity of Illinois at Urbana-Champaign1206 W. Gregory Dr.UrbanaIL 61801USA
- Department of MicrobiologyUniversity of Illinois at Urbana-Champaign, B103C&LSL601 S. GoodwinUrbanaIL 61801USA
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6
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Parkinson EI, Lakkis HG, Alwali AA, Metcalf MEM, Modi R, Metcalf WW. An Unusual Oxidative Rearrangement Catalyzed by a Divergent Member of the 2‐Oxoglutarate‐Dependent Dioxygenase Superfamily during Biosynthesis of Dehydrofosmidomycin. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | - Ramya Modi
- Purdue University Chemistry UNITED STATES
| | - William W. Metcalf
- University of Illinois Urbana-Champaign Microbiology 601 S. GoodwinB103 CLSL 61801 Urbana UNITED STATES
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7
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Schmidl D, Jonasson NSW, Menke A, Schneider S, Daumann L. Spectroscopic and in vitro investigations of Fe2+/α-Ketoglutarate-dependent enzymes involved in nucleic acid repair and modification. Chembiochem 2022; 23:e202100605. [PMID: 35040547 PMCID: PMC9401043 DOI: 10.1002/cbic.202100605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/14/2022] [Indexed: 11/08/2022]
Abstract
The activation of molecular oxygen for the highly selective functionalization and repair of DNA and RNA nucleobases is achieved by α-ketoglutarate (α-KG)/iron-dependent dioxygenases. Enzymes of special interest are the human homologs AlkBH of Escherichia coli EcAlkB and ten-eleven translocation (TET) enzymes. These enzymes are involved in demethylation or dealkylation of DNA and RNA, although additional physiological functions are continuously being revealed. Given their importance, studying enzyme-substrate interactions, turnover and kinetic parameters is pivotal for the understanding of the mode of action of these enzymes. Diverse analytical methods, including X-ray crystallography, UV/Vis absorption, electron paramagnetic resonance (EPR), circular dichroism (CD) and NMR spectroscopy have been employed to study the changes in the active site and the overall enzyme structure upon substrate, cofactor and inhibitor addition. Several methods are now available to assess activity of these enzymes. By discussing limitations and possibilities of these techniques for EcAlkB, AlkBH and TET we aim to give a comprehensive synopsis from a bioinorganic point of view, addressing researchers from different disciplines working in the highly interdisciplinary and rapidly evolving field of epigenetic processes and DNA/RNA repair and modification.
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Affiliation(s)
- David Schmidl
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Niko S W Jonasson
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Annika Menke
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Sabine Schneider
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Lena Daumann
- Ludwig-Maximilians-Universität München, Department of Chemistry, Butenandtstr. 5-13, 81377, München, GERMANY
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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: 0.5] [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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Hermann L, Mais CN, Czech L, Smits SHJ, Bange G, Bremer E. The ups and downs of ectoine: structural enzymology of a major microbial stress protectant and versatile nutrient. Biol Chem 2021; 401:1443-1468. [PMID: 32755967 DOI: 10.1515/hsz-2020-0223] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/22/2020] [Indexed: 12/13/2022]
Abstract
Ectoine and its derivative 5-hydroxyectoine are compatible solutes and chemical chaperones widely synthesized by Bacteria and some Archaea as cytoprotectants during osmotic stress and high- or low-growth temperature extremes. The function-preserving attributes of ectoines led to numerous biotechnological and biomedical applications and fostered the development of an industrial scale production process. Synthesis of ectoines requires the expenditure of considerable energetic and biosynthetic resources. Hence, microorganisms have developed ways to exploit ectoines as nutrients when they are no longer needed as stress protectants. Here, we summarize our current knowledge on the phylogenomic distribution of ectoine producing and consuming microorganisms. We emphasize the structural enzymology of the pathways underlying ectoine biosynthesis and consumption, an understanding that has been achieved only recently. The synthesis and degradation pathways critically differ in the isomeric form of the key metabolite N-acetyldiaminobutyric acid (ADABA). γ-ADABA serves as preferred substrate for the ectoine synthase, while the α-ADABA isomer is produced by the ectoine hydrolase as an intermediate in catabolism. It can serve as internal inducer for the genetic control of ectoine catabolic genes via the GabR/MocR-type regulator EnuR. Our review highlights the importance of structural enzymology to inspire the mechanistic understanding of metabolic networks at the biological scale.
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Affiliation(s)
- Lucas Hermann
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von Frisch Str. 8, D-35043 Marburg, Germany.,Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology, Karl-von Frisch Str. 10, D-35043 Marburg, Germany
| | - Christopher-Nils Mais
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
| | - Laura Czech
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von Frisch Str. 8, D-35043 Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
| | - Sander H J Smits
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany.,Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von Frisch Str. 8, D-35043 Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
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10
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Wang J, Wang X, Ouyang Q, Liu W, Shan J, Tan H, Li X, Chen G. N-Nitrosation Mechanism Catalyzed by Non-heme Iron-Containing Enzyme SznF Involving Intramolecular Oxidative Rearrangement. Inorg Chem 2021; 60:7719-7731. [PMID: 34004115 DOI: 10.1021/acs.inorgchem.1c00057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The non-heme iron-dependent enzyme SznF catalyzes a critical N-nitrosation step during the N-nitrosourea pharmacophore biosynthesis in streptozotocin. The intramolecular oxidative rearrangement process is known to proceed at the FeII-containing active site in the cupin domain of SznF, but its mechanism has not been elucidated to date. In this study, based on the density functional theory calculations, a unique mechanism was proposed for the N-nitrosation reaction catalyzed by SznF in which a four-electron oxidation process is accomplished through a series of complicated electron transferring between the iron center and substrate to bypass the high-valent FeIV═O species. In the catalytic reaction pathway, the O2 binds to the iron center and attacks on the substrate to form the peroxo bridge intermediate by obtaining two electrons from the substrate exclusively. Then, instead of cleaving the peroxo bridge, the Cε-Nω bond of the substrate is homolytically cleaved first to form a carbocation intermediate, which polarizes the peroxo bridge and promotes its heterolysis. After O-O bond cleavage, the following reaction steps proceed effortlessly so that the N-nitrosation is accomplished without NO exchange among reaction species.
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Affiliation(s)
- Junkai Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xixi Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Qingwen Ouyang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wei Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jiankai Shan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Hongwei Tan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xichen Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Guangju Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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11
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John CW, Swain GM, Hausinger RP, Proshlyakov DA. Strongly Coupled Redox-Linked Conformational Switching at the Active Site of the Non-Heme Iron-Dependent Dioxygenase, TauD. J Phys Chem B 2019; 123:7785-7793. [PMID: 31433947 PMCID: PMC7092797 DOI: 10.1021/acs.jpcb.9b05866] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
2-Oxoglutarate (2OG)-dependent dioxygenases catalyze C-H activation while performing a wide range of chemical transformations. In contrast to their heme analogues, non-heme iron centers afford greater structural flexibility with important implications for their diverse catalytic mechanisms. We characterize an in situ structural model of the putative transient ferric intermediate of 2OG:taurine dioxygenase (TauD) by using a combination of spectroelectrochemical and semiempirical computational methods, demonstrating that the Fe(III/II) transition involves a substantial, fully reversible, redox-linked conformational change at the active site. This rearrangement alters the apparent redox potential of the active site between -127 mV for reduction of the ferric state and +171 mV for oxidation of the ferrous state of the 2OG-Fe-TauD complex. Structural perturbations exhibit limited sensitivity to mediator concentrations and potential pulse duration. Similar changes were observed in the Fe-TauD and taurine-2OG-Fe-TauD complexes, thus attributing the reorganization to the protein moiety rather than the cosubstrates. Redox-difference infrared spectra indicate a reorganization of the protein backbone in addition to the involvement of carboxylate and histidine ligands. Quantitative modeling of the transient redox response using two alternative reaction schemes across a variety of experimental conditions strongly supports the proposal for intrinsic protein reorganization as the origin of the experimental observations.
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Affiliation(s)
- Christopher W. John
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Greg M. Swain
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Robert P. Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Denis A. Proshlyakov
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
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12
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Herr CQ, Macomber L, Kalliri E, Hausinger RP. Glutarate L-2-hydroxylase (CsiD/GlaH) is an archetype Fe(II)/2-oxoglutarate-dependent dioxygenase. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 117:63-90. [PMID: 31564307 DOI: 10.1016/bs.apcsb.2019.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The Escherichia coli gene initially named ygaT is located adjacent to lhgO, encoding L-2-hydroxyglutarate oxidase/dehydrogenase, and the gabDTP gene cluster, utilized for γ-aminobutyric acid (GABA) metabolism. Because this gene is transcribed specifically during periods of carbon starvation, it was renamed csiD for carbon starvation induced. The CsiD protein was structurally characterized and shown to possess a double-stranded ß-helix fold, characteristic of a large family of non-heme Fe(II)- and 2-oxoglutarate (2OG)-dependent oxygenases. Consistent with a role in producing the substrate for LhgO, CsiD was shown to be a glutarate L-2-hydroxylase. We review the kinetic and structural properties of glutarate L-2-hydroxylase from E. coli and other species, and we propose a catalytic mechanism for this archetype 2OG-dependent hydroxylase. Glutarate can be derived from l-lysine within the cell, with the gabDT genes exhibiting expanded reactivities beyond those known for GABA metabolism. The complete CsiD-containing pathway provides a means for the cell to obtain energy from the metabolism of l-lysine during periods of carbon starvation. To reflect the role of this protein in the cell, a renaming of csiD to glaH has been proposed.
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Affiliation(s)
- Caitlyn Q Herr
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Lee Macomber
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Efthalia Kalliri
- Department of Chemistry, Michigan State University, East Lansing, MI, United States
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
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13
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Drummond MJ, Ford CL, Gray DL, Popescu CV, Fout AR. Radical Rebound Hydroxylation Versus H-Atom Transfer in Non-Heme Iron(III)-Hydroxo Complexes: Reactivity and Structural Differentiation. J Am Chem Soc 2019; 141:6639-6650. [PMID: 30969766 DOI: 10.1021/jacs.9b01516] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The characterization of high-valent iron centers in enzymes has been aided by synthetic model systems that mimic their reactivity or structural and spectral features. For example, the cleavage of dioxygen often produces an iron(IV)-oxo that has been characterized in a number of enzymatic and synthetic systems. In non-heme 2-oxogluterate dependent (iron-2OG) enzymes, the ferryl species abstracts an H-atom from bound substrate to produce the proposed iron(III)-hydroxo and caged substrate radical. Most iron-2OG enzymes perform a radical rebound hydroxylation at the site of the H-atom abstraction (HAA); however, recent reports have shown that certain substrates can be desaturated through the loss of a second H atom at a site adjacent to a heteroatom (N or O) for most native desaturase substrates. One proposed mechanism for the removal of the second H-atom involves a polar-cleavage mechanism (electron transfer-proton transfer) by the iron(III)-hydroxo, as opposed to a second HAA. Herein we report the synthesis and characterization of a series of iron complexes with hydrogen bonding interactions between bound aquo or hydroxo ligands and the secondary coordination sphere in ferrous and ferric complexes. Interconversion among the iron species is accomplished by stepwise proton or electron addition or subtraction, as well as H-atom transfer (HAT). The calculated bond dissociation free energies (BDFEs) of two ferric hydroxo complexes, differentiated by their noncovalent interactions and reactivity, suggest that neither complex is capable of activating even weak C-H bonds, lending further support to the proposed mechanism for desaturation in iron-2OG desaturase enzymes. Additionally, the ferric hydroxo species are differentiated by their reactivity toward performing a radical rebound hydroxylation of triphenylmethylradical. Our findings should encourage further study of the desaturase systems that may contain unique H-bonding motifs proximal to the active site that help bias substrate desaturation over hydroxylation.
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Affiliation(s)
- Michael J Drummond
- School of Chemical Sciences , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States
| | - Courtney L Ford
- School of Chemical Sciences , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States
| | - Danielle L Gray
- School of Chemical Sciences , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States
| | - Codrina V Popescu
- Department of Chemistry , University of Saint Thomas , 2115 Summit Avenue , Saint Paul , Minnesota 55105 , United States
| | - Alison R Fout
- School of Chemical Sciences , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States
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14
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Mitchell AJ, Weng JK. Unleashing the Synthetic Power of Plant Oxygenases: From Mechanism to Application. PLANT PHYSIOLOGY 2019; 179:813-829. [PMID: 30670605 PMCID: PMC6393811 DOI: 10.1104/pp.18.01223] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/14/2019] [Indexed: 05/23/2023]
Abstract
The functions and biochemical mechanisms of major classes of plant oxygenases are discussed, and their potential utility for plant synthetic biology is explored.
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Affiliation(s)
- Andrew J Mitchell
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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15
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Chang HC, Mondal B, Fang H, Neese F, Bill E, Ye S. Electron Paramagnetic Resonance Signature of Tetragonal Low Spin Iron(V)-Nitrido and -Oxo Complexes Derived from the Electronic Structure Analysis of Heme and Non-Heme Archetypes. J Am Chem Soc 2019; 141:2421-2434. [PMID: 30620571 PMCID: PMC6728100 DOI: 10.1021/jacs.8b11429] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Iron(V)-nitrido and -oxo complexes
have been proposed as key intermediates
in a diverse array of chemical transformations. Herein we present
a detailed electronic-structure analysis of [FeV(N)(TPP)]
(1, TPP2– = tetraphenylporphyrinato),
and [FeV(N)(cyclam-ac)]+ (2, cyclam-ac
= 1,4,8,11-tetraazacyclotetradecane-1-acetato) using electron paramagnetic
resonance (EPR) and 57Fe Mössbauer spectroscopy
coupled with wave function based complete active-space self-consistent
field (CASSCF) calculations. The findings were compared with all other
well-characterized genuine iron(V)-nitrido and -oxo complexes, [FeV(N)(MePy2tacn)](PF6)2 (3, MePy2tacn = methyl-N′,N″-bis(2-picolyl)-1,4,7-triazacyclononane), [FeV(N){PhB(t-BuIm)3}]+ (4, PhB(tBuIm)3– = phenyltris(3-tert-butylimidazol-2-ylidene)borate),
and [FeV(O)(TAML)]− (5,
TAML4– = tetraamido macrocyclic ligand). Our results
revealed that complex 1 is an authenticated iron(V)-nitrido
species and contrasts with its oxo congener, compound I, which contains
a ferryl unit interacting with a porphyrin radical. More importantly,
tetragonal iron(V)-nitrido and -oxo complexes 1–3 and 5 all possess an orbitally nearly doubly
degenerate S = 1/2 ground state. Consequently, analogous
near-axial EPR spectra with g|| < g⊥ ≤ 2 were measured for them,
and their g|| and g⊥ values were found to obey a simple relation of g⊥2 + (2 – g∥)2 = 4. However, the bonding situation for trigonal iron(V)-nitrido
complex 4 is completely different as evidenced by its
distinct EPR spectrum with g|| < 2
< g⊥. Further in-depth analyses
suggested that tetragonal low spin iron(V)-nitrido and -oxo complexes
feature electronic structures akin to those found for complexes 1–3 and 5. Therefore, the
characteristic EPR signals determined for 1–3 and 5 can be used as a spectroscopic marker
to identify such highly reactive intermediates in catalytic processes.
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Affiliation(s)
- Hao-Ching Chang
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , D-45470 Mülheim an der Ruhr , Germany
| | - Bhaskar Mondal
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstr. 34-36 , D-45470 Mülheim an der Ruhr , Germany
| | - Huayi Fang
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstr. 34-36 , D-45470 Mülheim an der Ruhr , Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , D-45470 Mülheim an der Ruhr , Germany
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstr. 34-36 , D-45470 Mülheim an der Ruhr , Germany
| | - Shengfa Ye
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , D-45470 Mülheim an der Ruhr , Germany
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16
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Klinman JP, Offenbacher AR. Understanding Biological Hydrogen Transfer Through the Lens of Temperature Dependent Kinetic Isotope Effects. Acc Chem Res 2018; 51:1966-1974. [PMID: 30152685 DOI: 10.1021/acs.accounts.8b00226] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Hydrogen atom transfer (HAT) is a salient feature of many enzymatic C-H cleavage mechanisms. In systems where kinetic isolation of HAT is achieved, selective labeling of substrate with hydrogen isotopes, such as deuterium, enables the determination of intrinsic kinetic isotope effects (KIEs). While the magnitude of the KIE is itself informative, ultimately the size of the temperature dependence of the KIE, Δ Ea = Ea(D) - Ea(H), serves as a critical, and often misinterpreted (or even ignored) descriptor of the reaction coordinate. As will be highlighted in this Account, Δ Ea is one of the most robust parameters to emerge from studies of enzyme catalyzed hydrogen transfer. Kinetic parameters for C-H reactions via HAT can appear consistent with either classical "over-the-barrier" or "Bell-like tunneling correction" models. However, neither of these models is able to explain the observation of near-zero Δ Ea values with many native enzymes that increase upon extrinsic or intrinsic perturbations to function. Instead, a full tunneling model has been developed that can account for the aggregate trends in the temperature dependence of the KIE. This model is reminiscent of Marcus-like theory for electron tunneling, with the additional incorporation of an H atom donor-acceptor distance (DAD) sampling term for effective wave function overlap; the role of the latter term is manifested in the experimentally determined Δ Ea. Three enzyme systems from this laboratory that illustrate different aspects of HAT are presented: taurine dioxygenase, the dual copper β-monooxygenases, and soybean lipoxygenase (SLO). The latter provides a particularly compelling system for understanding the properties of hydrogen tunneling, showing systematic increases in Δ Ea upon reduction in the size of hydrophobic residues both proximal and distal from the active site iron cofactor. Of note, recent ENDOR-based studies of enzyme-substrate complexes with SLO indicate an increase in DAD for mutants with increased Δ Ea, observations that are inconsistent with "Bell-like correction" models. Overall, the surmounting kinetic and biophysical evidence corroborates a multidimensional approach for understanding HAT, offering a robust mechanistic explanation for the magnitude and trends of the KIE and Δ Ea. Recent DFT and QM/MM computations on SLO are compared to the developed nonadiabatic analytical constructs, providing considerable insight into ground state structures and reactivity. However, QM/MM is unable to readily reproduce the small Δ Ea values characteristic of native enzymes. Future theoretical developments to capture these experimental observations may necessitate a parsing of protein motions for local, substrate deuteration-sensitive modes from isotope-insensitive modes within the larger conformational landscape, in the process providing deeper understanding of how native enzymes have evolved to transiently optimize their active site configurations.
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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, United States
| | - Adam R. Offenbacher
- Department of Chemistry, Department of Molecular and Cell Biology and California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
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17
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Chang WC, Liu P, Guo Y. Mechanistic Elucidation of Two Catalytically Versatile Iron(II)- and α-Ketoglutarate-Dependent Enzymes: Cases Beyond Hydroxylation. COMMENT INORG CHEM 2018. [DOI: 10.1080/02603594.2018.1509856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Wei-chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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18
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Herr CQ, Hausinger RP. Amazing Diversity in Biochemical Roles of Fe(II)/2-Oxoglutarate Oxygenases. Trends Biochem Sci 2018; 43:517-532. [PMID: 29709390 DOI: 10.1016/j.tibs.2018.04.002] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 03/21/2018] [Accepted: 04/01/2018] [Indexed: 12/13/2022]
Abstract
Since their discovery in the 1960s, the family of Fe(II)/2-oxoglutarate-dependent oxygenases has undergone a tremendous expansion to include enzymes catalyzing a vast diversity of biologically important reactions. Recent examples highlight roles in controlling chromatin modification, transcription, mRNA demethylation, and mRNA splicing. Others generate modifications in tRNA, translation factors, ribosomes, and other proteins. Thus, oxygenases affect all components of molecular biology's central dogma, in which information flows from DNA to RNA to proteins. These enzymes also function in biosynthesis and catabolism of cellular metabolites, including antibiotics and signaling molecules. Due to their critical importance, ongoing efforts have targeted family members for the development of specific therapeutics. This review provides a general overview of recently characterized oxygenase reactions and their key biological roles.
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Affiliation(s)
- Caitlyn Q Herr
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
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19
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Guo M, Lee YM, Gupta R, Seo MS, Ohta T, Wang HH, Liu HY, Dhuri SN, Sarangi R, Fukuzumi S, Nam W. Dioxygen Activation and O-O Bond Formation Reactions by Manganese Corroles. J Am Chem Soc 2017; 139:15858-15867. [PMID: 29056043 PMCID: PMC5711437 DOI: 10.1021/jacs.7b08678] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Activation of dioxygen (O2) in enzymatic and biomimetic reactions has been intensively investigated over the past several decades. More recently, O-O bond formation, which is the reverse of the O2-activation reaction, has been the focus of current research. Herein, we report the O2-activation and O-O bond formation reactions by manganese corrole complexes. In the O2-activation reaction, Mn(V)-oxo and Mn(IV)-peroxo intermediates were formed when Mn(III) corroles were exposed to O2 in the presence of base (e.g., OH-) and hydrogen atom (H atom) donor (e.g., THF or cyclic olefins); the O2-activation reaction did not occur in the absence of base and H atom donor. Moreover, formation of the Mn(V)-oxo and Mn(IV)-peroxo species was dependent on the amounts of base present in the reaction solution. The role of the base was proposed to lower the oxidation potential of the Mn(III) corroles, thereby facilitating the binding of O2 and forming a Mn(IV)-superoxo species. The putative Mn(IV)-superoxo species was then converted to the corresponding Mn(IV)-hydroperoxo species by abstracting a H atom from H atom donor, followed by the O-O bond cleavage of the putative Mn(IV)-hydroperoxo species to form a Mn(V)-oxo species. We have also shown that addition of hydroxide ion to the Mn(V)-oxo species afforded the Mn(IV)-peroxo species via O-O bond formation and the resulting Mn(IV)-peroxo species reverted to the Mn(V)-oxo species upon addition of proton, indicating that the O-O bond formation and cleavage reactions between the Mn(V)-oxo and Mn(IV)-peroxo complexes are reversible. The present study reports the first example of using the same manganese complex in both O2-activation and O-O bond formation reactions.
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Affiliation(s)
- Mian Guo
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Yong-Min Lee
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Ranjana Gupta
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Mi Sook Seo
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Takehiro Ohta
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH LP Center, Hyogo 679-5148, Japan
| | - Hua-Hua Wang
- Department of Chemistry, South China University of Technology, Guangzhou 510641, China
| | - Hai-Yang Liu
- Department of Chemistry, South China University of Technology, Guangzhou 510641, China
| | - Sunder N. Dhuri
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
- Department of Chemistry, Goa University, Goa 403 206, India
| | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Shunichi Fukuzumi
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, China
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20
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Miao C, Li XX, Lee YM, Xia C, Wang Y, Nam W, Sun W. Manganese complex-catalyzed oxidation and oxidative kinetic resolution of secondary alcohols by hydrogen peroxide. Chem Sci 2017; 8:7476-7482. [PMID: 29163900 PMCID: PMC5676093 DOI: 10.1039/c7sc00891k] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 09/06/2017] [Indexed: 12/14/2022] Open
Abstract
The highly efficient catalytic oxidation and oxidative kinetic resolution (OKR) of secondary alcohols has been achieved using a synthetic manganese catalyst with low loading and hydrogen peroxide as an environmentally benign oxidant in the presence of a small amount of sulfuric acid as an additive. The product yields were high (up to 93%) for alcohol oxidation and the enantioselectivity was excellent (>90% ee) for the OKR of secondary alcohols. Mechanistic studies revealed that alcohol oxidation occurs via hydrogen atom (H-atom) abstraction from an α-CH bond of the alcohol substrate and a two-electron process by an electrophilic Mn-oxo species. Density functional theory calculations revealed the difference in reaction energy barriers for H-atom abstraction from the α-CH bonds of R- and S-enantiomers by a chiral high-valent manganese-oxo complex, supporting the experimental result from the OKR of secondary alcohols.
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Affiliation(s)
- Chengxia Miao
- State Key Laboratory for Oxo Synthesis and Selective Oxidation , Suzhou Research Institute of LICP , Lanzhou Institute of Chemical Physics (LICP) , Chinese Academy of Sciences , Lanzhou 730000 , China .
- College of Chemistry and Material Science , Shandong Agricultural University , Tai'an 271018 , China
| | - Xiao-Xi Li
- State Key Laboratory for Oxo Synthesis and Selective Oxidation , Suzhou Research Institute of LICP , Lanzhou Institute of Chemical Physics (LICP) , Chinese Academy of Sciences , Lanzhou 730000 , China .
- Department of Chemistry and Nano Science , Ewha Womans University , Seoul 03760 , Korea .
| | - Yong-Min Lee
- Department of Chemistry and Nano Science , Ewha Womans University , Seoul 03760 , Korea .
| | - Chungu Xia
- State Key Laboratory for Oxo Synthesis and Selective Oxidation , Suzhou Research Institute of LICP , Lanzhou Institute of Chemical Physics (LICP) , Chinese Academy of Sciences , Lanzhou 730000 , China .
| | - Yong Wang
- State Key Laboratory for Oxo Synthesis and Selective Oxidation , Suzhou Research Institute of LICP , Lanzhou Institute of Chemical Physics (LICP) , Chinese Academy of Sciences , Lanzhou 730000 , China .
| | - Wonwoo Nam
- State Key Laboratory for Oxo Synthesis and Selective Oxidation , Suzhou Research Institute of LICP , Lanzhou Institute of Chemical Physics (LICP) , Chinese Academy of Sciences , Lanzhou 730000 , China .
- Department of Chemistry and Nano Science , Ewha Womans University , Seoul 03760 , Korea .
| | - Wei Sun
- State Key Laboratory for Oxo Synthesis and Selective Oxidation , Suzhou Research Institute of LICP , Lanzhou Institute of Chemical Physics (LICP) , Chinese Academy of Sciences , Lanzhou 730000 , China .
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21
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Hong S, Lu X, Lee YM, Seo MS, Ohta T, Ogura T, Clémancey M, Maldivi P, Latour JM, Sarangi R, Nam W. Achieving One-Electron Oxidation of a Mononuclear Nonheme Iron(V)-Imido Complex. J Am Chem Soc 2017; 139:14372-14375. [PMID: 28960973 DOI: 10.1021/jacs.7b08161] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A mononuclear nonheme iron(V)-imido complex bearing a tetraamido macrocyclic ligand (TAML), [FeV(NTs)(TAML)]- (1), was oxidized by one-electron oxidants, affording formation of an iron(V)-imido TAML cation radical species, [FeV(NTs)(TAML+•)] (2); 2 is a diamagnetic (S = 0) complex, resulting from the antiferromagnetic coupling of the low-spin iron(V) ion (S = 1/2) with the one-electron oxidized ligand (TAML+•). 2 is a competent oxidant in C-H bond functionalization and nitrene transfer reaction, showing that the reactivity of 2 is greater than that of 1.
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Affiliation(s)
- Seungwoo Hong
- Department of Chemistry and Nano Science, Ewha Womans University , Seoul 03760, Korea.,Department of Chemistry, Sookmyung Women's University , Seoul 04310, Korea
| | - Xiaoyan Lu
- Department of Chemistry and Nano Science, Ewha Womans University , Seoul 03760, Korea
| | - Yong-Min Lee
- Department of Chemistry and Nano Science, Ewha Womans University , Seoul 03760, Korea
| | - Mi Sook Seo
- Department of Chemistry and Nano Science, Ewha Womans University , Seoul 03760, Korea
| | - Takehiro Ohta
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH LP Center , Hyogo 679-5148, Japan
| | - Takashi Ogura
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH LP Center , Hyogo 679-5148, Japan
| | - Martin Clémancey
- LCBM/PMB and CEA/BIG/CBM/and CNRS UMR 5249, Université Grenoble Alpes , Grenoble 38054, France
| | - Pascale Maldivi
- CEA, CNRS, INAC, SYMMES, Université Grenoble Alpes , Grenoble 38000, France
| | - Jean-Marc Latour
- LCBM/PMB and CEA/BIG/CBM/and CNRS UMR 5249, Université Grenoble Alpes , Grenoble 38054, France
| | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory , California 94025, United States
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University , Seoul 03760, Korea.,State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences , Lanzhou 730000, China
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22
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Mitchell AJ, Dunham NP, Martinie RJ, Bergman JA, Pollock CJ, Hu K, Allen BD, Chang WC, Silakov A, Bollinger JM, Krebs C, Boal AK. Visualizing the Reaction Cycle in an Iron(II)- and 2-(Oxo)-glutarate-Dependent Hydroxylase. J Am Chem Soc 2017; 139:13830-13836. [PMID: 28823155 DOI: 10.1021/jacs.7b07374] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Iron(II)- and 2-(oxo)-glutarate-dependent oxygenases catalyze diverse oxidative transformations that are often initiated by abstraction of hydrogen from carbon by iron(IV)-oxo (ferryl) complexes. Control of the relative orientation of the substrate C-H and ferryl Fe-O bonds, primarily by direction of the oxo group into one of two cis-related coordination sites (termed inline and offline), may be generally important for control of the reaction outcome. Neither the ferryl complexes nor their fleeting precursors have been crystallographically characterized, hindering direct experimental validation of the offline hypothesis and elucidation of the means by which the protein might dictate an alternative oxo position. Comparison of high-resolution X-ray crystal structures of the substrate complex, an Fe(II)-peroxysuccinate ferryl precursor, and a vanadium(IV)-oxo mimic of the ferryl intermediate in the l-arginine 3-hydroxylase, VioC, reveals coordinated motions of active site residues that appear to control the intermediate geometries to determine reaction outcome.
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Affiliation(s)
- Andrew J Mitchell
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Noah P Dunham
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Ryan J Martinie
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Jonathan A Bergman
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Christopher J Pollock
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Kai Hu
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States.,The Huck Institutes for the Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Benjamin D Allen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States.,The Huck Institutes for the Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Wei-Chen Chang
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Alexey Silakov
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - J Martin Bollinger
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States.,Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States.,Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Amie K Boal
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States.,Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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23
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24
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Wang Y, Li J, Liu A. Oxygen activation by mononuclear nonheme iron dioxygenases involved in the degradation of aromatics. J Biol Inorg Chem 2017; 22:395-405. [PMID: 28084551 DOI: 10.1007/s00775-017-1436-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/03/2017] [Indexed: 11/25/2022]
Abstract
Molecular oxygen is utilized in numerous metabolic pathways fundamental for life. Mononuclear nonheme iron-dependent oxygenase enzymes are well known for their involvement in some of these pathways, activating O2 so that oxygen atoms can be incorporated into their primary substrates. These reactions often initiate pathways that allow organisms to use stable organic molecules as sources of carbon and energy for growth. From the myriad of reactions in which these enzymes are involved, this perspective recounts the general mechanisms of aromatic dihydroxylation and oxidative ring cleavage, both of which are ubiquitous chemical reactions found in life-sustaining processes. The organic substrate provides all four electrons required for oxygen activation and insertion in the reactions mediated by extradiol and intradiol ring-cleaving catechol dioxygenases. In contrast, two of the electrons are provided by NADH in the cis-dihydroxylation mechanism of Rieske dioxygenases. The catalytic nonheme Fe center, with the aid of active site residues, facilitates these electron transfers to O2 as key elements of the activation processes. This review discusses some general questions for the catalytic strategies of oxygen activation and insertion into aromatic compounds employed by mononuclear nonheme iron-dependent dioxygenases. These include: (1) how oxygen is activated, (2) whether there are common intermediates before oxygen transfer to the aromatic substrate, and (3) are these key intermediates unique to mononuclear nonheme iron dioxygenases?
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Affiliation(s)
- Yifan Wang
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Jiasong Li
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA.
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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: 174] [Impact Index Per Article: 21.8] [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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