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Vennelakanti V, Jeon M, Kulik HJ. How Do Differences in Electronic Structure Affect the Use of Vanadium Intermediates as Mimics in Nonheme Iron Hydroxylases? Inorg Chem 2024; 63:4997-5011. [PMID: 38428015 DOI: 10.1021/acs.inorgchem.3c04421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
We study active-site models of nonheme iron hydroxylases and their vanadium-based mimics using density functional theory to determine if vanadyl is a faithful structural mimic. We identify crucial structural and energetic differences between ferryl and vanadyl isomers owing to the differences in their ground electronic states, i.e., high spin (HS) for Fe and low spin (LS) for V. For the succinate cofactor bound to the ferryl intermediate, we predict facile interconversion between monodentate and bidentate coordination isomers for ferryl species but difficult rearrangement for vanadyl mimics. We study isomerization of the oxo intermediate between axial and equatorial positions and find the ferryl potential energy surface to be characterized by a large barrier of ca. 10 kcal/mol that is completely absent for the vanadyl mimic. This analysis reveals even starker contrasts between Fe and V in hydroxylases than those observed for this metal substitution in nonheme halogenases. Analysis of the relative bond strengths of coordinating carboxylate ligands for Fe and V reveals that all of the ligands show stronger binding to V than Fe owing to the LS ground state of V in contrast to the HS ground state of Fe, highlighting the limitations of vanadyl mimics of native nonheme iron hydroxylases.
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Affiliation(s)
- Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mugyeom Jeon
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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2
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Monkcom EC, Gómez L, Lutz M, Ye S, Bill E, Costas M, Klein Gebbink RJM. Synthesis, Structure and Reactivity of a Mononuclear N,N,O-Bound Fe(II) α-Keto-Acid Complex. Chemistry 2024; 30:e202302710. [PMID: 37882223 DOI: 10.1002/chem.202302710] [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: 08/18/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 10/27/2023]
Abstract
A bulky, tridentate phenolate ligand (ImPh2 NNOtBu ) was used to synthesise the first example of a mononuclear, facial, N,N,O-bound iron(II) benzoylformate complex, [Fe(ImPh2 NNOtBu )(BF)] (2). The X-ray crystal structure of 2 reveals that the iron centre is pentacoordinate (τ=0.5), with a vacant site located cis to the bidentate BF ligand. The Mössbauer parameters of 2 are consistent with high-spin iron(II), and are very close to those reported for α-ketoglutarate-bound non-heme iron enzyme active sites. According to NMR and UV-vis spectroscopies, the structural integrity of 2 is retained in both coordinating and non-coordinating solvents. Cyclic voltammetry studies show that the iron centre has a very low oxidation potential and is more prone to electrochemical oxidation than the redox-active phenolate ligand. Complex 2 reacts with NO to form a S=3 /2 {FeNO}7 adduct in which NO binds directly to the iron centre, according to EPR, UV-vis, IR spectroscopies and DFT analysis. Upon O2 exposure, 2 undergoes oxidative decarboxylation to form a diiron(III) benzoate complex, [Fe2 (ImPh2 NNOtBu )2 (μ2 -OBz)(μ2 -OH)2 ]+ (3). A small amount of hydroxylated ligand was also observed by ESI-MS, hinting at the formation of a high-valent iron(IV)-oxo intermediate. Initial reactivity studies show that 2 is capable of oxygen atom transfer reactivity with O2 , converting methyl(p-tolyl)sulfide to sulfoxide.
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Affiliation(s)
- Emily C Monkcom
- Organic Chemistry and Catalysis, Institute for Sustainable and Circular Chemistry, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Laura Gómez
- Serveis Tècnics de Recerca, Universitat de Girona, Pic de Peguera 15, Parc Cientific, 17003, Girona, Spain
| | - Martin Lutz
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Shengfa Ye
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion, 45470, Mülheim an der Ruhr, Germany
| | - Miquel Costas
- Institut de Química Computacional i Catàlisi, Universitat de Girona, Pic de Peguera 15, Parc Cientific, 17003, Girona, Spain
| | - Robertus J M Klein Gebbink
- Organic Chemistry and Catalysis, Institute for Sustainable and Circular Chemistry, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
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3
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Vennelakanti V, Li GL, Kulik HJ. Why Nonheme Iron Halogenases Do Not Fluorinate C-H Bonds: A Computational Investigation. Inorg Chem 2023; 62:19758-19770. [PMID: 37972340 DOI: 10.1021/acs.inorgchem.3c03215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Selective halogenation is necessary for a range of fine chemical applications, including the development of therapeutic drugs. While synthetic processes to achieve C-H halogenation require harsh conditions, enzymes such as nonheme iron halogenases carry out some types of C-H halogenation, i.e., chlorination or bromination, with ease, while others, i.e., fluorination, have never been observed in natural or engineered nonheme iron enzymes. Using density functional theory and correlated wave function theory, we investigate the differences in structural and energetic preferences of the smaller fluoride and the larger chloride or bromide intermediates throughout the catalytic cycle. Although we find that the energetics of rate-limiting hydrogen atom transfer are not strongly impacted by fluoride substitution, the higher barriers observed during the radical rebound reaction for fluoride relative to chloride and bromide contribute to the difficulty of C-H fluorination. We also investigate the possibility of isomerization playing a role in differences in reaction selectivity, and our calculations reveal crucial differences in terms of isomer energetics of the key ferryl intermediate between fluoride and chloride/bromide intermediates. While formation of monodentate isomers believed to be involved in selective catalysis is shown for chloride and bromide intermediates, we find that formation of the fluoride monodentate intermediate is not possible in our calculations, which lack additional stabilizing interactions with the greater protein environment. Furthermore, the shorter Fe-F bonds are found to increase isomerization reaction barriers, suggesting that incorporation of residues that form a halogen bond with F and elongate Fe-F bonds could make selective C-H fluorination possible in nonheme iron halogenases. Our work highlights the differences between the fluoride and chloride/bromide intermediates and suggests potential steps toward engineering nonheme iron halogenases to enable selective C-H fluorination.
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Affiliation(s)
- Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Grace L Li
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Biosynthesizing structurally diverse diols via a general route combining oxidative and reductive formations of OH-groups. Nat Commun 2022; 13:1595. [PMID: 35332143 PMCID: PMC8948231 DOI: 10.1038/s41467-022-29216-5] [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: 07/03/2021] [Accepted: 03/02/2022] [Indexed: 11/09/2022] Open
Abstract
Diols encompass important bulk and fine chemicals for the chemical, pharmaceutical and cosmetic industries. During the past decades, biological production of C3-C5 diols from renewable feedstocks has received great interest. Here, we elaborate a general principle for effectively synthesizing structurally diverse diols by expanding amino acid metabolism. Specifically, we propose to combine oxidative and reductive formations of hydroxyl groups from amino acids in a thermodynamically favorable order of four reactions catalyzed by amino acid hydroxylase, L-amino acid deaminase, α-keto acid decarboxylase and aldehyde reductase consecutively. The oxidative formation of hydroxyl group from an alkyl group is energetically more attractive than the reductive pathway, which is exclusively used in the synthetic pathways of diols reported so far. We demonstrate this general route for microbial production of branched-chain diols in E. coli. Ten C3-C5 diols are synthesized. Six of them, namely isopentyldiol (IPDO), 2-methyl-1,3-butanediol (2-M-1,3-BDO), 2-methyl-1,4-butanediol (2-M-1,4-BDO), 2-methyl-1,3-propanediol (MPO), 2-ethyl-1,3-propanediol (2-E-1,3-PDO), 1,4-pentanediol (1,4-PTD), have not been biologically synthesized before. This work opens up opportunities for synthesizing structurally diverse diols and triols, especially by genome mining, rational design or directed evolution of proper enzymes. Diols are important bulk and fine chemicals, but bioproduciton of branch-chain diols is hampered by the unknown biological route. Here, the authors report the expanding of amino acid metabolism for biosynthesis of branch-chain diols via a general route of combined oxidative and reductive formations of hydroxyl groups.
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Tassano E, Moore C, Dussauge S, Vargas A, Snajdrova R. Discovery of New Fe(II)/α-Ketoglutarate-Dependent Dioxygenases for Oxidation of l-Proline. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.1c00405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Erika Tassano
- Global Discovery Chemistry, Novartis Institute for Biomedical Research, 4056 Basel, Switzerland
| | - Charles Moore
- Global Discovery Chemistry, Novartis Institute for Biomedical Research, 4056 Basel, Switzerland
| | - Solene Dussauge
- Global Discovery Chemistry, Novartis Institute for Biomedical Research, 4056 Basel, Switzerland
| | - Alexandra Vargas
- Global Discovery Chemistry, Novartis Institute for Biomedical Research, 4056 Basel, Switzerland
| | - Radka Snajdrova
- Global Discovery Chemistry, Novartis Institute for Biomedical Research, 4056 Basel, Switzerland
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Mrugała B, Miłaczewska A, Porebski PJ, Niedzialkowska E, Guzik M, Minor W, Borowski T. A study on the structure, mechanism, and biochemistry of kanamycin B dioxygenase (KanJ)-an enzyme with a broad range of substrates. FEBS J 2020; 288:1366-1386. [PMID: 32592631 DOI: 10.1111/febs.15462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/09/2020] [Accepted: 06/09/2020] [Indexed: 02/06/2023]
Abstract
Kanamycin A is an aminoglycoside antibiotic isolated from Streptomyces kanamyceticus and used against a wide spectrum of bacteria, including Mycobacterium tuberculosis. Biosynthesis of kanamycin involves an oxidative deamination step catalyzed by kanamycin B dioxygenase (KanJ), thereby the C2' position of kanamycin B is transformed into a keto group upon release of ammonia. Here, we present for the first time, structural models of KanJ with several ligands, which along with the results of ITC binding assays and HPLC activity tests explain substrate specificity of the enzyme. The large size of the binding pocket suggests that KanJ can accept a broad range of substrates, which was confirmed by activity tests. Specificity of the enzyme with respect to its substrate is determined by the hydrogen bond interactions between the methylamino group of the antibiotic and highly conserved Asp134 and Cys150 as well as between hydroxyl groups of the substrate and Asn120 and Gln80. Upon antibiotic binding, the C terminus loop is significantly rearranged and Gln80 and Asn120, which are directly involved in substrate recognition, change their conformations. Based on reaction energy profiles obtained by density functional theory (DFT) simulations, we propose a mechanism of ketone formation involving the reactive FeIV = O and proceeding either via OH rebound, which yields a hemiaminal intermediate or by abstraction of two hydrogen atoms, which leads to an imine species. At acidic pH, the latter involves a lower barrier than the OH rebound, whereas at basic pH, the barrier leading to an imine vanishes completely. DATABASES: Structural data are available in PDB database under the accession numbers: 6S0R, 6S0T, 6S0U, 6S0W, 6S0V, 6S0S. Diffraction images are available at the Integrated Resource for Reproducibility in Macromolecular Crystallography at http://proteindiffraction.org under DOIs: 10.18430/m36s0t, 10.18430/m36s0u, 10.18430/m36s0r, 10.18430/m36s0s, 10.18430/m36s0v, 10.18430/m36s0w. A data set collection of computational results is available in the Mendeley Data database under DOI: 10.17632/sbyzssjmp3.1 and in the ioChem-BD database under DOI: 10.19061/iochem-bd-4-18.
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Affiliation(s)
- Beata Mrugała
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| | - Anna Miłaczewska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| | - Przemyslaw Jerzy Porebski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Ewa Niedzialkowska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Maciej Guzik
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
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7
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Liang W, Zhang W, Lv Z, Li C. 4-Hydroxyphenylpyruvate dioxygenase from sea cucumber Apostichopus japonicus negatively regulates reactive oxygen species production. FISH & SHELLFISH IMMUNOLOGY 2020; 101:261-268. [PMID: 32276034 DOI: 10.1016/j.fsi.2020.04.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 04/02/2020] [Accepted: 04/04/2020] [Indexed: 06/11/2023]
Abstract
As a wide distribution molecule, 4-hydroxyphenylpyruvate dioxygenase (4-HPPD) catalyzes the second step in the tyrosine catabolism pathway. This process commonly occurs in all aerobic life forms. The broad distribution of these metabolites suggests that they have an important role in many organisms. A portion of the 4-HPPD homology sequence was also identified in Apostichopus japonicus transcriptome. However, the functional roles of A. japonicus 4-HPPD remain unclear. In the current study, a 4-HPPD homolog was cloned from A. japonicus (designated as AjHPPD). The nucleotide sequence analysis showed that the open reading frame of AjHPPD was 1149 bp and encoded a 382-amino-acid residue polyprotein with glyoxalase_4 (residues 20-133) and glyoxalase (residues 180-335) domains. The spatial expression analysis revealed that AjHPPD was ubiquitously expressed in all examined tissues with large-magnitude in the respiratory tree and was minimally expressed in coelomocytes. Compared with a control group, the significant increase in transcription of AjHPPD mRNA in the Vibrio splendidus-challenged sea cucumber was 2.10-fold (p < 0.01) at 48 h and returned to the normal level at 72 and 96 h. Similarly, compared with a control group, the significant increase in the transcription of AjHPPD mRNA was 3.36-fold (p < 0.01) at 24 h after stimulation with 10 mg mL-1 of LPS. On the one hand, silencing AjHPPD in vitro could inhibit the expression of pentose phosphate pathway (PPP) flux enzyme glucose-6-phosphate dehydrogenase (G6PD) at the mRNA level and prevent the clearance of reactive oxygen species (ROS) in sea cucumbers. On the other hand, interference of AjHPPD by using specific siRNA can result in the significant promotion of coelomocyte apoptosis with a 1.61-fold increase in vitro. AjHPPD negatively regulated ROS levels by modulating tyrosine catabolism on AjG6PD expression and coelomocyte apoptosis in response to pathogen infection.
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Affiliation(s)
- Weikang Liang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, PR China
| | - Weiwei Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, PR China
| | - Zhimeng Lv
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, PR China
| | - Chenghua Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, PR China.
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8
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Zeb N, Rashid MH, Mubarak MQE, Ghafoor S, de Visser SP. Flavonol biosynthesis by nonheme iron dioxygenases: A computational study into the structure and mechanism. J Inorg Biochem 2019; 198:110728. [PMID: 31203088 DOI: 10.1016/j.jinorgbio.2019.110728] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/13/2019] [Accepted: 05/29/2019] [Indexed: 12/20/2022]
Abstract
Plants produce flavonol compounds for vital functions regarding plant growth, fruit and flower colouring as well as fruit ripening processes. Several of these biosynthesis steps are stereo- and regioselective and are being carried out by nonheme iron enzymes. Using density functional theory calculations on a large active site model complex of flavanone-3β-hydroxylase (FHT), we established the mechanism for conversion of naringenin to its dihydroflavonol, which is a key step in the mechanism of flavonol biosynthesis. The reaction starts with dioxygen binding to the iron(II) centre and a reaction with α-ketoglutarate co-substrate gives succinate, an iron(IV)-oxo species and CO2 with large exothermicity and small reaction barriers. The rate-determining reaction step in the mechanism; however, is hydrogen atom abstraction of an aliphatic CH bond by the iron(IV)-oxo species. We identify a large kinetic isotope effect for the replacement of the transferring hydrogen atom by deuterium. In a final step the OH and substrate radicals combine to form the alcohol product with a barrier of several kcal mol-1. We show that the latter is the result of geometric constraints in the active site pocket. Furthermore, the calculations show that a weak tertiary CH bond is shielded from the iron(IV)-oxo species in the substrate binding position and therefore the enzyme is able to activate a stronger CH bond. As such, the flavanone-3β-hydroxylase enzyme reacts regioselectively with one specific CH bond of naringenin by avoiding activation of weaker bonds through tight substrate and oxidant positioning.
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Affiliation(s)
- Neelam Zeb
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom; National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P.O. Box 577, Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Muhammad H Rashid
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P.O. Box 577, Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - M Qadri E Mubarak
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Sidra Ghafoor
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom; Department of Chemistry, Government College University Faisalabad, Jhang Road, 3800 Faisalabad, Pakistan
| | - Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.
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Xue J, Lu J, Lai W. Mechanistic insights into a non-heme 2-oxoglutarate-dependent ethylene-forming enzyme: selectivity of ethylene-formation versusl-Arg hydroxylation. Phys Chem Chem Phys 2019; 21:9957-9968. [PMID: 31041955 DOI: 10.1039/c9cp00794f] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The ethylene-forming enzyme (EFE) is a unique member of the Fe(ii)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenases. It converts 2OG into ethylene plus three CO2 molecules (ethylene-forming reaction) and also catalyzes the C5 hydroxylation of l-arginine coupled to the oxidative decarboxylation of 2OG (l-Arg hydroxylation reaction). To uncover the mechanisms of the dual transformations by EFE, quantum mechanical/molecular mechanical (QM/MM) calculations were carried out. Based on the results, a branched mechanism was proposed. An FeII-peroxysuccinate complex with a dissociated CO2 generated through the nucleophilic attack of the superoxo moiety of the Fe-O2 species on the keto carbon of 2OG is the key common intermediate in both reactions. A competition between the subsequent CO2 insertion (a key step in the ethylene-forming pathway) and the O-O bond cleavage (leading to the formation of succinate) governs the product selectivity. The calculated reaction barriers suggested that the CO2 insertion is favored over the O-O bond cleavage. This is consistent with the product preference observed in experiments. By comparison with the results of AsqJ (an Fe/2OG oxygenase that leads to substrate oxidation exclusively), the protein environment was found to be crucial for the selectivity. Further calculations demonstrated that the local electric field of the protein environment in EFE promotes ethylene formation by acting as a charge template, exemplifying the importance of the electrostatic interaction in enzyme catalysis. These findings offer mechanistic insights into the EFE catalysis and provide important clues for better understanding the unique ethylene-forming capability of EFE compared with other Fe/2OG oxygenases.
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Affiliation(s)
- Junqin Xue
- Department of Chemistry, Renmin University of China, Beijing, 100872, China.
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Liu X. Hydrolysing the soluble protein secreted by Escherichia coli in trans-4-hydroxy-L-proline fermentation increased dissolve oxygen to promote high-level trans-4-hydroxy-L-proline production. Bioengineered 2019; 10:52-58. [PMID: 30955438 PMCID: PMC6527073 DOI: 10.1080/21655979.2019.1600966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Trans-4-hydroxy-L-proline (Hyp) production by Escherichia coli (E. coli) in fermentation is a high-oxygen-demand process. E. coli secretes large amounts of soluble protein, especially in the anaphase of fermentation, which is an important factor leading to inadequate oxygen supply. And acetic acid that is the major by-product of Hyp production accumulates under low dissolved oxygen (DO). To increase DO and achieve high-level Hyp production, soluble protein was hydrolysed by adding protease in Hyp fermentation. The optimal protease, concentration, and addition time were trypsin, 0.2 g/L, and 18 h, respectively. With the addition of trypsin, the soluble protein in Hyp fermentation decreased by 43.5%. The DO could be maintained at 20–30% throughout fermentation. Hyp production and glucose conversion rate were 45.3 g/L and 18.1%, which were increases of 24.1% and 8.4%, respectively. The accumulation of acetic acid was decreased by 52.1%. The metabolic flux of Hyp was increased by 44.2% and the flux of acetate was decreased by 51.0%.
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Affiliation(s)
- Xiaocui Liu
- a School of Life Sciences of Shanxi Datong University , Datong Shanxi , China
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11
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Sun D, Gao D, Xu P, Guo Q, Zhu Z, Cheng X, Bai S, Qin HM, Lu F. A novel l -leucine 5-hydroxylase from Nostoc piscinale unravels unexpected sulfoxidation activity toward l -methionine. Protein Expr Purif 2018; 149:1-6. [DOI: 10.1016/j.pep.2018.04.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/26/2018] [Accepted: 04/13/2018] [Indexed: 01/21/2023]
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12
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Gao SS, Naowarojna N, Cheng R, Liu X, Liu P. Recent examples of α-ketoglutarate-dependent mononuclear non-haem iron enzymes in natural product biosyntheses. Nat Prod Rep 2018; 35:792-837. [PMID: 29932179 PMCID: PMC6093783 DOI: 10.1039/c7np00067g] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: up to 2018 α-Ketoglutarate (αKG, also known as 2-oxoglutarate)-dependent mononuclear non-haem iron (αKG-NHFe) enzymes catalyze a wide range of biochemical reactions, including hydroxylation, ring fragmentation, C-C bond cleavage, epimerization, desaturation, endoperoxidation and heterocycle formation. These enzymes utilize iron(ii) as the metallo-cofactor and αKG as the co-substrate. Herein, we summarize several novel αKG-NHFe enzymes involved in natural product biosyntheses discovered in recent years, including halogenation reactions, amino acid modifications and tailoring reactions in the biosynthesis of terpenes, lipids, fatty acids and phosphonates. We also conducted a survey of the currently available structures of αKG-NHFe enzymes, in which αKG binds to the metallo-centre bidentately through either a proximal- or distal-type binding mode. Future structure-function and structure-reactivity relationship investigations will provide crucial information regarding how activities in this large class of enzymes have been fine-tuned in nature.
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Affiliation(s)
- Shu-Shan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | | | - Ronghai Cheng
- Department of Chemistry, Boston University, Boston, MA 02215, USA.
| | - Xueting Liu
- Department of Chemistry, Boston University, Boston, MA 02215, USA. and State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, MA 02215, USA.
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13
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Liang W, Zhang W, Shao Y, Zhao X, Li C. Dual functions of a 4-hydroxyphenylpyruvate dioxygenase for Vibrio splendidus survival and infection. Microb Pathog 2018; 120:47-54. [DOI: 10.1016/j.micpath.2018.04.055] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/25/2018] [Accepted: 04/26/2018] [Indexed: 01/08/2023]
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14
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Song X, Lu J, Lai W. Mechanistic insights into dioxygen activation, oxygen atom exchange and substrate epoxidation by AsqJ dioxygenase from quantum mechanical/molecular mechanical calculations. Phys Chem Chem Phys 2018; 19:20188-20197. [PMID: 28726913 DOI: 10.1039/c7cp02687k] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Herein, we use in-protein quantum mechanical/molecular mechanical (QM/MM) calculations to elucidate the mechanism of dioxygen activation, oxygen atom exchange and substrate epoxidation processes by AsqJ, an FeII/α-ketoglutarate-dependent dioxygenase (α-KGD) using a 2-His-1-Asp facial triad. Our results demonstrated that the whole reaction proceeds through a quintet surface. The dioxygen activation by AsqJ leads to a quintet penta-coordinated FeIV-oxo species, which has a square pyramidal geometry with the oxo group trans to His134. This penta-coordinated FeIV-oxo species is not the reactive one in the substrate epoxidation reaction since its oxo group is pointing away from the target C[double bond, length as m-dash]C bond. Instead, it can undergo the oxo group isomerization followed by water binding or the water binding followed by oxygen atom exchange to form the reactive hexa-coordinated FeIV-oxo species with the oxo group trans to His211. The calculated parameters of Mössbauer spectra for this hexa-coordinated FeIV-oxo intermediate are in excellent agreement with the experimental values, suggesting that it is most likely the experimentally trapped species. The calculated energetics indicated that the rate-limiting step is the substrate C[double bond, length as m-dash]C bond activation. This work improves our understanding of the dioxygen activation by α-KGD and provides important structural information about the reactive FeIV-oxo species.
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Affiliation(s)
- Xudan Song
- Department of Chemistry, Renmin University of China, Beijing, 100872, China.
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Rigid scaffolds for the design of molecular catalysts and biomimetic active sites: A case study of anthracene-based ligands for modeling mono-iron hydrogenase (Hmd). Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.09.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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16
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Su H, Sheng X, Zhu W, Ma G, Liu Y. Mechanistic Insights into the Decoupled Desaturation and Epoxidation Catalyzed by Dioxygenase AsqJ Involved in the Biosynthesis of Quinolone Alkaloids. ACS Catal 2017. [DOI: 10.1021/acscatal.7b01606] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Hao Su
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Xiang Sheng
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Wenyou Zhu
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Guangcai Ma
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, Shandong 250100, China
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Elwell CE, Gagnon NL, Neisen BD, Dhar D, Spaeth AD, Yee GM, Tolman WB. Copper-Oxygen Complexes Revisited: Structures, Spectroscopy, and Reactivity. Chem Rev 2017; 117:2059-2107. [PMID: 28103018 PMCID: PMC5963733 DOI: 10.1021/acs.chemrev.6b00636] [Citation(s) in RCA: 445] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A longstanding research goal has been to understand the nature and role of copper-oxygen intermediates within copper-containing enzymes and abiological catalysts. Synthetic chemistry has played a pivotal role in highlighting the viability of proposed intermediates and expanding the library of known copper-oxygen cores. In addition to the number of new complexes that have been synthesized since the previous reviews on this topic in this journal (Mirica, L. M.; Ottenwaelder, X.; Stack, T. D. P. Chem. Rev. 2004, 104, 1013-1046 and Lewis, E. A.; Tolman, W. B. Chem. Rev. 2004, 104, 1047-1076), the field has seen significant expansion in the (1) range of cores synthesized and characterized, (2) amount of mechanistic work performed, particularly in the area of organic substrate oxidation, and (3) use of computational methods for both the corroboration and prediction of proposed intermediates. The scope of this review has been limited to well-characterized examples of copper-oxygen species but seeks to provide a thorough picture of the spectroscopic characteristics and reactivity trends of the copper-oxygen cores discussed.
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Affiliation(s)
- Courtney E Elwell
- Department of Chemistry, Center for Metals in Biocatalysis, University of Minnesota , 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Nicole L Gagnon
- Department of Chemistry, Center for Metals in Biocatalysis, University of Minnesota , 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Benjamin D Neisen
- Department of Chemistry, Center for Metals in Biocatalysis, University of Minnesota , 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Debanjan Dhar
- Department of Chemistry, Center for Metals in Biocatalysis, University of Minnesota , 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Andrew D Spaeth
- Department of Chemistry, Center for Metals in Biocatalysis, University of Minnesota , 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Gereon M Yee
- Department of Chemistry, Center for Metals in Biocatalysis, University of Minnesota , 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - William B Tolman
- Department of Chemistry, Center for Metals in Biocatalysis, University of Minnesota , 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
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Wu LF, Meng S, Tang GL. Ferrous iron and α-ketoglutarate-dependent dioxygenases in the biosynthesis of microbial natural products. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:453-70. [DOI: 10.1016/j.bbapap.2016.01.012] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/22/2016] [Accepted: 01/29/2016] [Indexed: 01/29/2023]
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Sheet D, Paine TK. Aerobic alcohol oxidation and oxygen atom transfer reactions catalyzed by a nonheme iron(ii)-α-keto acid complex. Chem Sci 2016; 7:5322-5331. [PMID: 30155184 PMCID: PMC6020522 DOI: 10.1039/c6sc01476c] [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: 04/04/2016] [Accepted: 04/23/2016] [Indexed: 11/21/2022] Open
Abstract
An iron(ii)-benzoylformate complex of a monoanionic facial tridentate ligand catalyzes the aerobic oxidation of sulfides to sulfoxides, alkenes to epoxides, and alcohols to the corresponding carbonyl compounds.
α-Ketoglutarate-dependent enzymes catalyze many important biological oxidation/oxygenation reactions. Iron(iv)–oxo intermediates have been established as key oxidants in these oxidation reactions. While most reported model iron(ii)–α-keto acid complexes exhibit stoichiometric reactivity, selective oxidation of substrates with dioxygen catalyzed by biomimetic iron(ii)–α-keto acid complexes remains unexplored. In this direction, we have investigated the ability of an iron(ii) complex [(TpPh,Me)FeII(BF)] (1) (TpPh,Me = hydrotris(3-phenyl-5-methylpyrazolyl)borate and BF = monoanionic benzoylformate) to catalyze the aerobic oxidation of organic substrates. An iron–oxo oxidant, intercepted in the reaction of 1 with O2, selectively oxidizes sulfides to sulfoxides, alkenes to epoxides, and alcohols to the corresponding carbonyl compounds. The oxidant from 1 is able to hydroxylate the benzylic carbon of phenylacetic acid to afford mandelic acid with the incorporation of one oxygen atom from O2 into the product. The iron(ii)–benzoylformate complex oxidatively converts phenoxyacetic acids to the corresponding phenols, thereby mimicking the function of iron(ii)–α-ketoglutarate-dependent 2,4-dichlorophenoxyacetate dioxygenase (TfdA). Furthermore, complex 1 exhibits catalytic aerobic oxidation of alcohols and oxygen atom transfer reactions with multiple turnovers.
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Affiliation(s)
- Debobrata Sheet
- Department of Inorganic Chemistry , Indian Association for the Cultivation of Science , 2A & 2B Raja S. C. Mullick Road, Jadavpur , Kolkata 700032 , India . ; ; Tel: +91-33-2473-4971
| | - Tapan Kanti Paine
- Department of Inorganic Chemistry , Indian Association for the Cultivation of Science , 2A & 2B Raja S. C. Mullick Road, Jadavpur , Kolkata 700032 , India . ; ; Tel: +91-33-2473-4971
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Zhang J, Liu Z, Liang J, Wu J, Cheng F, Wang X. Three genes encoding AOP2, a protein involved in aliphatic glucosinolate biosynthesis, are differentially expressed in Brassica rapa. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:6205-18. [PMID: 26188204 PMCID: PMC4588880 DOI: 10.1093/jxb/erv331] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The glucosinolate biosynthetic gene AOP2 encodes an enzyme that plays a crucial role in catalysing the conversion of beneficial glucosinolates into anti-nutritional ones. In Brassica rapa, three copies of BrAOP2 have been identified, but their function in establishing the glucosinolate content of B. rapa is poorly understood. Here, we used phylogenetic and gene structure analyses to show that BrAOP2 proteins have evolved via a duplication process retaining two highly conserved domains at the N-terminal and C-terminal regions, while the middle part has experienced structural divergence. Heterologous expression and in vitro enzyme assays and Arabidopsis mutant complementation studies showed that all three BrAOP2 genes encode functional BrAOP2 proteins that convert the precursor methylsulfinyl alkyl glucosinolate to the alkenyl form. Site-directed mutagenesis showed that His356, Asp310, and Arg376 residues are required for the catalytic activity of one of the BrAOP2 proteins (BrAOP2.1). Promoter-β-glucuronidase lines revealed that the BrAOP2.3 gene displayed an overlapping but distinct tissue- and cell-specific expression profile compared with that of the BrAOP2.1 and BrAOP2.2 genes. Quantitative real-time reverse transcription-PCR assays demonstrated that BrAOP2.1 showed a slightly different pattern of expression in below-ground tissue at the seedling stage and in the silique at the reproductive stage compared with BrAOP2.2 and BrAOP2.3 genes in B. rapa. Taken together, our results revealed that all three BrAOP2 paralogues are active in B. rapa but have functionally diverged.
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Affiliation(s)
- Jifang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No. 12, Haidian District, Beijing 100081, PR China
| | - Zhiyuan Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No. 12, Haidian District, Beijing 100081, PR China
| | - Jianli Liang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No. 12, Haidian District, Beijing 100081, PR China
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No. 12, Haidian District, Beijing 100081, PR China
| | - Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No. 12, Haidian District, Beijing 100081, PR China
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No. 12, Haidian District, Beijing 100081, PR China
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Ibarra-Laclette E, Zamudio-Hernández F, Pérez-Torres CA, Albert VA, Ramírez-Chávez E, Molina-Torres J, Fernández-Cortes A, Calderón-Vázquez C, Olivares-Romero JL, Herrera-Estrella A, Herrera-Estrella L. De novo sequencing and analysis of Lophophora williamsii transcriptome, and searching for putative genes involved in mescaline biosynthesis. BMC Genomics 2015; 16:657. [PMID: 26330142 PMCID: PMC4557841 DOI: 10.1186/s12864-015-1821-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 08/07/2015] [Indexed: 12/04/2022] Open
Abstract
Background Lophophora williamsii (commonly named peyote) is a small, spineless cactus with psychoactive alkaloids, particularly mescaline. Peyote utilizes crassulacean acid metabolism (CAM), an alternative form of photosynthesis that exists in succulents such as cacti and other desert plants. Therefore, its transcriptome can be considered an important resource for future research focused on understanding how these plants make more efficient use of water in marginal environments and also for research focused on better understanding of the overall mechanisms leading to production of plant natural products and secondary metabolites. Results In this study, two cDNA libraries were generated from L. williamsii. These libraries, representing buttons (tops of stems) and roots were sequenced using different sequencing platforms (GS-FLX, GS-Junior and PGM, respectively). A total of 5,541,550 raw reads were generated, which were assembled into 63,704 unigenes with an average length of 564.04 bp. A total of 25,149 unigenes (62.19 %) was annotated using public databases. 681 unigenes were found to be differentially expressed when comparing the two libraries, where 400 were preferentially expressed in buttons and 281 in roots. Some of the major alkaloids, including mescaline, were identified by GC-MS and relevant metabolic pathways were reconstructed using the Kyoto encyclopedia of genes and genomes database (KEGG). Subsequently, the expression patterns of preferentially expressed genes putatively involved in mescaline production were examined and validated by qRT-PCR. Conclusions High throughput transcriptome sequencing (RNA-seq) analysis allowed us to efficiently identify candidate genes involved in mescaline biosynthetic pathway in L. williamsii; these included tyrosine/DOPA decarboxylase, hydroxylases, and O-methyltransferases. This study sets the theoretical foundation for bioassay design directed at confirming the participation of these genes in mescaline production. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1821-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Enrique Ibarra-Laclette
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México. .,Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070, Xalapa, Veracruz, México.
| | - Flor Zamudio-Hernández
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México.
| | - Claudia Anahí Pérez-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México. .,Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070, Xalapa, Veracruz, México. .,Investigador Cátedra CONACyT, Instituto de Ecología A.C., 91070, Xalapa, Veracruz, México.
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, 14260, USA.
| | - Enrique Ramírez-Chávez
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, 36821, Irapuato, Guanajuato, México.
| | - Jorge Molina-Torres
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, 36821, Irapuato, Guanajuato, México.
| | - Araceli Fernández-Cortes
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México.
| | - Carlos Calderón-Vázquez
- Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Instituto Politécnico Nacional, 81000, Guasave, Sinaloa, México.
| | | | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México.
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México.
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Theodosiou E, Frick O, Bühler B, Schmid A. Metabolic network capacity of Escherichia coli for Krebs cycle-dependent proline hydroxylation. Microb Cell Fact 2015. [PMID: 26215086 PMCID: PMC4517350 DOI: 10.1186/s12934-015-0298-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Background Understanding the metabolism of the microbial host is essential for the development and optimization of whole-cell based biocatalytic processes, as it dictates production efficiency. This is especially true for redox biocatalysis where metabolically active cells are employed because of the cofactor/cosubstrate regenerative capacity endogenous in the host. Recombinant Escherichia coli was used for overproducing proline-4-hydroxylase (P4H), a dioxygenase catalyzing the hydroxylation of free l-proline into trans-4-hydroxy-l-proline with a-ketoglutarate (a-KG) as cosubstrate. In this whole-cell biocatalyst, central carbon metabolism provides the required cosubstrate a-KG, coupling P4H biocatalytic performance directly to carbon metabolism and metabolic activity. By applying both experimental and computational biology tools, such as metabolic engineering and 13C-metabolic flux analysis (13C-MFA), we investigated and quantitatively described the physiological, metabolic, and bioenergetic response of the whole-cell biocatalyst to the targeted bioconversion and identified possible metabolic bottlenecks for further rational pathway engineering. Results A proline degradation-deficient E. coli strain was constructed by deleting the putA gene encoding proline dehydrogenase. Whole-cell biotransformations with this mutant strain led not only to quantitative proline hydroxylation but also to a doubling of the specific trans-4-l-hydroxyproline (hyp) formation rate, compared to the wild type. Analysis of carbon flux through central metabolism of the mutant strain revealed that the increased a-KG demand for P4H activity did not enhance the a-KG generating flux, indicating a tightly regulated TCA cycle operation under the conditions studied. In the wild type strain, P4H synthesis and catalysis caused a reduction in biomass yield. Interestingly, the ΔputA strain additionally compensated the associated ATP and NADH loss by reducing maintenance energy demands at comparably low glucose uptake rates, instead of increasing the TCA activity. Conclusions The putA knockout in recombinant E. coli BL21(DE3)(pLysS) was found to be promising for productive P4H catalysis not only in terms of biotransformation yield, but also regarding the rates for biotransformation and proline uptake and the yield of hyp on the energy source. The results indicate that, upon a putA knockout, the coupling of the TCA-cycle to proline hydroxylation via the cosubstrate a-KG becomes a key factor constraining and a target to further improve the efficiency of a-KG-dependent biotransformations. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0298-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eleni Theodosiou
- Department of Biochemical and Chemical Engineering, Laboratory of Chemical Biotechnology, TU Dortmund University, Emil-Figge-Strasse 66, 44227, Dortmund, Germany. .,Department of Solar Materials, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.
| | - Oliver Frick
- Department of Solar Materials, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.
| | - Bruno Bühler
- Department of Biochemical and Chemical Engineering, Laboratory of Chemical Biotechnology, TU Dortmund University, Emil-Figge-Strasse 66, 44227, Dortmund, Germany. .,Department of Solar Materials, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.
| | - Andreas Schmid
- Department of Solar Materials, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.
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Andersson I, Valegård K. 2-Oxoglutarate-Dependent Oxygenases of Cephalosporin Synthesis. 2-OXOGLUTARATE-DEPENDENT OXYGENASES 2015. [DOI: 10.1039/9781782621959-00385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Central steps in the biosynthetic pathways of some of the most commonly used antibiotics, the cephalosporins, are catalysed by 2-oxoglutarate (2OG)-dependent oxygenases. Deacetoxycephalosporin C synthase (DAOCS) catalyses the 2OG-dependent oxidative expansion of the five-membered thiazolidine ring of the penicillin nucleus into the six-membered dihydrothiazine ring of the cephalosporin nucleus. DAOCS uses dioxygen to create a reactive iron–oxygen intermediate from ferrous ion to drive the reaction. In prokaryotic cephalosporin producers, the cephalosporin product, DAOC, is hydroxylated at the 3′-position to form deacetylcephalosporin C (DAC) as catalysed by a second 2OG-dependent enzyme, DAC synthase (DACS). In eukaryotic cephalosporin producers, the reaction is catalysed by a bifunctional enzyme, DAOC/DACS, that catalyses both the ring expansion and the 3′-hydroxylation reactions. The prokaryotic and eukaryotic enzymes are closely related to DAOCS by sequence, suggesting these enzymes may have evolved by gene duplication. Cephamycin C-producing microorganisms use two enzymes, encoded by the genes cmcI/J, to convert cephalosporins to their 7α-methoxy derivatives that are less vulnerable to β-lactam hydrolysing enzymes. The methoxylation reaction is dependent on Fe(ii), 2OG and S-adenosylmethionine, suggesting the involvement of another 2OG-dependent oxygenase. Herein, structural and mechanistic features are summarized for these 2OG enzymes that utilize this common and flexible mode of dioxygen activation.
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Affiliation(s)
- Inger Andersson
- Department of Cell and Molecular Biology, Uppsala University Box 596, S-751 24 Uppsala Sweden
| | - Karin Valegård
- Department of Cell and Molecular Biology, Uppsala University Box 596, S-751 24 Uppsala Sweden
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Shah DD, Moran GR. 4-Hydroxyphenylpyruvate Dioxygenase and Hydroxymandelate Synthase: 2-Oxo Acid-Dependent Oxygenases of Importance to Agriculture and Medicine. 2-OXOGLUTARATE-DEPENDENT OXYGENASES 2015. [DOI: 10.1039/9781782621959-00438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Despite a separate evolutionary lineage, 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate synthase (HMS) are appropriately grouped with the 2-oxo acid-dependent oxygenase (2OADO) family of enzymes. HPPD and HMS accomplish highly similar overall chemistry to that observed in the majority of 2OADOs but require only two substrates rather than three. 2OADOs typically use the 2-oxo acid of 2-oxoglutarate (2OG) as a source of electrons to reduce and activate dioxygen in order to oxidize a third specific substrate. HPPD and HMS use instead the pyruvate substituent of 4-hydroxyphenylpyruvate to activate dioxygen and then proceed to also hydroxylate this substrate, each yielding a distinctly different aromatic product. HPPD catalyses the second and committed step of tyrosine catabolism, a pathway common to nearly all aerobes. Plants require the HPPD reaction to biosynthesize plastoquinones and therefore HPPD inhibitors can have potent herbicidal activity. The ubiquity of the HPPD reaction, however, has meant that HPPD-specific molecules developed as herbicides have other uses in different forms of life. In humans herbicidal HPPD inhibitors can be used therapeutically to alleviate specific inborn defects and also to retard the progress of certain bacterial and fungal infections. This review is intended as a concise overview of the contextual and catalytic chemistries of HPPD and HMS.
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Affiliation(s)
- Dhara D. Shah
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee 3210 N. Cramer St Milwaukee WI 53211-3209 USA
| | - Graham R. Moran
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee 3210 N. Cramer St Milwaukee WI 53211-3209 USA
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Sheet D, Bhattacharya S, Paine TK. Dioxygen activation and two consecutive oxidative decarboxylations of phenylpyruvate by nonheme iron(II) complexes: functional models of hydroxymandelate synthase (HMS) and CloR. Chem Commun (Camb) 2015; 51:7681-4. [PMID: 25850011 DOI: 10.1039/c5cc01652e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two mononuclear iron(ii)-phenylpyruvate complexes of monoanionic facial N3 ligands are reported to react with dioxygen to undergo two consecutive oxidative decarboxylation steps via an iron-mandelate complex mimicking the function of HMS and CloR.
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Affiliation(s)
- Debobrata Sheet
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A&2B Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India.
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Tsugawa T, Furutachi H, Marunaka M, Endo T, Hashimoto K, Fujinami S, Akine S, Sakata Y, Nagatomo S, Tosha T, Nomura T, Kitagawa T, Ogura T, Suzuki M. Oxidation Reactivity of a Structurally and Spectroscopically Well-defined Mononuclear Peroxocarbonato–Iron(III) Complex. CHEM LETT 2015. [DOI: 10.1246/cl.141058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Tomohiro Tsugawa
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University
| | - Hideki Furutachi
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University
| | - Megumi Marunaka
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University
| | - Taichi Endo
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University
| | - Koji Hashimoto
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University
| | - Shuhei Fujinami
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University
| | - Shigehisa Akine
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University
| | - Yoko Sakata
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University
| | - Shigenori Nagatomo
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba
| | | | - Takashi Nomura
- Picobiology Institute, Graduate School of Life Science, University of Hyogo
| | - Teizo Kitagawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo
| | - Takashi Ogura
- Picobiology Institute, Graduate School of Life Science, University of Hyogo
| | - Masatatsu Suzuki
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University
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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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Zou XW, Liu YC, Hsu NS, Huang CJ, Lyu SY, Chan HC, Chang CY, Yeh HW, Lin KH, Wu CJ, Tsai MD, Li TL. Structure and mechanism of a nonhaem-iron SAM-dependent C-methyltransferase and its engineering to a hydratase and an O-methyltransferase. ACTA ACUST UNITED AC 2014; 70:1549-60. [PMID: 24914966 DOI: 10.1107/s1399004714005239] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 03/06/2014] [Indexed: 12/16/2022]
Abstract
In biological systems, methylation is most commonly performed by methyltransferases (MTs) using the electrophilic methyl source S-adenosyl-L-methionine (SAM) via the S(N)2 mechanism. (2S,3S)-β-Methylphenylalanine, a nonproteinogenic amino acid, is a building unit of the glycopeptide antibiotic mannopeptimycin. The gene product of mppJ from the mannopeptimycin-biosynthetic gene cluster is the MT that methylates the benzylic C atom of phenylpyruvate (Ppy) to give βMePpy. Although the benzylic C atom of Ppy is acidic, how its nucleophilicity is further enhanced to become an acceptor for C-methylation has not conclusively been determined. Here, a structural approach is used to address the mechanism of MppJ and to engineer it for new functions. The purified MppJ displays a turquoise colour, implying the presence of a metal ion. The crystal structures reveal MppJ to be the first ferric ion SAM-dependent MT. An additional four structures of binary and ternary complexes illustrate the molecular mechanism for the metal ion-dependent methyltransfer reaction. Overall, MppJ has a nonhaem iron centre that bind, orients and activates the α-ketoacid substrate and has developed a sandwiched bi-water device to avoid the formation of the unwanted reactive oxo-iron(IV) species during the C-methylation reaction. This discovery further prompted the conversion of the MT into a structurally/functionally unrelated new enzyme. Through stepwise mutagenesis and manipulation of coordination chemistry, MppJ was engineered to perform both Lewis acid-assisted hydration and/or O-methyltransfer reactions to give stereospecific new compounds. This process was validated by six crystal structures. The results reported in this study will facilitate the development and design of new biocatalysts for difficult-to-synthesize biochemicals.
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Affiliation(s)
- Xiao-Wei Zou
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Chen Liu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ning-Shian Hsu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | | | - Syue-Yi Lyu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hsiu-Chien Chan
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chin-Yuan Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hsien-Wei Yeh
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Kuan-Hung Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chang-Jer Wu
- Department of Food Science, National Taiwan Ocean University, Keelung 202, Taiwan
| | - Ming-Daw Tsai
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Tsung-Lin Li
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
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4-Hydroxyphenylpyruvate dioxygenase and hydroxymandelate synthase: exemplars of the α-keto acid dependent oxygenases. Arch Biochem Biophys 2013; 544:58-68. [PMID: 24211436 DOI: 10.1016/j.abb.2013.10.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 10/28/2013] [Accepted: 10/30/2013] [Indexed: 11/23/2022]
Abstract
4-Hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate synthase (HMS) are outliers within the α-keto acid dependent oxygenase (αKAO) family. HPPD and HMS catalyze the chemistry of the majority of enzymes within the αKAO family but are clearly mechanistically convergent, having a grossly different structural topology. Some of the unique characteristics of HPPD and HMS have elucidated select parts of the catalytic cycle that are obscured in other family members. Moreover, the inhibitory chemistry of HPPD is a phenomenon with ever-expanding relevance across all kingdoms of life. This review is a synopsis of the literature pertaining to HPPD and HMS. It is not intended as an exhaustive compilation of all observations made for these enzymes but rather a condensed narrative that connects those studies that have advanced the understanding of the chemistry of both enzymes.
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Epigenetic control of the immune system: histone demethylation as a target for drug discovery. DRUG DISCOVERY TODAY. TECHNOLOGIES 2013; 7:e1-e94. [PMID: 24103687 DOI: 10.1016/j.ddtec.2010.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Casey TM, Grzyska PK, Hausinger RP, McCracken J. Measuring the orientation of taurine in the active site of the non-heme Fe(II)/α-ketoglutarate-dependent taurine hydroxylase (TauD) using electron spin echo envelope modulation (ESEEM) spectroscopy. J Phys Chem B 2013; 117:10384-94. [PMID: 23937570 PMCID: PMC3854568 DOI: 10.1021/jp404743d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The position and orientation of taurine near the non-heme Fe(II) center of the α-ketoglutarate (α-KG)-dependent taurine hydroxylase (TauD) was measured using Electron Spin Echo Envelope Modulation (ESEEM) spectroscopy. TauD solutions containing Fe(II), α-KG, and natural abundance taurine or specifically deuterated taurine were prepared anaerobically and treated with nitric oxide (NO) to make an S = 3/2 {FeNO}(7) complex that is suitable for robust analysis with EPR spectroscopy. Using ratios of ESEEM spectra collected for TauD samples having natural abundance taurine or deuterated taurine, (1)H and (14)N modulations were filtered out of the spectra and interactions with specific deuterons on taurine could be studied separately. The Hamiltonian parameters used to calculate the amplitudes and line shapes of frequency spectra containing isolated deuterium ESEEM were obtained with global optimization algorithms. Additional statistical analysis was performed to validate the interpretation of the optimized parameters. The strongest (2)H hyperfine coupling was to a deuteron on the C1 position of taurine and was characterized by an effective dipolar distance of 3.90 ± 0.25 Å from the {FeNO}(7) paramagnetic center. The principal axes of this C1-(2)H hyperfine coupling and nuclear quadrupole interaction tensors were found to make angles of 26 ± 5 and 52 ± 17°, respectively, with the principal axis of the {FeNO}(7) zero-field splitting tensor. These results are discussed within the context of the orientation of substrate taurine prior to the initiation of hydrogen abstraction.
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Affiliation(s)
- Thomas M. Casey
- Department of Chemistry, Michigan State University, East Lansing MI-48824
| | - Piotr K. Grzyska
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing MI-48824
| | - Robert P. Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing MI-48824
| | - John McCracken
- Department of Chemistry, Michigan State University, East Lansing MI-48824
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Xu Q, Grant J, Chiu HJ, Farr CL, Jaroszewski L, Knuth MW, Miller MD, Lesley SA, Godzik A, Elsliger MA, Deacon AM, Wilson IA. Crystal structure of a member of a novel family of dioxygenases (PF10014) reveals a conserved cupin fold and active site. Proteins 2013; 82:164-70. [PMID: 23852666 DOI: 10.1002/prot.24362] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 06/24/2013] [Accepted: 06/27/2013] [Indexed: 12/12/2022]
Abstract
PF10014 is a novel family of 2-oxyglutarate-Fe(2+) -dependent dioxygenases that are involved in biosynthesis of antibiotics and regulation of biofilm formation, likely by catalyzing hydroxylation of free amino acids or other related ligands. The crystal structure of a PF10014 member from Methylibium petroleiphilum at 1.9 Å resolution shows strong structural similarity to cupin dioxygenases in overall fold and active site, despite very remote homology. However, one of the β-strands of the cupin catalytic core is replaced by a loop that displays conformational isomerism that likely regulates the active site.
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Affiliation(s)
- Qingping Xu
- Joint Center for Structural Genomics, La Jolla, California (http://www.jcsg.org); Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, 94025
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Shah DD, Conrad JA, Moran GR. Intermediate Partitioning Kinetic Isotope Effects for the NIH Shift of 4-Hydroxyphenylpyruvate Dioxygenase and the Hydroxylation Reaction of Hydroxymandelate Synthase Reveal Mechanistic Complexity. Biochemistry 2013; 52:6097-107. [DOI: 10.1021/bi400534q] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Dhara D. Shah
- Department of Chemistry
and Biochemistry, University of Wisconsin—Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211-3209, United
States
| | - John A. Conrad
- Department
of Chemistry, University of Nebraska—Omaha,
6001 Dodge Street, Omaha, Nebraska 68182-0109, United States
| | - Graham R. Moran
- Department of Chemistry
and Biochemistry, University of Wisconsin—Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211-3209, United
States
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Farrow SC, Facchini PJ. Dioxygenases catalyze O-demethylation and O,O-demethylenation with widespread roles in benzylisoquinoline alkaloid metabolism in opium poppy. J Biol Chem 2013; 288:28997-9012. [PMID: 23928311 DOI: 10.1074/jbc.m113.488585] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In opium poppy, the antepenultimate and final steps in morphine biosynthesis are catalyzed by the 2-oxoglutarate/Fe(II)-dependent dioxygenases, thebaine 6-O-demethylase (T6ODM) and codeine O-demethylase (CODM). Further investigation into the biochemical functions of CODM and T6ODM revealed extensive and unexpected roles for such enzymes in the metabolism of protopine, benzo[c]phenanthridine, and rhoeadine alkaloids. When assayed with a wide range of benzylisoquinoline alkaloids, CODM, T6ODM, and the functionally unassigned paralog DIOX2, renamed protopine O-dealkylase, showed novel and efficient dealkylation activities, including regio- and substrate-specific O-demethylation and O,O-demethylenation. Enzymes catalyzing O,O-demethylenation, which cleave a methylenedioxy bridge leaving two hydroxyl groups, have previously not been reported in plants. Similar cleavage of methylenedioxy bridges on substituted amphetamines is catalyzed by heme-dependent cytochromes P450 in mammals. Preferred substrates for O,O-demethylenation by CODM and protopine O-dealkylase were protopine alkaloids that serve as intermediates in the biosynthesis of benzo[c]phenanthridine and rhoeadine derivatives. Virus-induced gene silencing used to suppress the abundance of CODM and/or T6ODM transcripts indicated a direct physiological role for these enzymes in the metabolism of protopine alkaloids, and they revealed their indirect involvement in the formation of the antimicrobial benzo[c]phenanthridine sanguinarine and certain rhoeadine alkaloids in opium poppy.
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Affiliation(s)
- Scott C Farrow
- From the Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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Hüttel W. Biocatalytic Production of Chemical Building Blocks in Technical Scale with α-Ketoglutarate-Dependent Dioxygenases. CHEM-ING-TECH 2013. [DOI: 10.1002/cite.201300008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Das O, Chatterjee S, Paine TK. Functional models of α-keto acid dependent nonheme iron oxygenases: synthesis and reactivity of biomimetic iron(II) benzoylformate complexes supported by a 2,9-dimethyl-1,10-phenanthroline ligand. J Biol Inorg Chem 2013; 18:401-10. [PMID: 23417539 DOI: 10.1007/s00775-013-0984-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 01/31/2013] [Indexed: 01/12/2023]
Abstract
Two biomimetic iron(II) benzoylformate complexes, [LFe(II)(BF)(2)] (2) and [LFe(II)(NO(3))(BF)] (3) (L is 2,9-dimethyl-1,10-phenanthroline and BF is monoanionic benzoylformate), have been synthesized from an iron(II)-dichloro complex [LFe(II)Cl(2)] (1). All the iron(II) complexes have been structurally and spectroscopically characterized. The iron(II) center in 2 is coordinated by a bidentate NN ligand (2,9-dimethyl-1,10-phenanthroline) and two monoanionic benzoylformates to form a distorted octahedral coordination geometry. One of the benzoylformates binds to the iron in 2 via both carboxylate oxygens but the other one binds in a chelating bidentate fashion via one carboxylate oxygen and the keto oxygen. On the other hand, the iron(II) center in 3 is ligated by one NN ligand, one bidentate nitrate, and one monoanionic chelating benzoylformate. Both iron(II) benzoylformate complexes exhibit the facial NNO donor environment in their solid-state structures. Complexes 2 and 3 are stable in noncoordinating solvents under an inert atmosphere, but react with dioxygen under ambient conditions to undergo oxidative decarboxylation of benzoylformate to benzoate in high yields. Evidence for the formation of an iron(IV)-oxo intermediate upon oxidative decarboxylation of benzoylformate was obtained by interception and labeling experiments. The iron(II) benzoylformate complexes represent the functional models of α-keto acid dependent oxygenases.
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Affiliation(s)
- Oindrila Das
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, 700032, Kolkata, India
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Chakraborty B, Halder P, Banerjee PR, Paine TK. Oxidative C–C Bond Cleavage of α‐Keto Acids by Cobalt(II) Complexes of Nitrogen Donor Ligands. Eur J Inorg Chem 2012. [DOI: 10.1002/ejic.201200663] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Biswarup Chakraborty
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India, Fax: +91‐33‐2473‐2805
| | - Partha Halder
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India, Fax: +91‐33‐2473‐2805
| | - Priya Ranjan Banerjee
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India, Fax: +91‐33‐2473‐2805
| | - Tapan Kanti Paine
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India, Fax: +91‐33‐2473‐2805
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Schmid A, Fu J, Buehler K. Herstellung von Hydroxyprolin mit rekombinanten Escherichia coli. CHEM-ING-TECH 2012. [DOI: 10.1002/cite.201250293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Klein C, Hüttel W. Tertiary alcohol preferred: Hydroxylation of trans-3-methyl-L-proline with proline hydroxylases. Beilstein J Org Chem 2012; 7:1643-7. [PMID: 22238542 PMCID: PMC3252868 DOI: 10.3762/bjoc.7.193] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 11/14/2011] [Indexed: 01/17/2023] Open
Abstract
The enzymatic synthesis of tertiary alcohols by the stereospecific oxidation of tertiary alkyl centers is a most-straightforward but challenging approach, since these positions are sterically hindered. In contrast to P450-monooxygenases, there is little known about the potential of non-heme iron(II) oxygenases to catalyze such reactions. We have studied the hydroxylation of trans-3-methyl-L-proline with the α-ketoglutarate (α-KG) dependent oxygenases, cis-3-proline hydroxylase type II and cis-4-proline hydroxylase (cis-P3H_II and cis-P4H). With cis-P3H_II, the tertiary alcohol product (3R)-3-hydroxy-3-methyl-L-proline was obtained exclusively but in reduced yield (~7%) compared to the native substrate L-proline. For cis-P4H, a complete shift in regioselectivity from C-4 to C-3 was observed so that the same product as with cis-P3H_II was obtained. Moreover, the yields were at least as good as in control reactions with L-proline (~110% relative yield). This result demonstrates a remarkable potential of non-heme iron(II) oxygenases to oxidize substrates selectively at sterically hindered positions.
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Affiliation(s)
- Christian Klein
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical and Medicinal Chemistry, Albert-Ludwigs-Universität Freiburg, Albertstr. 25, 79104 Freiburg, Germany
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40
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Diebold AR, Brown-Marshall CD, Neidig ML, Brownlee JM, Moran GR, Solomon EI. Activation of α-keto acid-dependent dioxygenases: application of an {FeNO}7/{FeO2}8 methodology for characterizing the initial steps of O2 activation. J Am Chem Soc 2011; 133:18148-60. [PMID: 21981763 PMCID: PMC3212634 DOI: 10.1021/ja202549q] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The α-keto acid-dependent dioxygenases are a major subgroup within the O(2)-activating mononuclear nonheme iron enzymes. For these enzymes, the resting ferrous, the substrate plus cofactor-bound ferrous, and the Fe(IV)═O states of the reaction have been well studied. The initial O(2)-binding and activation steps are experimentally inaccessible and thus are not well understood. In this study, NO is used as an O(2) analogue to probe the effects of α-keto acid binding in 4-hydroxyphenylpyruvate dioxygenase (HPPD). A combination of EPR, UV-vis absorption, magnetic circular dichroism (MCD), and variable-temperature, variable-field (VTVH) MCD spectroscopies in conjunction with computational models is used to explore the HPPD-NO and HPPD-HPP-NO complexes. New spectroscopic features are present in the α-keto acid bound {FeNO}(7) site that reflect the strong donor interaction of the α-keto acid with the Fe. This promotes the transfer of charge from the Fe to NO. The calculations are extended to the O(2) reaction coordinate where the strong donation associated with the bound α-keto acid promotes formation of a new, S = 1 bridged Fe(IV)-peroxy species. These studies provide insight into the effects of a strong donor ligand on O(2) binding and activation by Fe(II) in the α-keto acid-dependent dioxygenases and are likely relevant to other subgroups of the O(2) activating nonheme ferrous enzymes.
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Affiliation(s)
- Adrienne R. Diebold
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | | | - Michael L. Neidig
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - June M. Brownlee
- Department of Chemistry and Biochemistry, University of Wisconsin-Madison, Milwaukee, Wisconsin 53211, USA
| | - Graham R. Moran
- Department of Chemistry and Biochemistry, University of Wisconsin-Madison, Milwaukee, Wisconsin 53211, USA
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
- Stanford Synchrotron Radiation Lightsource, SLAC, Stanford, CA 94309
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Abstract
Nickel has long been known to be an important human toxicant, including having the ability to form carcinomas, but until recently nickel was believed to be an issue only to microorganisms living in nickel-rich serpentine soils or areas contaminated by industrial pollution. This assumption was overturned by the discovery of a nickel defense system (RcnR/RcnA) found in microorganisms that live in a wide range of environmental niches, suggesting that nickel homeostasis is a general biological concern. To date, the mechanisms of nickel toxicity in microorganisms and higher eukaryotes are poorly understood. In this review, we summarize nickel homeostasis processes used by microorganisms and highlight in vivo and in vitro effects of exposure to elevated concentrations of nickel. On the basis of this evidence we propose four mechanisms of nickel toxicity: (1) nickel replaces the essential metal of metalloproteins, (2) nickel binds to catalytic residues of non-metalloenzymes; (3) nickel binds outside the catalytic site of an enzyme to inhibit allosterically and (4) nickel indirectly causes oxidative stress.
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Affiliation(s)
- Lee Macomber
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824-4320, USA
| | - Robert P. Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824-4320, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, USA
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Diebold AR, Straganz GD, Solomon EI. Spectroscopic and computational studies of α-keto acid binding to Dke1: understanding the role of the facial triad and the reactivity of β-diketones. J Am Chem Soc 2011; 133:15979-91. [PMID: 21870808 PMCID: PMC3191879 DOI: 10.1021/ja203005j] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The O(2) activating mononuclear nonheme iron enzymes generally have a common facial triad (two histidine and one carboxylate (Asp or Glu) residue) ligating Fe(II) at the active site. Exceptions to this motif have recently been identified in nonheme enzymes, including a 3His triad in the diketone cleaving dioxygenase Dke1. This enzyme is used to explore the role of the facial triad in directing reactivity. A combination of spectroscopic studies (UV-vis absorption, MCD, and resonance Raman) and DFT calculations is used to define the nature of the binding of the α-keto acid, 4-hydroxyphenlpyruvate (HPP), to the active site in Dke1 and the origin of the atypical cleavage (C2-C3 instead of C1-C2) pattern exhibited by this enzyme in the reaction of α-keto acids with dioxygen. The reduced charge of the 3His triad induces α-keto acid binding as the enolate dianion, rather than the keto monoanion, found for α-keto acid binding to the 2His/1 carboxylate facial triad enzymes. The mechanistic insight from the reactivity of Dke1 with the α-keto acid substrate is then extended to understand the reaction mechanism of this enzyme with its native substrate, acac. This study defines a key role for the 2His/1 carboxylate facial triad in α-keto acid-dependent mononuclear nonheme iron enzymes in stabilizing the bound α-keto acid as a monoanion for its decarboxylation to provide the two additional electrons required for O(2) activation.
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Affiliation(s)
- Adrienne R. Diebold
- Department of Chemistry, Stanford University, Stanford, California 94305, USA and Stanford Synchrotron Radiation Lightsource, SLAC, Stanford, CA 94309
| | - Grit D. Straganz
- Institute for Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, USA and Stanford Synchrotron Radiation Lightsource, SLAC, Stanford, CA 94309
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43
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He P, Moran GR. Structural and mechanistic comparisons of the metal-binding members of the vicinal oxygen chelate (VOC) superfamily. J Inorg Biochem 2011; 105:1259-72. [DOI: 10.1016/j.jinorgbio.2011.06.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 06/21/2011] [Accepted: 06/24/2011] [Indexed: 11/30/2022]
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Traber MG, Stevens JF. Vitamins C and E: beneficial effects from a mechanistic perspective. Free Radic Biol Med 2011; 51:1000-13. [PMID: 21664268 PMCID: PMC3156342 DOI: 10.1016/j.freeradbiomed.2011.05.017] [Citation(s) in RCA: 508] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 05/13/2011] [Accepted: 05/17/2011] [Indexed: 02/07/2023]
Abstract
The mechanistic properties of two dietary antioxidants that are required by humans, vitamins C and E, are discussed relative to their biological effects. Vitamin C (ascorbic acid) is an essential cofactor for α-ketoglutarate-dependent dioxygenases. Examples are prolyl hydroxylases, which play a role in the biosynthesis of collagen and in down-regulation of hypoxia-inducible factor (HIF)-1, a transcription factor that regulates many genes responsible for tumor growth, energy metabolism, and neutrophil function and apoptosis. Vitamin C-dependent inhibition of the HIF pathway may provide alternative or additional approaches for controlling tumor progression, infections, and inflammation. Vitamin E (α-tocopherol) functions as an essential lipid-soluble antioxidant, scavenging hydroperoxyl radicals in a lipid milieu. Human symptoms of vitamin E deficiency suggest that its antioxidant properties play a major role in protecting erythrocyte membranes and nervous tissues. As an antioxidant, vitamin C provides protection against oxidative stress-induced cellular damage by scavenging of reactive oxygen species, by vitamin E-dependent neutralization of lipid hydroperoxyl radicals, and by protecting proteins from alkylation by electrophilic lipid peroxidation products. These bioactivities bear relevance to inflammatory disorders. Vitamin C also plays a role in the function of endothelial nitric oxide synthase (eNOS) by recycling the eNOS cofactor, tetrahydrobiopterin, which is relevant to arterial elasticity and blood pressure regulation. Evidence from plants supports a role for vitamin C in the formation of covalent adducts with electrophilic secondary metabolites. Mechanism-based effects of vitamin C and E supplementation on biomarkers and on clinical outcomes from randomized, placebo-controlled trials are emphasized in this review.
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Affiliation(s)
- Maret G Traber
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA.
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Shah DD, Conrad JA, Heinz B, Brownlee JM, Moran GR. Evidence for the Mechanism of Hydroxylation by 4-Hydroxyphenylpyruvate Dioxygenase and Hydroxymandelate Synthase from Intermediate Partitioning in Active Site Variants. Biochemistry 2011; 50:7694-704. [DOI: 10.1021/bi2009344] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dhara D. Shah
- Department of Chemistry
and Biochemistry, University of Wisconsin—Milwaukee, 3210 N. Cramer
St., Milwaukee, Wisconsin 53211-3029, United States
| | - John A. Conrad
- Department of Chemistry
and Biochemistry, University of Wisconsin—Milwaukee, 3210 N. Cramer
St., Milwaukee, Wisconsin 53211-3029, United States
| | - Brian Heinz
- Department of Chemistry
and Biochemistry, University of Wisconsin—Milwaukee, 3210 N. Cramer
St., Milwaukee, Wisconsin 53211-3029, United States
| | - June M. Brownlee
- Department of Chemistry
and Biochemistry, University of Wisconsin—Milwaukee, 3210 N. Cramer
St., Milwaukee, Wisconsin 53211-3029, United States
| | - Graham R. Moran
- Department of Chemistry
and Biochemistry, University of Wisconsin—Milwaukee, 3210 N. Cramer
St., Milwaukee, Wisconsin 53211-3029, United States
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Bjørnstad L, Zoppellaro G, Tomter A, Falnes P, Andersson K. Spectroscopic and magnetic studies of wild-type and mutant forms of the Fe(II)- and 2-oxoglutarate-dependent decarboxylase ALKBH4. Biochem J 2011; 434:391-8. [PMID: 21166655 PMCID: PMC3048578 DOI: 10.1042/bj20101667] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 12/14/2010] [Accepted: 12/20/2010] [Indexed: 11/24/2022]
Abstract
The Fe(II)/2OG (2-oxoglutarate)-dependent dioxygenase superfamily comprises proteins that couple substrate oxidation to decarboxylation of 2OG to succinate. A member of this class of mononuclear non-haem Fe proteins is the Escherichia coli DNA/RNA repair enzyme AlkB. In the present work, we describe the magnetic and optical properties of the yet uncharacterized human ALKBH4 (AlkB homologue). Through EPR and UV-visible spectroscopy studies, we address the Fe-binding environment of the proposed catalytic centre of wild-type ALKBH4 and an Fe(II)-binding mutant. We could observe a novel unusual Fe(III) high-spin EPR-active species in the presence of sulfide with a g(max) of 8.2. The Fe(II) site was probed with NO. An intact histidine-carboxylate site is necessary for productive Fe binding. We also report the presence of a unique cysteine-rich motif conserved in the N-terminus of ALKBH4 orthologues, and investigate its possible Fe-binding ability. Furthermore, we show that recombinant ALKBH4 mediates decarboxylation of 2OG in absence of primary substrate. This activity is dependent on Fe as well as on residues predicted to be involved in Fe(II) co-ordination. The present results demonstrate that ALKBH4 represents an active Fe(II)/2OG-dependent decarboxylase and suggest that the cysteine cluster is involved in processes other than Fe co-ordination.
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Key Words
- alkb
- alkb homologue (alkbh4)
- epr
- non-haem fe
- uv–visible spectroscopy
- alkbh, alkb homologue
- fto, fat mass and obesity-associated protein
- gst, glutathione transferase
- icp-aep, inductively coupled plasma atomic emission spectroscopy
- ipns, isopenicillin n synthase
- iptg, isopropyl β-d-thiogalactopyranoside
- mv•+, methyl viologen radical cation
- 2og, 2-oxoglutarate
- pah, phenylalanine hydroxylase
- 4,5-pcd, protocatechuate 4,5-dioxygenase
- taud, taurine dioxygenase
- uv–vis, uv–visible
- zfs, zero-field splitting
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Affiliation(s)
- Linn G. Bjørnstad
- Department of Molecular Biosciences, University of Oslo, P.O. Box 1041, Blindern, NO-0316 Oslo, Norway
| | - Giorgio Zoppellaro
- Department of Molecular Biosciences, University of Oslo, P.O. Box 1041, Blindern, NO-0316 Oslo, Norway
| | - Ane B. Tomter
- Department of Molecular Biosciences, University of Oslo, P.O. Box 1041, Blindern, NO-0316 Oslo, Norway
| | - Pål Ø. Falnes
- Department of Molecular Biosciences, University of Oslo, P.O. Box 1041, Blindern, NO-0316 Oslo, Norway
| | - K. Kristoffer Andersson
- Department of Molecular Biosciences, University of Oslo, P.O. Box 1041, Blindern, NO-0316 Oslo, Norway
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Abstract
Whole-cell biocatalysis utilizes native or recombinant enzymes produced by cellular metabolism to perform synthetically interesting reactions. Besides hydrolases, oxidoreductases represent the most applied enzyme class in industry. Oxidoreductases are attributed a high future potential, especially for applications in the chemical and pharmaceutical industries, as they enable highly interesting chemistry (e.g., the selective oxyfunctionalization of unactivated C-H bonds). Redox reactions are characterized by electron transfer steps that often depend on redox cofactors as additional substrates. Their regeneration typically is accomplished via the metabolism of whole-cell catalysts. Traditionally, studies towards productive redox biocatalysis focused on the biocatalytic enzyme, its activity, selectivity, and specificity, and several successful examples of such processes are running commercially. However, redox cofactor regeneration by host metabolism was hardly considered for the optimization of biocatalytic rate, yield, and/or titer. This article reviews molecular mechanisms of oxidoreductases with synthetic potential and the host redox metabolism that fuels biocatalytic reactions with redox equivalents. The tools discussed in this review for investigating redox metabolism provide the basis for studies aiming at a deeper understanding of the interplay between synthetically active enzymes and metabolic networks. The ultimate goal of rational whole-cell biocatalyst engineering and use for fine chemical production is discussed.
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Hagel JM, Facchini PJ. Biochemistry and occurrence of o-demethylation in plant metabolism. Front Physiol 2010; 1:14. [PMID: 21423357 PMCID: PMC3059935 DOI: 10.3389/fphys.2010.00014] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 06/05/2010] [Indexed: 12/03/2022] Open
Abstract
Demethylases play a pivitol role in numerous biological processes from covalent histone modification and DNA repair to specialized metabolism in plants and microorganisms. Enzymes that catalyze O- and N-demethylation include 2-oxoglutarate (2OG)/Fe(II)-dependent dioxygenases, cytochromes P450, Rieske-domain proteins and flavin adenine dinucleotide (FAD)-dependent oxidases. Proposed mechanisms for demethylation by 2OG/Fe(II)-dependent enzymes involve hydroxylation at the O- or N-linked methyl group followed by formaldehyde elimination. Members of this enzyme family catalyze a wide variety of reactions in diverse plant metabolic pathways. Recently, we showed that 2OG/Fe(II)-dependent dioxygenases catalyze the unique O-demethylation steps of morphine biosynthesis in opium poppy, which provides a rational basis for the widespread occurrence of demethylases in benzylisoquinoline alkaloid metabolism.
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Affiliation(s)
- Jillian M Hagel
- Department of Biological Sciences, University of Calgary Calgary, AB, Canada
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Reuter K, Pittelkow M, Bursy J, Heine A, Craan T, Bremer E. Synthesis of 5-hydroxyectoine from ectoine: crystal structure of the non-heme iron(II) and 2-oxoglutarate-dependent dioxygenase EctD. PLoS One 2010; 5:e10647. [PMID: 20498719 PMCID: PMC2871039 DOI: 10.1371/journal.pone.0010647] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Accepted: 04/19/2010] [Indexed: 12/15/2022] Open
Abstract
As a response to high osmolality, many microorganisms synthesize various types of compatible solutes. These organic osmolytes aid in offsetting the detrimental effects of low water activity on cell physiology. One of these compatible solutes is ectoine. A sub-group of the ectoine producer's enzymatically convert this tetrahydropyrimidine into a hydroxylated derivative, 5-hydroxyectoine. This compound also functions as an effective osmostress protectant and compatible solute but it possesses properties that differ in several aspects from those of ectoine. The enzyme responsible for ectoine hydroxylation (EctD) is a member of the non-heme iron(II)-containing and 2-oxoglutarate-dependent dioxygenases (EC 1.14.11). These enzymes couple the decarboxylation of 2-oxoglutarate with the formation of a high-energy ferryl-oxo intermediate to catalyze the oxidation of the bound organic substrate. We report here the crystal structure of the ectoine hydroxylase EctD from the moderate halophile Virgibacillus salexigens in complex with Fe3+ at a resolution of 1.85 Å. Like other non-heme iron(II) and 2-oxoglutarate dependent dioxygenases, the core of the EctD structure consists of a double-stranded β-helix forming the main portion of the active-site of the enzyme. The positioning of the iron ligand in the active-site of EctD is mediated by an evolutionarily conserved 2-His-1-carboxylate iron-binding motif. The side chains of the three residues forming this iron-binding site protrude into a deep cavity in the EctD structure that also harbours the 2-oxoglutarate co-substrate-binding site. Database searches revealed a widespread occurrence of EctD-type proteins in members of the Bacteria but only in a single representative of the Archaea, the marine crenarchaeon Nitrosopumilus maritimus. The EctD crystal structure reported here can serve as a template to guide further biochemical and structural studies of this biotechnologically interesting enzyme family.
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Affiliation(s)
- Klaus Reuter
- Department of Pharmacy, Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
- * E-mail: (KR); (EB)
| | - Marco Pittelkow
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Jan Bursy
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Andreas Heine
- Department of Pharmacy, Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Tobias Craan
- Department of Pharmacy, Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- * E-mail: (KR); (EB)
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50
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Gupta AK, Tolman WB. Copper/alpha-ketocarboxylate chemistry with supporting peralkylated diamines: reactivity of copper(I) complexes and dicopper-oxygen intermediates. Inorg Chem 2010; 49:3531-9. [PMID: 20218646 PMCID: PMC2878206 DOI: 10.1021/ic100032n] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To further understand copper-promoted oxidation reactions, the Cu(I) complexes LCuX (L = N,N'-di-tert-butyl-N,N'-dimethylethylenediamine; X = benzoylformate (BF) or p-nitro-benzoylformate) were synthesized, fully characterized by X-ray crystallography and spectroscopy in solution, and their reactivity with O(2) at -80 degrees C examined. Oxidative decarboxylation of the alpha-ketocarboxylate ligand was observed, but only to a significant extent when cyclohexene, cyclooctene, or acetonitrile was present. Spectroscopic and conductivity data are consistent with mechanistic postulates involving displacement of the alpha-ketocarboxylate by the additives to a small extent, followed by oxygenation of the LCu(I) moiety to yield copper-oxygen species that subsequently induce decarboxylation. To test these hypotheses, spectroscopic and kinetic studies of the reactions of Bu(4)NBF with preformed mu-eta(2):eta(2)-peroxodicopper(II) and/or bis(mu-oxo)dicopper(III) complexes supported by L or N,N,N',N'-tetramethylpropylenediamine were performed. In an illustration of a new mode of reactivity for such dicopper-oxygen cores, decarboxylation of the added alpha-ketocarboxylate was observed and the intermediacy of a carboxylate-bridged mu-eta(2):eta(2)-peroxodicopper(II) complex was implicated.
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Affiliation(s)
- Aalo K. Gupta
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455
| | - William B. Tolman
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455
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