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Fu Y, Wang B, Cao Z. Biodegradation of 2,5-Dihydroxypyridine by 2,5-Dihydroxypyridine Dioxygenase and Its Mutants: Insights into O–O Bond Activation and Flexible Reaction Mechanisms from QM/MM Simulations. Inorg Chem 2022; 61:20501-20512. [DOI: 10.1021/acs.inorgchem.2c03229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yuzhuang Fu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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2
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Dunham NP, Arnold FH. Nature's Machinery, Repurposed: Expanding the Repertoire of Iron-Dependent Oxygenases. ACS Catal 2020; 10:12239-12255. [PMID: 33282461 PMCID: PMC7710332 DOI: 10.1021/acscatal.0c03606] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Iron is an especially important redox-active cofactor in biology because of its ability to mediate reactions with atmospheric O2. Iron-dependent oxygenases exploit this earth-abundant transition metal for the insertion of oxygen atoms into organic compounds. Throughout the astounding diversity of transformations catalyzed by these enzymes, the protein framework directs reactive intermediates toward the precise formation of products, which, in many cases, necessitates the cleavage of strong C-H bonds. In recent years, members of several iron-dependent oxygenase families have been engineered for new-to-nature transformations that offer advantages over conventional synthetic methods. In this Perspective, we first explore what is known about the reactivity of heme-dependent cytochrome P450 oxygenases and nonheme iron-dependent oxygenases bearing the 2-His-1-carboxylate facial triad by reviewing mechanistic studies with an emphasis on how the protein scaffold maximizes the catalytic potential of the iron-heme and iron cofactors. We then review how these cofactors have been repurposed for abiological transformations by engineering the protein frameworks of these enzymes. Finally, we discuss contemporary challenges associated with engineering these platforms and comment on their roles in biocatalysis moving forward.
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Affiliation(s)
- Noah P. Dunham
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
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3
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Monika, Ansari A. Mechanistic insights into the allylic oxidation of aliphatic compounds by tetraamido iron( v) species: A C–H vs. O–H bond activation. NEW J CHEM 2020. [DOI: 10.1039/d0nj03095c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work is based on a deep insight into a comparative study of C–H vs. O–H bond activation of allylic compound by the high valent iron complex. Our theoretical findings can help to design catalysts with better efficiency for catalytic reactions.
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Affiliation(s)
- Monika
- Department of Chemistry
- Central University of Haryana
- Mahendergarh-123031
- India
| | - Azaj Ansari
- Department of Chemistry
- Central University of Haryana
- Mahendergarh-123031
- India
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4
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Mono- and binuclear non-heme iron chemistry from a theoretical perspective. J Biol Inorg Chem 2016; 21:619-44. [DOI: 10.1007/s00775-016-1357-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/29/2016] [Indexed: 10/21/2022]
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Raba A, Cokoja M, Herrmann WA, Kühn FE. Catalytic hydroxylation of benzene and toluene by an iron complex bearing a chelating di-pyridyl-di-NHC ligand. Chem Commun (Camb) 2015; 50:11454-7. [PMID: 24840886 DOI: 10.1039/c4cc02178a] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work reports on iron-catalysed hydroxylation of benzene and toluene using aqueous H2O2. While benzene is hydroxylated with a high selectivity to phenol, toluene is hydroxylated to cresols with a high selectivity for the ortho and para-position. An inverse KIE indicates the presence of a high valent Fe=O species during catalysis.
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Affiliation(s)
- Andreas Raba
- Chair of Inorganic Chemistry/Molecular Catalysis, Catalysis Research Center, Technische Universität München, Ernst-Otto-Fischer-Straße 1, D-85747 Garching bei München, Germany.
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6
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Ansari A, Rajaraman G. ortho-Hydroxylation of aromatic acids by a non-heme Fe(V)=O species: how important is the ligand design? Phys Chem Chem Phys 2015; 16:14601-13. [PMID: 24812659 DOI: 10.1039/c3cp55430a] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
There is a growing interest in probing the mechanism of catalytic transformations effected by non-heme iron-oxo complexes as these reactions set a platform for understanding the relevant enzymatic reactions. The ortho-hydroxylation of aromatic compounds is one such reaction catalysed by iron-oxo complexes. Experimentally [Fe(II)(BPMEN)(CH3CN)2](2+) (1) and [Fe(II)(TPA)(CH3CN)2](2+) (2) (where TPA = tris(2-pyridylmethyl)amine and BPMEN = N,N′-dimethyl-N,N′-bis(2-pyridylmethyl)ethane-1,2-diamine) complexes containing amino pyridine ligands along with H2O2 are employed to carry out these transformations where complex 1 is found to be more reactive than complex 2. Herein, using density functional methods employing B3LYP and dispersion corrected B3LYP (B3LYP-D) functionals, we have explored the mechanism of this reaction to reason out the importance of ligand design in fine-tuning the reactivity of such catalytic transformations. Dispersion corrected B3LYP is found to be superior to B3LYP in predicting the correct ground state of these species and also yields lower barrier heights than the B3LYP functional. Starting the reaction from the Fe(III)–OOH species, both homolytic and heterolytic cleavage of the O···O bond is explored leading to the formation of the transient Fe(IV)=O and Fe(V)=O species. For both the ligand systems, heterolytic cleavage was energetically preferable and our calculations suggest that both the reactions are catalyzed by an elusive high-valent Fe(V)=O species. The Fe(V)=O species undergoes the reaction via an electrophilic attack of the benzene ring to effect the ortho-hydroxylation reaction. The reactivity pattern observed for 1 and 2 are reflected in the computed barrier heights for the ortho-hydroxylation reaction. Electronic structure analysis reveals that the difference in reactivity between the ligand architectures described in complex 1 and 2 arise due to orientation of the pyridine ring(s) parallel or perpendicular to the Fe(V)=O bond. The parallel orientation of the pyridine ring is found to mix with the (πFe(dyz)–O(py))* orbital of the Fe-oxo bond leading to a reduction in the electrophilicity of the ferryl oxygen atom. Our calculations highlight the importance of ligand design in this chemistry and suggest that this concept can be used to (i) stabilize high-valent intermediates which can be trapped and thoroughly characterized (ii) enhance the reactivity and efficiency of the oxidants by increasing the electrophilicity of the ferryl oxygen containing FeVO species. Our computed results are in general agreement with the experimental results.
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Affiliation(s)
- Azaj Ansari
- Department of Chemistry, Indian Institute of Technology-Bombay, Powai, Mumbai, India.
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Fuchs JE, Huber RG, von Grafenstein S, Wallnoefer HG, Spitzer GM, Fuchs D, Liedl KR. Dynamic regulation of phenylalanine hydroxylase by simulated redox manipulation. PLoS One 2012; 7:e53005. [PMID: 23300845 PMCID: PMC3534100 DOI: 10.1371/journal.pone.0053005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 11/26/2012] [Indexed: 01/06/2023] Open
Abstract
Recent clinical studies revealed increased phenylalanine levels and phenylalanine to tyrosine ratios in patients suffering from infection, inflammation and general immune activity. These data implicated down-regulation of activity of phenylalanine hydroxylase by oxidative stress upon in vivo immune activation. Though the structural damage of oxidative stress is expected to be comparably small, a structural rationale for this experimental finding was lacking. Hence, we investigated the impact of side chain oxidation at two vicinal cysteine residues on local conformational flexibility in the protein by comparative molecular dynamics simulations. Analysis of backbone dynamics revealed a highly flexible loop region (Tyr138-loop) in proximity to the active center of phenylalanine hydroxylase. We observed elevated loop dynamics in connection with a loop movement towards the active site in the oxidized state, thereby partially blocking access for the substrate phenylalanine. These findings were confirmed by extensive replica exchange molecular dynamics simulations and serve as a first structural explanation for decreased enzyme turnover in situations of oxidative stress.
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Affiliation(s)
- Julian E. Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Roland G. Huber
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Susanne von Grafenstein
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Hannes G. Wallnoefer
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Gudrun M. Spitzer
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Dietmar Fuchs
- Division of Biological Chemistry, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
- * E-mail:
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Flydal MI, Chatfield CH, Zheng H, Gunderson FF, Aubi O, Cianciotto NP, Martinez A. Phenylalanine hydroxylase from Legionella pneumophila is a thermostable enzyme with a major functional role in pyomelanin synthesis. PLoS One 2012; 7:e46209. [PMID: 23049981 PMCID: PMC3458870 DOI: 10.1371/journal.pone.0046209] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 08/29/2012] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Legionella pneumophila is a pathogenic bacterium that can cause Legionnaires' disease and other non-pneumonic infections in humans. This bacterium produces a pyomelanin pigment, a potential virulence factor with ferric reductase activity. In this work, we have investigated the role of phenylalanine hydroxylase from L. pneumophila (lpPAH), the product of the phhA gene, in the synthesis of the pyomelanin pigment and the growth of the bacterium in defined compositions. METHODOLOGY/PRINCIPAL FINDINGS Comparative studies of wild-type and phhA mutant corroborate that lpPAH provides the excess tyrosine for pigment synthesis. phhA and letA (gacA) appear transcriptionally linked when bacteria were grown in buffered yeast extract medium at 37°C. phhA is expressed in L. pneumophila growing in macrophages. We also cloned and characterized lpPAH, which showed many characteristics of other PAHs studied so far, including Fe(II) requirement for activity. However, it also showed many particular properties such as dimerization, a high conformational thermal stability, with a midpoint denaturation temperature (T(m)) = 79 ± 0.5°C, a high specific activity at 37°C (10.2 ± 0.3 µmol L-Tyr/mg/min) and low affinity for the substrate (K(m) (L-Phe) = 735 ± 50 µM. CONCLUSIONS/SIGNIFICANCE lpPAH has a major functional role in the synthesis of pyomelanin and promotes growth in low-tyrosine media. The high thermal stability of lpPAH might reflect the adaptation of the enzyme to withstand relatively high survival temperatures.
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Affiliation(s)
- Marte I. Flydal
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Christa H. Chatfield
- Department of Microbiology-Immunology, Northwestern University Medical School, Chicago, Illinois, United States of America
| | - Huaixin Zheng
- Department of Microbiology-Immunology, Northwestern University Medical School, Chicago, Illinois, United States of America
| | - Felizza F. Gunderson
- Department of Microbiology-Immunology, Northwestern University Medical School, Chicago, Illinois, United States of America
| | - Oscar Aubi
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Nicholas P. Cianciotto
- Department of Microbiology-Immunology, Northwestern University Medical School, Chicago, Illinois, United States of America
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Bergen, Norway
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Hirao H, Li F, Que L, Morokuma K. Theoretical study of the mechanism of oxoiron(IV) formation from H2O2 and a nonheme iron(II) complex: O-O cleavage involving proton-coupled electron transfer. Inorg Chem 2011; 50:6637-48. [PMID: 21678930 PMCID: PMC3136038 DOI: 10.1021/ic200522r] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It has recently been shown that the nonheme oxoiron(IV) species supported by the 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane ligand (TMC) can be generated in near-quantitative yield by reacting [Fe(II)(TMC)(OTf)(2)] with a stoichiometric amount of H(2)O(2) in CH(3)CN in the presence of 2,6-lutidine (Li, F.; England, J.; Que, L., Jr. J. Am. Chem. Soc. 2010, 132, 2134-2135). This finding has major implications for O-O bond cleavage events in both Fenton chemistry and nonheme iron enzymes. To understand the mechanism of this process, especially the intimate details of the O-O bond cleavage step, a series of density functional theory (DFT) calculations and analyses have been carried out. Two distinct reaction paths (A and B) were identified. Path A consists of two principal steps: (1) coordination of H(2)O(2) to Fe(II) and (2) a combination of partial homolytic O-O bond cleavage and proton-coupled electron transfer (PCET). The latter combination renders the rate-limiting O-O cleavage effectively a heterolytic process. Path B proceeds via a simultaneous homolytic O-O bond cleavage of H(2)O(2) and Fe-O bond formation. This is followed by H abstraction from the resultant Fe(III)-OH species by an •OH radical. Calculations suggest that path B is plausible in the absence of base. However, once 2,6-lutidine is added to the reacting system, the reaction barrier is lowered and more importantly the mechanistic path switches to path A, where 2,6-lutidine plays an essential role as an acid-base catalyst in a manner similar to how the distal histidine or glutamate residue assists in compound I formation in heme peroxidases. The reaction was found to proceed predominantly on the quintet spin state surface, and a transition to the triplet state, the experimentally known ground state for the TMC-oxoiron(IV) species, occurs in the last stage of the oxoiron(IV) formation process.
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Affiliation(s)
- Hajime Hirao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Feifei Li
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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Olsson E, Martinez A, Teigen K, Jensen VR. Substrate Hydroxylation by the Oxido-Iron Intermediate in Aromatic Amino Acid Hydroxylases: A DFT Mechanistic Study. Eur J Inorg Chem 2011. [DOI: 10.1002/ejic.201001218] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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