1
|
Biosynthesis of alkanes/alkenes from fatty acids or derivatives (triacylglycerols or fatty aldehydes). Biotechnol Adv 2022; 61:108045. [DOI: 10.1016/j.biotechadv.2022.108045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/27/2022]
|
2
|
Yeh CCG, Mokkawes T, Bradley J, Le Brun NE, de Visser S. Second coordination sphere effects on the mechanistic pathways for dioxygen activation by a ferritin: involvement of a Tyr radical and the identification of a cation binding site. Chembiochem 2022; 23:e202200257. [PMID: 35510795 PMCID: PMC9401865 DOI: 10.1002/cbic.202200257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/05/2022] [Indexed: 11/09/2022]
Abstract
Ferritins are ubiquitous diiron enzymes involved in iron(II) detoxification and oxidative stress responses and can act as metabolic iron stores. The overall reaction mechanisms of ferritin enzymes are still unclear, particularly concerning the role of the conserved, near catalytic center Tyr residue. Thus, we carried out a computational study of a ferritin using a large cluster model of well over 300 atoms including its first- and second-coordination sphere. The calculations reveal important insight into the structure and reactivity of ferritins. Specifically, the active site Tyr residue delivers a proton and electron in the catalytic cycle prior to iron(II) oxidation. In addition, the calculations highlight a likely cation binding site at Asp65, which through long-range electrostatic interactions, influences the electronic configuration and charge distributions of the metal center. The results are consistent with experimental observations but reveal novel detail of early mechanistic steps that lead to an unusual mixed-valent iron(III)-iron(II) center.
Collapse
Affiliation(s)
- Chieh-Chih George Yeh
- The University of Manchester, Department of Chemical Engineering, Oxford Road, Manchester, UNITED KINGDOM
| | - Thirakorn Mokkawes
- The University of Manchester, Department of Chemical Engineering, Manchester, UNITED KINGDOM
| | - Justin Bradley
- University of East Anglia, School of Chemistry, UNITED KINGDOM
| | - Nick E Le Brun
- University of East Anglia, School of Chemistry, UNITED KINGDOM
| | - Samuel de Visser
- The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, M1 7DN, Manchester, UNITED KINGDOM
| |
Collapse
|
3
|
A mixed-valent Fe(II)Fe(III) species converts cysteine to an oxazolone/thioamide pair in methanobactin biosynthesis. Proc Natl Acad Sci U S A 2022; 119:e2123566119. [PMID: 35320042 PMCID: PMC9060507 DOI: 10.1073/pnas.2123566119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Methanobactins (Mbns), copper-binding peptidic compounds produced by some bacteria, are candidate therapeutics for human diseases of copper overload. The paired oxazolone-thioamide bidentate ligands of methanobactins are generated from cysteine residues in a precursor peptide, MbnA, by the MbnBC enzyme complex. MbnBC activity depends on the presence of iron and oxygen, but the catalytically active form has not been identified. Here, we provide evidence that a dinuclear Fe(II)Fe(III) center in MbnB, which is the only representative of a >13,000-member protein family to be characterized, is responsible for this reaction. These findings expand the known roles of diiron enzymes in biology and set the stage for mechanistic understanding, and ultimately engineering, of the MbnBC biosynthetic complex. The iron-containing heterodimeric MbnBC enzyme complex plays a central role in the biosynthesis of methanobactins (Mbns), ribosomally synthesized, posttranslationally modified natural products that bind copper with high affinity. MbnBC catalyzes a four-electron oxidation of a cysteine residue in its precursor-peptide substrate, MbnA, to an oxazolone ring and an adjacent thioamide group. Initial studies of MbnBC indicated the presence of both diiron and triiron species, complicating identification of the catalytically active species. Here, we present evidence through activity assays combined with electron paramagnetic resonance (EPR) and Mössbauer spectroscopic analysis that the active species is a mixed-valent, antiferromagnetically coupled Fe(II)Fe(III) center. Consistent with this assignment, heterologous expression of the MbnBC complex in culture medium containing less iron yielded purified protein with less bound iron but greater activity in vitro. The maximally activated MbnBC prepared in this manner could modify both cysteine residues in MbnA, in contrast to prior findings that only the first cysteine could be processed. Site-directed mutagenesis and multiple crystal structures clearly identify the two essential Fe ions in the active cluster as well as the location of the previously detected third Fe site. Moreover, structural modeling indicates a role for MbnC in recognition of the MbnA leader peptide. These results add a biosynthetic oxidative rearrangement reaction to the repertoire of nonheme diiron enzymes and provide a foundation for elucidating the MbnBC mechanism.
Collapse
|
4
|
Paik A, Paul S, Bhowmik S, Das R, Naveen T, Rana S. Recent Advances in First Row Transition Metal Mediated C‐H Halogenation of (Hetero)arenes and Alkanes. ASIAN J ORG CHEM 2022. [DOI: 10.1002/ajoc.202200060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Aniruddha Paik
- University of North Bengal Department of Chemistry Raja Rammohunpur, DarjeelingWest Bengal, India - 734013 734013 Siliguri INDIA
| | - Sabarni Paul
- University of North Bengal Department of Chemistry Raja Rammohunpur, DarjeelingWest Bengal, India - 734013 734013 Siliguri INDIA
| | - Sabyasachi Bhowmik
- University of North Bengal Department of Chemistry Raja Rammohunpur, DarjeelingWest Bengal, India - 734013 734013 Siliguri INDIA
| | - Rahul Das
- University of North Bengal Department of Chemistry Raja Rammohunpur, DarjeelingWest Bengal, India - 734013 734013 Siliguri INDIA
| | - Togati Naveen
- Sardar Vallabhbhai National Institute of Technology Department of Chemistry 395007 Surat INDIA
| | - Sujoy Rana
- University of North Bengal Chemistry Raja Rammohunpur, DarjeelingWest Bengal, India, 734013 734013 Siliguri INDIA
| |
Collapse
|
5
|
Tupec M, Culka M, Machara A, Macháček S, Bím D, Svatoš A, Rulíšek L, Pichová I. Understanding desaturation/hydroxylation activity of castor stearoyl Δ9-Desaturase through rational mutagenesis. Comput Struct Biotechnol J 2022; 20:1378-1388. [PMID: 35386101 PMCID: PMC8940945 DOI: 10.1016/j.csbj.2022.03.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/11/2022] [Accepted: 03/11/2022] [Indexed: 01/17/2023] Open
Abstract
Rationally designed mutations in the Δ9 desaturase promoted hydroxylation activity. Proton and electron transfer to the active site is crucial for the Δ9D to desaturate Detailed analysis of all enzymatic products of the Δ9D was carried out Insight into the chemo-, and stereoselectivity of non-heme diiron enzymes was obtained
A recently proposed reaction mechanism of soluble Δ9 desaturase (Δ9D) allowed us to identify auxiliary residues His203, Asp101, Thr206 and Cys222 localized near the di-iron active site that are supposedly involved in the proton transfer (PT) to and from the active site. The PT, along with the electron transfer (ET), seems to be crucial for efficient desaturation. Thus, perturbing the major PT chains is expected to impair the native reaction and (potentially) amplify minor reaction channels, such as the substrate hydroxylation. To verify this hypothesis, we mutated the four residues mentioned above into their counterparts present in a soluble methane monooxygenase (sMMO), and determined the reaction products of mutants. We found that the mutations significantly promote residual monohydroxylation activities on stearoyl-CoA, often at the expense of native desaturation activity. The favored hydroxylation positions are C9, followed by C10 and C11. Reactions with unsaturated substrate, oleoyl-CoA, yield erythro-9,10-diol, cis-9,10-epoxide and a mixture of allylic alcohols. Additionally, using 9- and 11-hydroxystearoyl-CoA, we showed that the desaturation reaction can proceed only with the hydroxyl group at position C11, whereas the hydroxylation reaction is possible in both cases, i.e. with hydroxyl at position C9 or C11. Despite the fact that the overall outcome of hydroxylation is rather modest and that it is mostly the desaturation/hydroxylation ratio that is affected, our results broaden understanding of the origin of chemo- and stereoselectivity of the Δ9D and provide further insight into the catalytic action of the NHFe2 enzymes.
Collapse
Affiliation(s)
- Michal Tupec
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Martin Culka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Aleš Machara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Stanislav Macháček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Daniel Bím
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Aleš Svatoš
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
- Max-Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena 07745, Germany
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
- Corresponding authors.
| | - Iva Pichová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
- Corresponding authors.
| |
Collapse
|
6
|
Sinha SK, Roy TK, Modak A, Maiti D. Enabling the Facile Synthesis of Arenes by Transition Metal Catalyzed Decarbonylation Methodology. CHEM REC 2021; 21:3990-3999. [PMID: 34713555 DOI: 10.1002/tcr.202100244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 11/11/2022]
Abstract
Transition metal-catalyzed decarbonylation is an essential paradigm of synthetic organic chemistry. Decarbonylation offers a unique pathway to decoding the skeletal structure of arenes and enabling easy synthesis of structurally complicated molecules. Due to the omnipresence of carbonyl groups in a wide array of synthetically important complex molecules, the variety and scope of these transformations are enormous. As a result, the development of transition metal catalysts in such a simple decarbonylation reaction ranks among one of the most important topics in synthetic organic chemistry. Transition metals that have been employed range from 3d metals like V to second-row transition metals like Pd. The growing potential of this methodology has driven the pioneers of synthetic organic chemistry into delving into the details of this transition metal-catalyzed decarbonylation pathways. This review aims to take the readers through the employment of transition metals in various decarbonylation processes developed by our group, sticking not only to the scope and diversification of synthetically complex molecules, but also enabling the readers to understand the mechanistic insights, through computational and kinetic studies put forward in such reaction protocol, hoping to pave the way for future organic chemists to delve and hopefully solve the unique problems associated with this protocol.
Collapse
Affiliation(s)
- Soumya Kumar Sinha
- Department of Chemistry, Indian Institute of Technology Bombay Powai, Mumbai, 400076, India
| | - Triptesh Kumar Roy
- Department of Chemistry, Indian Institute of Technology Bombay Powai, Mumbai, 400076, India
| | - Atanu Modak
- Department of Chemistry, Indian Institute of Technology Bombay Powai, Mumbai, 400076, India
| | - Debabrata Maiti
- Department of Chemistry, Indian Institute of Technology Bombay Powai, Mumbai, 400076, India
| |
Collapse
|
7
|
Chandra A, Ansari M, Monte‐Pérez I, Kundu S, Rajaraman G, Ray K. Ligand‐Constraint‐Induced Peroxide Activation for Electrophilic Reactivity. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Anirban Chandra
- Department of Chemistry Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Mursaleem Ansari
- Department of Chemistry Indian Institute of Technology Bombay, Powai Mumbai Maharashtra 400 076 India
| | - Inés Monte‐Pérez
- Department of Chemistry Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Subrata Kundu
- Department of Chemistry Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Gopalan Rajaraman
- Department of Chemistry Indian Institute of Technology Bombay, Powai Mumbai Maharashtra 400 076 India
| | - Kallol Ray
- Department of Chemistry Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 12489 Berlin Germany
| |
Collapse
|
8
|
Chandra A, Ansari M, Monte-Pérez I, Kundu S, Rajaraman G, Ray K. Ligand-Constraint-Induced Peroxide Activation for Electrophilic Reactivity. Angew Chem Int Ed Engl 2021; 60:14954-14959. [PMID: 33843113 PMCID: PMC8252416 DOI: 10.1002/anie.202100438] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/26/2021] [Indexed: 12/16/2022]
Abstract
μ‐1,2‐peroxo‐bridged diiron(III) intermediates P are proposed as reactive intermediates in various biological oxidation reactions. In sMMO, P acts as an electrophile, and performs hydrogen atom and oxygen atom transfers to electron‐rich substrates. In cyanobacterial ADO, however, P is postulated to react by nucleophilic attack on electrophilic carbon atoms. In biomimetic studies, the ability of μ‐1,2‐peroxo‐bridged dimetal complexes of Fe, Co, Ni and Cu to act as nucleophiles that effect deformylation of aldehydes is documented. By performing reactivity and theoretical studies on an end‐on μ‐1,2‐peroxodicobalt(III) complex 1 involving a non‐heme ligand system, L1, supported on a Sn6O6 stannoxane core, we now show that a peroxo‐bridged dimetal complex can also be a reactive electrophile. The observed electrophilic chemistry, which is induced by the constraints provided by the Sn6O6 core, represents a new domain for metal−peroxide reactivity.
Collapse
Affiliation(s)
- Anirban Chandra
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
| | - Mursaleem Ansari
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra, 400 076, India
| | - Inés Monte-Pérez
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
| | - Subrata Kundu
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
| | - Gopalan Rajaraman
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra, 400 076, India
| | - Kallol Ray
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
| |
Collapse
|
9
|
Török P, Unjaroen D, Viktória Csendes F, Giorgi M, Browne WR, Kaizer J. A nonheme peroxo-diiron(III) complex exhibiting both nucleophilic and electrophilic oxidation of organic substrates. Dalton Trans 2021; 50:7181-7185. [PMID: 34019062 PMCID: PMC8168641 DOI: 10.1039/d1dt01502h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The complex [FeIII2(μ-O2)(L3)4(S)2]4+ (L3 = 2-(4-thiazolyl)benzimidazole, S = solvent) forms upon reaction of [FeII(L3)2] with H2O2 and is a functional model of peroxo-diiron intermediates invoked during the catalytic cycle of oxidoreductases. The spectroscopic properties of the complex are in line with those of complexes formed with N-donor ligands. [FeIII2(μ-O2)(L3)4(S)2]4+ shows both nucleophilic (aldehydes) and electrophilic (phenol, N,N-dimethylanilines) oxidative reactivity and unusually also electron transfer oxidation. A bidentate ligand based iron complex shows nucleophillic and electrophillice reactivity in the oxidation of organic substrates.![]()
Collapse
Affiliation(s)
- Patrik Török
- Research Group of Bioorganic and Biocoordination Chemistry, University of Pannonia, H-8200 Veszprém, Hungary.
| | - Duenpen Unjaroen
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
| | - Flóra Viktória Csendes
- Research Group of Bioorganic and Biocoordination Chemistry, University of Pannonia, H-8200 Veszprém, Hungary.
| | - Michel Giorgi
- Aix-Marseille Université, FR1739, Spectropole, Campus St Jérome, Avenue Escadrille Normandie-Niemen, 13397 Marseille Cedex 20, France
| | - Wesley R Browne
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
| | - József Kaizer
- Research Group of Bioorganic and Biocoordination Chemistry, University of Pannonia, H-8200 Veszprém, Hungary.
| |
Collapse
|
10
|
Mak WS, Wang X, Arenas R, Cui Y, Bertolani S, Deng WQ, Tagkopoulos I, Wilson DK, Siegel JB. Discovery, Design, and Structural Characterization of Alkane-Producing Enzymes across the Ferritin-like Superfamily. Biochemistry 2020; 59:3834-3843. [PMID: 32935984 DOI: 10.1021/acs.biochem.0c00665] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
To complement established rational and evolutionary protein design approaches, significant efforts are being made to utilize computational modeling and the diversity of naturally occurring protein sequences. Here, we combine structural biology, genomic mining, and computational modeling to identify structural features critical to aldehyde deformylating oxygenases (ADOs), an enzyme family that has significant implications in synthetic biology and chemoenzymatic synthesis. Through these efforts, we discovered latent ADO-like function across the ferritin-like superfamily in various species of Bacteria and Archaea. We created a machine learning model that uses protein structural features to discriminate ADO-like activity. Computational enzyme design tools were then utilized to introduce ADO-like activity into the small subunit of Escherichia coli class I ribonucleotide reductase. The integrated approach of genomic mining, structural biology, molecular modeling, and machine learning has the potential to be utilized for rapid discovery and modulation of functions across enzyme families.
Collapse
Affiliation(s)
- Wai Shun Mak
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - XiaoKang Wang
- Department of Biomedical Engineering, University of California, Davis, Davis, California 95616, United States
| | - Rigoberto Arenas
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States.,Chemistry Graduate Group, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Youtian Cui
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Steve Bertolani
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Wen Qiao Deng
- California College of Arts, 1111 Eighth Street, San Francisco, California 94107, United States
| | - Ilias Tagkopoulos
- Department of Biomedical Engineering, University of California, Davis, Davis, California 95616, United States.,Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California 95616, United States.,Department of Computer Science, University of California, Davis, Davis, California 95616, United States
| | - David K Wilson
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, California 95616, United States.,Chemistry Graduate Group, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Justin B Siegel
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States.,Department of Biochemistry and Molecular Medicine, University of California, Davis, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States.,Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California 95616, United States
| |
Collapse
|
11
|
Kripli B, Szávuly M, Csendes FV, Kaizer J. Functional models of nonheme diiron enzymes: reactivity of the μ-oxo-μ-1,2-peroxo-diiron(iii) intermediate in electrophilic and nucleophilic reactions. Dalton Trans 2020; 49:1742-1746. [PMID: 31967142 DOI: 10.1039/c9dt04551a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The reactivity of the previously reported peroxo-adduct [FeIII2(μ-O)(μ-1,2-O2)(IndH)2(solv)2]2+ (1) (IndH = 1,3-bis(2-pyridyl-imino)isoindoline) has been investigated in nucleophilic (e.g., deformylation of alkyl and aryl alkyl aldehydes) and electrophilic (e.g. oxidation of phenols) stoichiometric reactions as biomimics of ribonucleotide reductase (RNR-R2) and aldehyde deformylating oxygenase (ADO) enzymes. Based on detailed kinetic and mechanistic studies, we have found further evidence for the ambiphilic behaviour of the peroxo intermediates proposed for diferric oxidoreductase enzymes.
Collapse
Affiliation(s)
- Balázs Kripli
- Department of Chemistry, University of Pannonia, H-8201 Veszprém, Hungary.
| | | | | | | |
Collapse
|
12
|
Bím D, Chalupský J, Culka M, Solomon EI, Rulíšek L, Srnec M. Proton-Electron Transfer to the Active Site Is Essential for the Reaction Mechanism of Soluble Δ 9-Desaturase. J Am Chem Soc 2020; 142:10412-10423. [PMID: 32406236 DOI: 10.1021/jacs.0c01786] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A full understanding of the catalytic action of non-heme iron (NHFe) and non-heme diiron (NHFe2) enzymes is still beyond the grasp of contemporary computational and experimental techniques. Many of these enzymes exhibit fascinating chemo-, regio-, and stereoselectivity, in spite of employing highly reactive intermediates which are necessary for activations of most stable chemical bonds. Herein, we study in detail one intriguing representative of the NHFe2 family of enzymes: soluble Δ9 desaturase (Δ9D), which desaturates rather than performing the thermodynamically favorable hydroxylation of substrate. Its catalytic mechanism has been explored in great detail by using QM(DFT)/MM and multireference wave function methods. Starting from the spectroscopically observed 1,2-μ-peroxo diferric P intermediate, the proton-electron uptake by P is the favored mechanism for catalytic activation, since it allows a significant reduction of the barrier of the initial (and rate-determining) H-atom abstraction from the stearoyl substrate as compared to the "proton-only activated" pathway. Also, we ruled out that a Q-like intermediate (high-valent diamond-core bis-μ-oxo-[FeIV]2 unit) is involved in the reaction mechanism. Our mechanistic picture is consistent with the experimental data available for Δ9D and satisfies fairly stringent conditions required by Nature: the chemo-, stereo-, and regioselectivity of the desaturation of stearic acid. Finally, the mechanisms evaluated are placed into a broader context of NHFe2 chemistry, provided by an amino acid sequence analysis through the families of the NHFe2 enzymes. Our study thus represents an important contribution toward understanding the catalytic action of the NHFe2 enzymes and may inspire further work in NHFe(2) biomimetic chemistry.
Collapse
Affiliation(s)
- Daniel Bím
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, Prague 8 182 23, Czech Republic.,Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 166 10, Czech Republic
| | - Jakub Chalupský
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 166 10, Czech Republic
| | - Martin Culka
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 166 10, Czech Republic
| | - Edward I Solomon
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California 94305-5080, United States
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 166 10, Czech Republic
| | - Martin Srnec
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, Prague 8 182 23, Czech Republic
| |
Collapse
|
13
|
Hofmann AJ, Jandl C, Hess CR. Structural Differences and Redox Properties of Unsymmetric Diiron PDIxCy Complexes. Eur J Inorg Chem 2020. [DOI: 10.1002/ejic.201901173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Andreas J. Hofmann
- Department of Chemistry and Catalysis Research Center Technische Universität München Lichtenbergstraße 4 85748 Garching Germany
| | - Christian Jandl
- Department of Chemistry and Catalysis Research Center Technische Universität München Lichtenbergstraße 4 85748 Garching Germany
| | - Corinna R. Hess
- Department of Chemistry and Catalysis Research Center Technische Universität München Lichtenbergstraße 4 85748 Garching Germany
| |
Collapse
|
14
|
Walleck S, Glaser T. A Dinucleating Ligand System with Varying Terminal Donors to Mimic Diiron Active Sites. Isr J Chem 2020. [DOI: 10.1002/ijch.201900097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Stephan Walleck
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie Universität Bielefeld Universitätsstrasse 25 D-33615 Bielefeld Germany
| | - Thorsten Glaser
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie Universität Bielefeld Universitätsstrasse 25 D-33615 Bielefeld Germany
| |
Collapse
|
15
|
High-resolution iron X-ray absorption spectroscopic and computational studies of non-heme diiron peroxo intermediates. J Inorg Biochem 2019; 203:110877. [PMID: 31710865 DOI: 10.1016/j.jinorgbio.2019.110877] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/05/2019] [Accepted: 10/01/2019] [Indexed: 11/20/2022]
Abstract
Ferritin-like carboxylate-bridged non-heme diiron enzymes activate O2 for a variety of difficult reactions throughout nature. These reactions often begin by abstraction of hydrogen from strong CH bonds. The enzymes activate O2 at their diferrous cofactors to form canonical diferric peroxo intermediates, with a range of possible coordination modes. Herein, we explore the ability of high-energy resolution fluorescence detected X-ray absorption spectroscopy (HERFD XAS) to provide insight into the nature of peroxo level intermediates in non-heme diiron proteins. Freeze quenched (FQ) peroxo intermediates from p-aminobenzoate N-oxygenase (AurF), aldehyde-deformylating oxygenase (ADO), and the β subunit of class Ia ribonucleotide reductase from Escherichia coli (Ecβ) are investigated. All three intermediates are proposed to adopt different peroxo binding modes, and each exhibit different Fe Kα HERFD XAS pre-edge features and intensities. As these FQ-trapped samples consist of multiple species, deconvolution of HERFD XAS spectra based on speciation, as determined by Mössbauer spectroscopy, is also necessitated - yielding 'pure' diferric peroxo HERFD XAS spectra from dilute protein samples. Finally, the impact of a given peroxo coordination mode on the HERFD XAS pre-edge energy and intensity is evaluated through time-dependent density functional theory (TDDFT) calculations of the XAS spectra on a series of hypothetical model complexes, which span a full range of possible peroxo coordination modes to a diferric core. The utility of HERFD XAS for future studies of enzymatic intermediates is discussed.
Collapse
|
16
|
Kripli B, Csendes FV, Török P, Speier G, Kaizer J. Stoichiometric Aldehyde Deformylation Mediated by Nucleophilic Peroxo-diiron(III) Complex as a Functional Model of Aldehyde Deformylating Oxygenase. Chemistry 2019; 25:14290-14294. [PMID: 31448834 DOI: 10.1002/chem.201903727] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Indexed: 11/11/2022]
Abstract
The reactivity of the previously reported peroxo adduct [FeIII 2 (μ-O2 )(MeBzim-Py)4 (CH3 CN)2 ]4+ (1) (MeBzim-Py=2-(2'-pyridyl)-N-methylbenzimidazole) towards aldehyde substrates including phenylacetaldehyde (PAA), hydrocinnamaldehyde (HCA), propionaldehyde (PA), 2-phenylpropionaldehyde (PPA), cyclohexanecarboxaldehyde (CCA), and para-substituted benzaldehydes (benzoyl chlorides) has been investigated. Complex 1 proved to be a nucleophilic oxidant in aldehyde deformylation reaction. These models, including detailed kinetic and mechanistic studies, may serve as the first biomimics of aldehyde deformylating oxygenase (ADO) enzymes.
Collapse
Affiliation(s)
- Balázs Kripli
- Department of Chemistry, University of Pannonia, 8201, Veszprém, Hungary
| | | | - Patrik Török
- Department of Chemistry, University of Pannonia, 8201, Veszprém, Hungary
| | - Gábor Speier
- Department of Chemistry, University of Pannonia, 8201, Veszprém, Hungary
| | - József Kaizer
- Department of Chemistry, University of Pannonia, 8201, Veszprém, Hungary
| |
Collapse
|
17
|
A di-iron protein recruited as an Fe[II] and oxygen sensor for bacterial chemotaxis functions by stabilizing an iron-peroxy species. Proc Natl Acad Sci U S A 2019; 116:14955-14960. [PMID: 31270241 DOI: 10.1073/pnas.1904234116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Many bacteria contain cytoplasmic chemoreceptors that lack sensor domains. Here, we demonstrate that such cytoplasmic receptors found in 8 different bacterial and archaeal phyla genetically couple to metalloproteins related to β-lactamases and nitric oxide reductases. We show that this oxygen-binding di-iron protein (ODP) acts as a sensor for chemotactic responses to both iron and oxygen in the human pathogen Treponema denticola (Td). The ODP di-iron site binds oxygen at high affinity to reversibly form an unusually stable μ-peroxo adduct. Crystal structures of ODP from Td and the thermophile Thermotoga maritima (Tm) in the Fe[III]2-O2 2-, Zn[II], and apo states display differences in subunit association, conformation, and metal coordination that indicate potential mechanisms for sensing. In reconstituted systems, iron-peroxo ODP destabilizes the phosphorylated form of the receptor-coupled histidine kinase CheA, thereby providing a biochemical link between oxygen sensing and chemotaxis in diverse prokaryotes, including anaerobes of ancient origin.
Collapse
|
18
|
Jeon H, Hong S. Peroxide Bond Cleavage of Nonheme Iron-(Hydro/Alkyl)Peroxo Complexes Induced by Endogenous and Exogenous Factors. CHEM LETT 2019. [DOI: 10.1246/cl.180831] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Hyeri Jeon
- Department of Chemistry, Sookmyung Women’s University, Seoul 04310, Korea
| | - Seungwoo Hong
- Department of Chemistry, Sookmyung Women’s University, Seoul 04310, Korea
| |
Collapse
|
19
|
Weitz AC, Giri N, Frederick RE, Kurtz DM, Bominaar EL, Hendrich MP. Spectroscopy and DFT Calculations of Flavo-Diiron Nitric Oxide Reductase Identify Bridging Structures of NO-Coordinated Diiron Intermediates. ACS Catal 2018; 8:11704-11715. [PMID: 31263628 PMCID: PMC6602092 DOI: 10.1021/acscatal.8b03051] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Flavo-diiron proteins (FDPs) are widespread in anaerobic bacteria, archaea, and protozoa, where they serve as the terminal components of dioxygen and nitric oxide reductive scavenging pathways. FDPs contain an N,O-ligated diiron site adjacent to a flavin mononucleotide (FMN) cofactor. The diiron site is structurally similar to those in hemerythrin, ribonucleotide reductase, and methane monooxygenase. However, only FDPs turn over NO to N2O at significant rates and yields. Previous studies revealed sequential binding of two NO molecules to the diferrous site, forming mono- and dinitrosyl intermediates leading to N2O formation. In the present work, these mono- and dinitrosyl intermediates have been characterized by EPR and Mössbauer spectroscopies and DFT calculations. Our results show that the iron proximal to the cofactor binds the first NO to form the diiron mononitrosyl complex, implying the iron distal to the FMN binds the second NO to form the diiron dinitrosyl intermediate. The exchange-coupling constants, J (H = JS1·S2), were found to differ substantially, +17 cm-1 for the diiron mononitrosyl and +60 cm-1 for the diiron dinitrosyl. Notwithstanding this large difference, our findings indicate retention of at least one hydroxo bridge throughout the NOR catalytic cycle. The Mossbauer hyperfine parameters and DFT calculations confirmed a semibridging NO- ligand in the mononitrosyl intermediate that lowers the exchange parameter. The DFT calculations on the dinitrosyl intermediate suggest a contribution to J from direct exchange between the S = 1 spins on the NO- ligands, which could initiate N-N bond formation. Our results provide insight into why FDPs are the only known nonheme diiron enzymes that competently turn over NO to N2O.
Collapse
Affiliation(s)
- Andrew C. Weitz
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Nitai Giri
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Rosanne E. Frederick
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Donald M. Kurtz
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Emile L. Bominaar
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Michael P. Hendrich
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| |
Collapse
|
20
|
Arai M, Hayashi Y, Kudo H. Cyanobacterial Enzymes for Bioalkane Production. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1080:119-154. [PMID: 30091094 DOI: 10.1007/978-981-13-0854-3_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyanobacterial biosynthesis of alkanes is an attractive way of producing substitutes for petroleum-based fuels. Key enzymes for bioalkane production in cyanobacteria are acyl-ACP reductase (AAR) and aldehyde-deformylating oxygenase (ADO). AAR catalyzes the reduction of the fatty acyl-ACP/CoA substrates to fatty aldehydes, which are then converted into alkanes/alkenes by ADO. These enzymes have been widely used for biofuel production by metabolic engineering of cyanobacteria and other organisms. However, both proteins, particularly ADO, have low enzymatic activities, and their catalytic activities are desired to be improved for use in biofuel production. Recently, progress has been made in the basic sciences and in the application of AAR and ADO in alkane production. This chapter provides an overview of recent advances in the study of the structure and function of AAR and ADO, protein engineering of these enzymes for improving activity and modifying substrate specificities, and examples of metabolic engineering of cyanobacteria and other organisms using AAR and ADO for biofuel production.
Collapse
Affiliation(s)
- Munehito Arai
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.
| | - Yuuki Hayashi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Hisashi Kudo
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
21
|
Cleavage of a carbon-fluorine bond by an engineered cysteine dioxygenase. Nat Chem Biol 2018; 14:853-860. [PMID: 29942080 PMCID: PMC6103799 DOI: 10.1038/s41589-018-0085-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 05/04/2018] [Indexed: 11/08/2022]
Abstract
Cysteine dioxygenase (CDO) plays an essential role in sulfur metabolism by regulating homeostatic levels of cysteine. Human CDO contains a post-translationally generated Cys93-Tyr157 cross-linked cofactor. Here, we investigated this Cys-Tyr cross-linking by incorporating unnatural tyrosines in place of Tyr157 via a genetic method. The catalytically active variants were obtained with a thioether bond between Cys93 and the halogen-substituted Tyr157, and we determined the crystal structures of both wild-type and engineered CDO variants in the purely uncross-linked form and with a mature cofactor. Along with mass spectrometry and 19F NMR, these data indicated that the enzyme could catalyze oxidative C-F or C-Cl bond cleavage, resulting in a substantial conformational change of both Cys93 and Tyr157 during cofactor assembly. These findings provide insights into the mechanism of Cys-Tyr cofactor biogenesis and may aid the development of bioinspired aromatic carbon-halogen bond activation.
Collapse
|
22
|
Rose HR, Ghosh MK, Maggiolo AO, Pollock CJ, Blaesi EJ, Hajj V, Wei Y, Rajakovich LJ, Chang WC, Han Y, Hajj M, Krebs C, Silakov A, Pandelia ME, Bollinger JM, Boal AK. Structural Basis for Superoxide Activation of Flavobacterium johnsoniae Class I Ribonucleotide Reductase and for Radical Initiation by Its Dimanganese Cofactor. Biochemistry 2018; 57:2679-2693. [PMID: 29609464 DOI: 10.1021/acs.biochem.8b00247] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A ribonucleotide reductase (RNR) from Flavobacterium johnsoniae ( Fj) differs fundamentally from known (subclass a-c) class I RNRs, warranting its assignment to a new subclass, Id. Its β subunit shares with Ib counterparts the requirements for manganese(II) and superoxide (O2-) for activation, but it does not require the O2--supplying flavoprotein (NrdI) needed in Ib systems, instead scavenging the oxidant from solution. Although Fj β has tyrosine at the appropriate sequence position (Tyr 104), this residue is not oxidized to a radical upon activation, as occurs in the Ia/b proteins. Rather, Fj β directly deploys an oxidized dimanganese cofactor for radical initiation. In treatment with one-electron reductants, the cofactor can undergo cooperative three-electron reduction to the II/II state, in contrast to the quantitative univalent reduction to inactive "met" (III/III) forms seen with I(a-c) βs. This tendency makes Fj β unusually robust, as the II/II form can readily be reactivated. The structure of the protein rationalizes its distinctive traits. A distortion in a core helix of the ferritin-like architecture renders the active site unusually open, introduces a cavity near the cofactor, and positions a subclass-d-specific Lys residue to shepherd O2- to the Mn2II/II cluster. Relative to the positions of the radical tyrosines in the Ia/b proteins, the unreactive Tyr 104 of Fj β is held away from the cofactor by a hydrogen bond with a subclass-d-specific Thr residue. Structural comparisons, considered with its uniquely simple mode of activation, suggest that the Id protein might most closely resemble the primordial RNR-β.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Yifeng Wei
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | | | | | | | | | | | | | - Maria-Eirini Pandelia
- Department of Biochemistry , Brandeis University , Waltham , Massachusetts 02454 , United States
| | | | | |
Collapse
|
23
|
Shakeel T, Gupta M, Fatma Z, Kumar R, Kumar R, Singh R, Sharma M, Jade D, Gupta D, Fatma T, Yazdani SS. A consensus-guided approach yields a heat-stable alkane-producing enzyme and identifies residues promoting thermostability. J Biol Chem 2018; 293:9148-9161. [PMID: 29632075 PMCID: PMC6005442 DOI: 10.1074/jbc.ra117.000639] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 04/06/2018] [Indexed: 01/02/2023] Open
Abstract
Aldehyde-deformylating oxygenase (ADO) is an essential enzyme for production of long-chain alkanes as drop-in biofuels, which are compatible with existing fuel systems. The most active ADOs are present in mesophilic cyanobacteria, especially Nostoc punctiforme Given the potential applications of thermostable enzymes in biorefineries, here we generated a thermostable (Cts)-ADO based on a consensus of ADO sequences from several thermophilic cyanobacterial strains. Using an in silico design pipeline and a metagenome library containing 41 hot-spring microbial communities, we created Cts-ADO. Cts-ADO displayed a 3.8-fold increase in pentadecane production on raising the temperature from 30 to 42 °C, whereas ADO from N. punctiforme (Np-ADO) exhibited a 1.7-fold decline. 3D structure modeling and molecular dynamics simulations of Cts- and Np-ADO at different temperatures revealed differences between the two enzymes in residues clustered on exposed loops of these variants, which affected the conformation of helices involved in forming the ADO catalytic core. In Cts-ADO, this conformational change promoted ligand binding to its preferred iron, Fe2, in the di-iron cluster at higher temperature, but the reverse was observed in Np-ADO. Detailed mapping of residues conferring Cts-ADO thermostability identified four amino acids, which we substituted individually and together in Np-ADO. Among these substitution variants, A161E was remarkably similar to Cts-ADO in terms of activity optima, kinetic parameters, and structure at higher temperature. A161E was located in loop L6, which connects helices H5 and H6, and supported ligand binding to Fe2 at higher temperatures, thereby promoting optimal activity at these temperatures and explaining the increased thermostability of Cts-ADO.
Collapse
Affiliation(s)
- Tabinda Shakeel
- From the Microbial Engineering Group.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067 and
| | - Mayank Gupta
- From the Microbial Engineering Group.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067 and
| | - Zia Fatma
- From the Microbial Engineering Group.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067 and
| | | | | | - Rahul Singh
- From the Microbial Engineering Group.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067 and
| | - Medha Sharma
- From the Microbial Engineering Group.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067 and
| | | | | | - Tasneem Fatma
- the Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Syed Shams Yazdani
- From the Microbial Engineering Group, .,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067 and
| |
Collapse
|
24
|
Jasniewski AJ, Que L. Dioxygen Activation by Nonheme Diiron Enzymes: Diverse Dioxygen Adducts, High-Valent Intermediates, and Related Model Complexes. Chem Rev 2018; 118:2554-2592. [PMID: 29400961 PMCID: PMC5920527 DOI: 10.1021/acs.chemrev.7b00457] [Citation(s) in RCA: 298] [Impact Index Per Article: 49.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A growing subset of metalloenzymes activates dioxygen with nonheme diiron active sites to effect substrate oxidations that range from the hydroxylation of methane and the desaturation of fatty acids to the deformylation of fatty aldehydes to produce alkanes and the six-electron oxidation of aminoarenes to nitroarenes in the biosynthesis of antibiotics. A common feature of their reaction mechanisms is the formation of O2 adducts that evolve into more reactive derivatives such as diiron(II,III)-superoxo, diiron(III)-peroxo, diiron(III,IV)-oxo, and diiron(IV)-oxo species, which carry out particular substrate oxidation tasks. In this review, we survey the various enzymes belonging to this unique subset and the mechanisms by which substrate oxidation is carried out. We examine the nature of the reactive intermediates, as revealed by X-ray crystallography and the application of various spectroscopic methods and their associated reactivity. We also discuss the structural and electronic properties of the model complexes that have been found to mimic salient aspects of these enzyme active sites. Much has been learned in the past 25 years, but key questions remain to be answered.
Collapse
Affiliation(s)
- Andrew J. Jasniewski
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
25
|
Lindsay S, Mader SL, Kaila VRI, Hess CR. C-H Oxidation by a Diiron Complex with Facially Opposing Active Sites. ChemistrySelect 2018. [DOI: 10.1002/slct.201800192] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Stacey Lindsay
- Department of Chemistry; Durham University; South Rd Durham DH1 3LE UK
| | - Sophie L. Mader
- Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85747 Garching Germany
| | - Ville R. I. Kaila
- Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85747 Garching Germany
| | - Corinna R. Hess
- Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85747 Garching Germany
- Catalysis Research Center; Technische Universität München; Ernst-Otto-Fischer-Straße 1 85748 Garching Germany
| |
Collapse
|
26
|
Khenkin AM, Vedichi M, Shimon LJW, Cranswick MA, Klein JEMN, Que L, Neumann R. Hydrogen-Atom Transfer Oxidation with H 2O 2 Catalyzed by [FeII(1,2-bis(2,2'-bipyridyl-6-yl)ethane(H 2O) 2] 2+: Likely Involvement of a (μ-Hydroxo)(μ-1,2-peroxo)diiron(III) Intermediate. Isr J Chem 2018; 57:990-998. [PMID: 29335656 DOI: 10.1002/ijch.201700059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The iron(II) triflate complex (1) of 1,2-bis(2,2'-bipyridyl-6-yl)ethane, with two bipyridine moieties connected by an ethane bridge, was prepared. Addition of aqueous 30% H2O2 to an acetonitrile solution of 1 yielded 2, a green compound with λmax=710 nm. Moessbauer measurements on 2 showed a doublet with an isomer shift (δ) of 0.35 mm/s and a quadrupole splitting (ΔEQ) of 0.86 mm/s, indicative of an antiferromagnetically coupled diferric complex. Resonance Raman spectra showed peaks at 883, 556 and 451 cm-1 that downshifted to 832, 540 and 441 cm-1 when 1 was treated with H218O2. All the spectroscopic data support the initial formation of a (μ-hydroxo)(μ-1,2-peroxo)diiron(III) complex that oxidizes carbon-hydrogen bonds. At 0°C 2 reacted with cyclohexene to yield allylic oxidation products but not epoxide. Weak benzylic C-H bonds of alkylarenes were also oxidized. A plot of the logarithms of the second order rate constants versus the bond dissociation energies of the cleaved C-H bond showed an excellent linear correlation. Along with the observation that oxidation of the probe substrate 2,2-dimethyl-1-phenylpropan-1-ol yielded the corresponding ketone but no benzaldehyde, and the kinetic isotope effect, kH/kD , of 2.8 found for the oxidation of xanthene, the results support the hypothesis for a metal-based H-atom abstraction mechanism. Complex 2 is a rare example of a (μ-hydroxo)(μ-1,2-peroxo)diiron(III) complex that can elicit the oxidation of carbon-hydrogen bonds.
Collapse
Affiliation(s)
- Alexander M Khenkin
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel 76100, phone: +972-8-9343354
| | - Madhu Vedichi
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel 76100, phone: +972-8-9343354
| | - Linda J W Shimon
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel 76100
| | - Matthew A Cranswick
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, USA
| | - Johannes E M N Klein
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, USA
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, USA
| | - Ronny Neumann
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel 76100, phone: +972-8-9343354
| |
Collapse
|
27
|
Abdellaoui S, Macazo FC, Cai R, De Lacey AL, Pita M, Minteer SD. Enzymatic Electrosynthesis of Alkanes by Bioelectrocatalytic Decarbonylation of Fatty Aldehydes. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712890] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sofiene Abdellaoui
- Department of Chemistry University of Utah 315 S 1400 E Salt Lake City UT 84112 USA
| | - Florika C. Macazo
- Department of Chemistry University of Utah 315 S 1400 E Salt Lake City UT 84112 USA
| | - Rong Cai
- Department of Chemistry University of Utah 315 S 1400 E Salt Lake City UT 84112 USA
| | - Antonio L. De Lacey
- Instituto de Catalisis y Petroleoquimica CSIC C/ Marie Curie 2, L10 28049 Madrid Spain
| | - Marcos Pita
- Instituto de Catalisis y Petroleoquimica CSIC C/ Marie Curie 2, L10 28049 Madrid Spain
| | - Shelley D. Minteer
- Department of Chemistry University of Utah 315 S 1400 E Salt Lake City UT 84112 USA
| |
Collapse
|
28
|
Abdellaoui S, Macazo FC, Cai R, De Lacey AL, Pita M, Minteer SD. Enzymatic Electrosynthesis of Alkanes by Bioelectrocatalytic Decarbonylation of Fatty Aldehydes. Angew Chem Int Ed Engl 2018; 57:2404-2408. [DOI: 10.1002/anie.201712890] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Sofiene Abdellaoui
- Department of Chemistry University of Utah 315 S 1400 E Salt Lake City UT 84112 USA
| | - Florika C. Macazo
- Department of Chemistry University of Utah 315 S 1400 E Salt Lake City UT 84112 USA
| | - Rong Cai
- Department of Chemistry University of Utah 315 S 1400 E Salt Lake City UT 84112 USA
| | - Antonio L. De Lacey
- Instituto de Catalisis y Petroleoquimica CSIC C/ Marie Curie 2, L10 28049 Madrid Spain
| | - Marcos Pita
- Instituto de Catalisis y Petroleoquimica CSIC C/ Marie Curie 2, L10 28049 Madrid Spain
| | - Shelley D. Minteer
- Department of Chemistry University of Utah 315 S 1400 E Salt Lake City UT 84112 USA
| |
Collapse
|
29
|
Weitz AC, Giri N, Caranto JD, Kurtz DM, Bominaar EL, Hendrich MP. Spectroscopy and DFT Calculations of a Flavo-diiron Enzyme Implicate New Diiron Site Structures. J Am Chem Soc 2017; 139:12009-12019. [PMID: 28756660 PMCID: PMC5898632 DOI: 10.1021/jacs.7b06546] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Flavo-diiron proteins (FDPs) are non-heme iron containing enzymes that are widespread in anaerobic bacteria, archaea, and protozoa, serving as the terminal components to dioxygen and nitric oxide reductive scavenging pathways in these organisms. FDPs contain a dinuclear iron active site similar to that in hemerythrin, ribonucleotide reductase, and methane monooxygenase, all of which can bind NO and O2. However, only FDP competently turns over NO to N2O. Here, EPR and Mössbauer spectroscopies allow electronic characterization of the diferric and diferrous species of FDP. The exchange-coupling constant J (Hex = JS1·S2) was found to increase from +20 cm-1 to +32 cm-1 upon reduction of the diferric to the diferrous species, indicative of (1) at least one hydroxo bridge between the iron ions for both states and (2) a change to the diiron core structure upon reduction. In comparison to characterized diiron proteins and synthetic complexes, the experimental values were consistent with a dihydroxo bridged diferric core, which loses one hydroxo bridge upon reduction. DFT calculations of these structures gave values of J and Mössbauer parameters in agreement with experiment. Although the crystal structure shows a hydrogen bond between the iron bound aspartate and the bridging solvent molecule, the DFT calculations of structures consistent with the crystal structure gave calculated values of J incompatible with the spectroscopic results. We conclude that the crystal structure of the diferric state does not represent the frozen solution structure and that a mono-μ-hydroxo diferrous species is the catalytically functional state that reacts with NO and O2. The new EPR spectroscopic probe of the diferric state indicated that the diferric structure of FDP prior to and immediately after turnover with NO are flavin mononucleotide (FMN) dependent, implicating an additional proton transfer role for FMN in turnover of NO.
Collapse
Affiliation(s)
- Andrew C. Weitz
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Nitai Giri
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Jonathan D. Caranto
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Donald M. Kurtz
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Emile L. Bominaar
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Michael P. Hendrich
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| |
Collapse
|
30
|
Jasniewski AJ, Komor AJ, Lipscomb JD, Que L. Unprecedented (μ-1,1-Peroxo)diferric Structure for the Ambiphilic Orange Peroxo Intermediate of the Nonheme N-Oxygenase CmlI. J Am Chem Soc 2017; 139:10472-10485. [PMID: 28673082 PMCID: PMC5568637 DOI: 10.1021/jacs.7b05389] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The final step in the biosynthesis of the antibiotic chloramphenicol is the oxidation of an aryl-amine substrate to an aryl-nitro product catalyzed by the N-oxygenase CmlI in three two-electron steps. The CmlI active site contains a diiron cluster ligated by three histidine and four glutamate residues and activates dioxygen to perform its role in the biosynthetic pathway. It was previously shown that the active oxidant used by CmlI to facilitate this chemistry is a peroxo-diferric intermediate (CmlIP). Spectroscopic characterization demonstrated that the peroxo binding geometry of CmlIP is not consistent with the μ-1,2 mode commonly observed in nonheme diiron systems. Its geometry was tentatively assigned as μ-η2:η1 based on comparison with resonance Raman (rR) features of mixed-metal model complexes in the absence of appropriate diiron models. Here, X-ray absorption spectroscopy (XAS) and rR studies have been used to establish a refined structure for the diferric cluster of CmlIP. The rR experiments carried out with isotopically labeled water identified the symmetric and asymmetric vibrations of an Fe-O-Fe unit in the active site at 485 and 780 cm-1, respectively, which was confirmed by the 1.83 Å Fe-O bond observed by XAS. In addition, a unique Fe···O scatterer at 2.82 Å observed from XAS analysis is assigned as arising from the distal O atom of a μ-1,1-peroxo ligand that is bound symmetrically between the irons. The (μ-oxo)(μ-1,1-peroxo)diferric core structure associated with CmlIP is unprecedented among diiron cluster-containing enzymes and corresponding biomimetic complexes. Importantly, it allows the peroxo-diferric intermediate to be ambiphilic, acting as an electrophilic oxidant in the initial N-hydroxylation of an arylamine and then becoming a nucleophilic oxidant in the final oxidation of an aryl-nitroso intermediate to the aryl-nitro product.
Collapse
Affiliation(s)
- Andrew J. Jasniewski
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455
| | - Anna J. Komor
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455
| | - Lawrence Que
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455
| |
Collapse
|
31
|
Miller EK, Trivelas NE, Maugeri PT, Blaesi EJ, Shafaat HS. Time-Resolved Investigations of Heterobimetallic Cofactor Assembly in R2lox Reveal Distinct Mn/Fe Intermediates. Biochemistry 2017; 56:3369-3379. [PMID: 28574263 DOI: 10.1021/acs.biochem.7b00403] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The assembly mechanism of the Mn/Fe ligand-binding oxidases (R2lox), a family of proteins that are homologous to the nonheme diiron carboxylate enzymes, has been investigated using time-resolved techniques. Multiple heterobimetallic intermediates that exhibit unique spectral features, including visible absorption bands and exceptionally broad electron paramagnetic resonance signatures, are observed through optical and magnetic resonance spectroscopies. On the basis of comparison to known diiron species and model compounds, the spectra have been attributed to (μ-peroxo)-MnIII/FeIII and high-valent Mn/Fe species. Global spectral analysis coupled with isotopic substitution and kinetic modeling reveals elementary rate constants for the assembly of Mn/Fe R2lox under aerobic conditions. A complete reaction mechanism for cofactor maturation that is consistent with experimental data has been developed. These results suggest that the Mn/Fe cofactor can perform direct C-H bond abstraction, demonstrating the potential for potent chemical reactivity that remains unexplored.
Collapse
Affiliation(s)
| | | | | | - Elizabeth J Blaesi
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | | |
Collapse
|
32
|
Park K, Li N, Kwak Y, Srnec M, Bell CB, Liu LV, Wong SD, Yoda Y, Kitao S, Seto M, Hu M, Zhao J, Krebs C, Bollinger JM, Solomon EI. Peroxide Activation for Electrophilic Reactivity by the Binuclear Non-heme Iron Enzyme AurF. J Am Chem Soc 2017; 139:7062-7070. [PMID: 28457126 DOI: 10.1021/jacs.7b02997] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Binuclear non-heme iron enzymes activate O2 for diverse chemistries that include oxygenation of organic substrates and hydrogen atom abstraction. This process often involves the formation of peroxo-bridged biferric intermediates, only some of which can perform electrophilic reactions. To elucidate the geometric and electronic structural requirements to activate peroxo reactivity, the active peroxo intermediate in 4-aminobenzoate N-oxygenase (AurF) has been characterized spectroscopically and computationally. A magnetic circular dichroism study of reduced AurF shows that its electronic and geometric structures are poised to react rapidly with O2. Nuclear resonance vibrational spectroscopic definition of the peroxo intermediate formed in this reaction shows that the active intermediate has a protonated peroxo bridge. Density functional theory computations on the structure established here show that the protonation activates peroxide for electrophilic/single-electron-transfer reactivity. This activation of peroxide by protonation is likely also relevant to the reactive peroxo intermediates in other binuclear non-heme iron enzymes.
Collapse
Affiliation(s)
- Kiyoung Park
- Department of Chemistry, Stanford University , Stanford, California 94305-5080, United States.,Department of Chemistry, KAIST , Daejeon 34141, Republic of Korea
| | - Ning Li
- Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Yeonju Kwak
- Department of Chemistry, Stanford University , Stanford, California 94305-5080, United States
| | - Martin Srnec
- Department of Chemistry, Stanford University , Stanford, California 94305-5080, United States
| | - Caleb B Bell
- Department of Chemistry, Stanford University , Stanford, California 94305-5080, United States
| | - Lei V Liu
- Department of Chemistry, Stanford University , Stanford, California 94305-5080, United States
| | - Shaun D Wong
- Department of Chemistry, Stanford University , Stanford, California 94305-5080, United States
| | | | - Shinji Kitao
- Research Reactor Institute, Kyoto University , Kumatori-cho, Osaka 590-0494, Japan
| | - Makoto Seto
- Research Reactor Institute, Kyoto University , Kumatori-cho, Osaka 590-0494, Japan
| | - Michael Hu
- Advanced Photon Source, Argonne National Laboratory , Lemont, Illinois 60439, United States
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory , Lemont, Illinois 60439, United States
| | - Carsten Krebs
- Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States.,Department of Chemistry, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - J Martin Bollinger
- Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States.,Department of Chemistry, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Edward I Solomon
- Department of Chemistry, Stanford University , Stanford, California 94305-5080, United States.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory , Stanford, California 94309, United States
| |
Collapse
|
33
|
Patrikainen P, Carbonell V, Thiel K, Aro EM, Kallio P. Comparison of orthologous cyanobacterial aldehyde deformylating oxygenases in the production of volatile C3-C7 alkanes in engineered E. coli. Metab Eng Commun 2017; 5:9-18. [PMID: 29188180 PMCID: PMC5699528 DOI: 10.1016/j.meteno.2017.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 04/11/2017] [Accepted: 05/01/2017] [Indexed: 01/01/2023] Open
Abstract
Aldehyde deformylating oxygenase (ADO) is a unique enzyme found exclusively in photosynthetic cyanobacteria, which natively converts acyl aldehyde precursors into hydrocarbon products embedded in cellular lipid bilayers. This capacity has opened doors for potential biotechnological applications aiming at biological production of diesel-range alkanes and alkenes, which are compatible with the nonrenewable petroleum-derived end-products in current use. The development of production platforms, however, has been limited by the relative inefficiency of ADO enzyme, promoting research towards finding new strategies and information to be used for rational design of enhanced pathways for hydrocarbon over-expression. In this work we present an optimized approach to study different ADO orthologs derived from different cyanobacterial species in an in vivo set-up in Escherichia coli. The system enabled comparison of alternative ADOs for the production efficiency of short-chain volatile C3-C7 alkanes, propane, pentane and heptane, and provided insight on the differences in substrate preference, catalytic efficiency and limitations associated with the enzymes. The work concentrated on five ADO orthologs which represent the most extensively studied cyanobacterial species in the field, and revealed distinct differences between the enzymes. In most cases the ADO from Nostoc punctiforme PCC 73102 performed the best in respect to yields and initial rates for the production of the volatile hydrocarbons. At the other extreme, the system harboring the ADO form Synechococcus sp. RS9917 produced very low amounts of the short-chain alkanes, primarily due to poor accumulation of the enzyme in E. coli. The ADOs from Synechocystis sp. PCC 6803 and Prochlorococcus marinus MIT9313, and the corresponding variant A134F displayed less divergence, although variation between chain-length preferences could be observed. The results confirmed the general trend of ADOs having decreasing catalytic efficiency towards precursors of decreasing chain-length, while expanding the knowledge on the species-specific traits, which may aid future pathway design and structure-based engineering of ADO for more efficient hydrocarbon production systems. Five cyanobacterial aldehyde deformylating oxygenases were compared in E. coli. The engineered pathways produced volatile Cn-1 alkanes from supplemented fatty acids. The E. coli strains produced propane, pentane and heptane in the culture headspace. The results revealed clear differences in the catalytic performance between the ADOs.
Collapse
Affiliation(s)
- Pekka Patrikainen
- Molecular Plant Biology, Department of Biochemistry, University of Turku (Turun Yliopisto), 20014 TURUN YLIOPISTO, Finland
| | - Veronica Carbonell
- Molecular Plant Biology, Department of Biochemistry, University of Turku (Turun Yliopisto), 20014 TURUN YLIOPISTO, Finland
| | - Kati Thiel
- Molecular Plant Biology, Department of Biochemistry, University of Turku (Turun Yliopisto), 20014 TURUN YLIOPISTO, Finland
| | - Eva-Mari Aro
- Molecular Plant Biology, Department of Biochemistry, University of Turku (Turun Yliopisto), 20014 TURUN YLIOPISTO, Finland
| | - Pauli Kallio
- Molecular Plant Biology, Department of Biochemistry, University of Turku (Turun Yliopisto), 20014 TURUN YLIOPISTO, Finland
| |
Collapse
|
34
|
Waldman AJ, Ng TL, Wang P, Balskus EP. Heteroatom-Heteroatom Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5784-5863. [PMID: 28375000 PMCID: PMC5534343 DOI: 10.1021/acs.chemrev.6b00621] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Natural products that contain functional groups with heteroatom-heteroatom linkages (X-X, where X = N, O, S, and P) are a small yet intriguing group of metabolites. The reactivity and diversity of these structural motifs has captured the interest of synthetic and biological chemists alike. Functional groups containing X-X bonds are found in all major classes of natural products and often impart significant biological activity. This review presents our current understanding of the biosynthetic logic and enzymatic chemistry involved in the construction of X-X bond containing functional groups within natural products. Elucidating and characterizing biosynthetic pathways that generate X-X bonds could both provide tools for biocatalysis and synthetic biology, as well as guide efforts to uncover new natural products containing these structural features.
Collapse
Affiliation(s)
- Abraham J. Waldman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Tai L. Ng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Peng Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| |
Collapse
|
35
|
Yu P, Chen X, Li P. Enhancing microbial production of biofuels by expanding microbial metabolic pathways. Biotechnol Appl Biochem 2017; 64:606-619. [PMID: 27507087 DOI: 10.1002/bab.1529] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 07/31/2016] [Indexed: 12/29/2022]
Abstract
Fatty acid, isoprenoid, and alcohol pathways have been successfully engineered to produce biofuels. By introducing three genes, atfA, adhE, and pdc, into Escherichia coli to expand fatty acid pathway, up to 1.28 g/L of fatty acid ethyl esters can be achieved. The isoprenoid pathway can be expanded to produce bisabolene with a high titer of 900 mg/L in Saccharomyces cerevisiae. Short- and long-chain alcohols can also be effectively biosynthesized by extending the carbon chain of ketoacids with an engineered "+1" alcohol pathway. Thus, it can be concluded that expanding microbial metabolic pathways has enormous potential for enhancing microbial production of biofuels for future industrial applications. However, some major challenges for microbial production of biofuels should be overcome to compete with traditional fossil fuels: lowering production costs, reducing the time required to construct genetic elements and to increase their predictability and reliability, and creating reusable parts with useful and predictable behavior. To address these challenges, several aspects should be further considered in future: mining and transformation of genetic elements related to metabolic pathways, assembling biofuel elements and coordinating their functions, enhancing the tolerance of host cells to biofuels, and creating modular subpathways that can be easily interconnected.
Collapse
Affiliation(s)
- Ping Yu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Xingge Chen
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Peng Li
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province, People's Republic of China
| |
Collapse
|
36
|
Martinie RJ, Blaesi EJ, Krebs C, Bollinger JM, Silakov A, Pollock CJ. Evidence for a Di-μ-oxo Diamond Core in the Mn(IV)/Fe(IV) Activation Intermediate of Ribonucleotide Reductase from Chlamydia trachomatis. J Am Chem Soc 2017; 139:1950-1957. [PMID: 28075562 DOI: 10.1021/jacs.6b11563] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High-valent iron and manganese complexes effect some of the most challenging biochemical reactions known, including hydrocarbon and water oxidations associated with the global carbon cycle and oxygenic photosynthesis, respectively. Their extreme reactivity presents an impediment to structural characterization, but their biological importance and potential chemical utility have, nevertheless, motivated extensive efforts toward that end. Several such intermediates accumulate during activation of class I ribonucleotide reductase (RNR) β subunits, which self-assemble dimetal cofactors with stable one-electron oxidants that serve to initiate the enzyme's free-radical mechanism. In the class I-c β subunit from Chlamydia trachomatis, a heterodinuclear Mn(II)/Fe(II) complex reacts with dioxygen to form a Mn(IV)/Fe(IV) intermediate, which undergoes reduction of the iron site to produce the active Mn(IV)/Fe(III) cofactor. Herein, we assess the structure of the Mn(IV)/Fe(IV) activation intermediate using Fe- and Mn-edge extended X-ray absorption fine structure (EXAFS) analysis and multifrequency pulse electron paramagnetic resonance (EPR) spectroscopy. The EXAFS results reveal a metal-metal vector of 2.74-2.75 Å and an intense light-atom (C/N/O) scattering interaction 1.8 Å from the Fe. Pulse EPR data reveal an exchangeable deuterium hyperfine coupling of strength |T| = 0.7 MHz, but no stronger couplings. The results suggest that the intermediate possesses a di-μ-oxo diamond core structure with a terminal hydroxide ligand to the Mn(IV).
Collapse
Affiliation(s)
- Ryan J Martinie
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Elizabeth J Blaesi
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - J Martin Bollinger
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Alexey Silakov
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Christopher J Pollock
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| |
Collapse
|
37
|
Wang C, Zhao C, Hu L, Chen H. Calculated Mechanism of Cyanobacterial Aldehyde-Deformylating Oxygenase: Asymmetric Aldehyde Activation by a Symmetric Diiron Cofactor. J Phys Chem Lett 2016; 7:4427-4432. [PMID: 27775357 DOI: 10.1021/acs.jpclett.6b02061] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Cyanobacterial aldehyde-deformylating oxygenase (cADO) is a nonheme diiron enzyme that catalyzes the conversion of aldehyde to alk(a/e)ne, an important transformation in biofuel research. In this work, we report a highly desired computational study for probing the mechanism of cADO. By combining our QM/MM results with the available 57Fe Mössbauer spectroscopic data, the gained detailed structural information suggests construction of asymmetry from the symmetric diiron cofactor in an aldehyde substrate and O2 activation. His160, one of the two iron-coordinate histidine residues in cADO, plays a pivotal role in this asymmetric aldehyde activation process by unprecedented reversible dissociation from the diiron cofactor, a behavior unknown in any other nonheme dinuclear or mononuclear enzymes. The revealed intrinsically asymmetric interactions of the substrate/O2 with the symmetric cofactor in cADO are inspirational for exploring diiron subsite resolution in other nonheme diiron enzymes.
Collapse
Affiliation(s)
- Chao Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049, People's Republic of China
| | - Chongyang Zhao
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049, People's Republic of China
| | - Lianrui Hu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049, People's Republic of China
| | - Hui Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, People's Republic of China
| |
Collapse
|
38
|
Kim S, Lee JH, Seok JH, Park YH, Jung SW, Cho AE, Lee C, Chung MS, Kim KH. Structural Basis of Novel Iron-Uptake Route and Reaction Intermediates in Ferritins from Gram-Negative Bacteria. J Mol Biol 2016; 428:5007-5018. [PMID: 27777002 DOI: 10.1016/j.jmb.2016.10.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 10/17/2016] [Accepted: 10/18/2016] [Indexed: 10/20/2022]
Abstract
Iron and oxygen chemistry is mediated by iron proteins for many biological functions. Carboxylate-bridged diiron enzymes including ferritin have the common mechanism of oxygen activation via peroxodiferric intermediates. However, the route for iron uptake and the structural identification of intermediates still remain incomplete. The 4-fold symmetry channel of Helicobacter pylori ferritin was previously proposed as the iron-uptake route in eubacteria, but the amino acid residues at the 4-fold channel are not highly conserved. Here, we show evidence for a short path for iron uptake from His93 on the surface to the ferroxidase center in H. pylori ferritin and Escherichia coli ferritin. The amino acid residues along this path are highly conserved in Gram-negative bacteria and some archaea, and the mutants containing S20A and H93L showed significantly decreased iron oxidation. Surprisingly, the E. coli ferritin S20A crystal structure showed oxygen binding and side-on, symmetric μ-η2:η2 peroxodiferric and oxodiferric intermediates. The results provide the structural basis for understanding the chemical nature of intermediates in iron oxidation in bacteria and some of archaea.
Collapse
Affiliation(s)
- Sella Kim
- Department of Biotechnology & Bioinformatics, Korea University, Sejong 339-700, Korea
| | - Ji-Hye Lee
- Department of Biotechnology & Bioinformatics, Korea University, Sejong 339-700, Korea
| | - Jong Hyeon Seok
- Department of Biotechnology & Bioinformatics, Korea University, Sejong 339-700, Korea
| | - Yi-Ho Park
- Department of Biotechnology & Bioinformatics, Korea University, Sejong 339-700, Korea
| | - Sang Won Jung
- Department of Biotechnology & Bioinformatics, Korea University, Sejong 339-700, Korea
| | - Art E Cho
- Department of Biotechnology & Bioinformatics, Korea University, Sejong 339-700, Korea
| | - Cheolju Lee
- Functional Proteomics Center, Korea Institute of Science and Technology, Seoul 136-791, Korea
| | - Mi Sook Chung
- Department of Food and Nutrition, Duksung Women's University, Seoul 132-714, Korea
| | - Kyung Hyun Kim
- Department of Biotechnology & Bioinformatics, Korea University, Sejong 339-700, Korea.
| |
Collapse
|
39
|
Rana S, Pandey B, Dey A, Haque R, Rajaraman G, Maiti D. A Doubly Biomimetic Synthetic Transformation: Catalytic Decarbonylation and Halogenation at Room Temperature by Vanadium Pentoxide. ChemCatChem 2016. [DOI: 10.1002/cctc.201600843] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sujoy Rana
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai- 400076 India
| | - Bhawana Pandey
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai- 400076 India
| | - Aniruddha Dey
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai- 400076 India
| | - Rameezul Haque
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai- 400076 India
| | - Gopalan Rajaraman
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai- 400076 India
| | - Debabrata Maiti
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai- 400076 India
| |
Collapse
|
40
|
Jasniewski AJ, Engstrom LM, Vu VV, Park MH, Que L. X-ray absorption spectroscopic characterization of the diferric-peroxo intermediate of human deoxyhypusine hydroxylase in the presence of its substrate eIF5a. J Biol Inorg Chem 2016; 21:605-18. [PMID: 27380180 PMCID: PMC4990465 DOI: 10.1007/s00775-016-1373-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 06/16/2016] [Indexed: 11/29/2022]
Abstract
Human deoxyhypusine hydroxylase (hDOHH) is an enzyme that is involved in the critical post-translational modification of the eukaryotic translation initiation factor 5A (eIF5A). Following the conversion of a lysine residue on eIF5A to deoxyhypusine (Dhp) by deoxyhypusine synthase, hDOHH hydroxylates Dhp to yield the unusual amino acid residue hypusine (Hpu), a modification that is essential for eIF5A to promote peptide synthesis at the ribosome, among other functions. Purification of hDOHH overexpressed in E. coli affords enzyme that is blue in color, a feature that has been associated with the presence of a peroxo-bridged diiron(III) active site. To gain further insight into the nature of the diiron site and how it may change as hDOHH goes through the catalytic cycle, we have conducted X-ray absorption spectroscopic studies of hDOHH on five samples that represent different species along its reaction pathway. Structural analysis of each species has been carried out, starting with the reduced diferrous state, proceeding through its O2 adduct, and ending with a diferric decay product. Our results show that the Fe⋯Fe distances found for the five samples fall within a narrow range of 3.4-3.5 Å, suggesting that hDOHH has a fairly constrained active site. This pattern differs significantly from what has been associated with canonical dioxygen activating nonheme diiron enzymes, such as soluble methane monooxygenase and Class 1A ribonucleotide reductases, for which the Fe⋯Fe distance can change by as much as 1 Å during the redox cycle. These results suggest that the O2 activation mechanism for hDOHH deviates somewhat from that associated with the canonical nonheme diiron enzymes, opening the door to new mechanistic possibilities for this intriguing family of enzymes.
Collapse
Affiliation(s)
- Andrew J Jasniewski
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN, 55455, USA
| | - Lisa M Engstrom
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN, 55455, USA
| | - Van V Vu
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN, 55455, USA
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 298-300A Nguyen Tat Thanh Street, Ward 13, District 4, Ho Chi Minh City, Vietnam
| | - Myung Hee Park
- National Institute of Dental and Craniofacial Research, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN, 55455, USA.
| |
Collapse
|
41
|
Solomon EI, Park K. Structure/function correlations over binuclear non-heme iron active sites. J Biol Inorg Chem 2016; 21:575-88. [PMID: 27369780 PMCID: PMC5010389 DOI: 10.1007/s00775-016-1372-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/14/2016] [Indexed: 11/30/2022]
Abstract
Binuclear non-heme iron enzymes activate O2 to perform diverse chemistries. Three different structural mechanisms of O2 binding to a coupled binuclear iron site have been identified utilizing variable-temperature, variable-field magnetic circular dichroism spectroscopy (VTVH MCD). For the μ-OH-bridged Fe(II)2 site in hemerythrin, O2 binds terminally to a five-coordinate Fe(II) center as hydroperoxide with the proton deriving from the μ-OH bridge and the second electron transferring through the resulting μ-oxo superexchange pathway from the second coordinatively saturated Fe(II) center in a proton-coupled electron transfer process. For carboxylate-only-bridged Fe(II)2 sites, O2 binding as a bridged peroxide requires both Fe(II) centers to be coordinatively unsaturated and has good frontier orbital overlap with the two orthogonal O2 π* orbitals to form peroxo-bridged Fe(III)2 intermediates. Alternatively, carboxylate-only-bridged Fe(II)2 sites with only a single open coordination position on an Fe(II) enable the one-electron formation of Fe(III)-O2 (-) or Fe(III)-NO(-) species. Finally, for the peroxo-bridged Fe(III)2 intermediates, further activation is necessary for their reactivities in one-electron reduction and electrophilic aromatic substitution, and a strategy consistent with existing spectral data is discussed.
Collapse
Affiliation(s)
- Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, CA, 94305-5080, USA.
| | - Kiyoung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon, 34141, Republic of Korea
| |
Collapse
|
42
|
Zhang L, Liang Y, Wu W, Tan X, Lu X. Microbial synthesis of propane by engineering valine pathway and aldehyde-deformylating oxygenase. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:80. [PMID: 27042209 PMCID: PMC4818529 DOI: 10.1186/s13068-016-0496-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/22/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND Propane, a major component of liquid petroleum gas (LPG) derived from fossil fuels, has widespread applications in vehicles, cooking, and ambient heating. Given the concerns about fossil fuel depletion and carbon emission, exploiting alternative and renewable source of propane have become attractive. In this study, we report the construction of a novel propane biosynthetic pathway in Escherichia coli. RESULTS We constructed an aldehyde reductases (ALR)-deprived E. coli strain BW25113(DE3) Δ13 via genetic engineering, which produced sufficient isobutyraldehyde precursors and finally achieved de novo synthesis of propane (91 μg/L) by assembling the engineered valine pathway and cyanobacterial aldehyde-deformylating oxygenase (ADO). Additionally, after extensive screening of ADO mutants generated by engineering the active center to accommodate branched-chain isobutyraldehyde, we identified two ADO mutants (I127G, I127G/A48G) which exhibited higher catalytic activity for isobutyraldehyde and improved propane productivity by three times (267 μg/L). CONCLUSIONS The propane biosynthetic pathway constructed here through the engineered valine pathway can produce abundant isobutyraldehyde for ADO and overcome the low availability of precursors in propane production. Furthermore, the rational design aiming at the ADO active center illustrates the plasticity and catalytic potential of ADO. These results together highlight the potential for developing a microbial biomanufacturing platform for propane.
Collapse
Affiliation(s)
- Lei Zhang
- />Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
- />University of Chinese Academy of Sciences, Beijing, China
| | - Yajing Liang
- />Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
| | - Wei Wu
- />Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
| | - Xiaoming Tan
- />Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
| | - Xuefeng Lu
- />Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
| |
Collapse
|
43
|
Kwak Y, Schwartz JK, Huang VW, Boice E, Kurtz DM, Solomon EI. CD/MCD/VTVH-MCD Studies of Escherichia coli Bacterioferritin Support a Binuclear Iron Cofactor Site. Biochemistry 2015; 54:7010-8. [PMID: 26551523 DOI: 10.1021/acs.biochem.5b01033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ferritins and bacterioferritins (Bfrs) utilize a binuclear non-heme iron binding site to catalyze oxidation of Fe(II), leading to formation of an iron mineral core within a protein shell. Unlike ferritins, in which the diiron site binds Fe(II) as a substrate, which then autoxidizes and migrates to the mineral core, the diiron site in Bfr has a 2-His/4-carboxylate ligand set that is commonly found in diiron cofactor enzymes. Bfrs could, therefore, utilize the diiron site as a cofactor rather than for substrate iron binding. In this study, we applied circular dichroism (CD), magnetic CD (MCD), and variable-temperature, variable-field MCD (VTVH-MCD) spectroscopies to define the geometric and electronic structures of the biferrous active site in Escherichia coli Bfr. For these studies, we used an engineered M52L variant, which is known to eliminate binding of a heme cofactor but to have very minor effects on either iron oxidation or mineral core formation. We also examined an H46A/D50A/M52L Bfr variant, which additionally disrupts a previously observed mononuclear non-heme iron binding site inside the protein shell. The spectral analyses define a binuclear and an additional mononuclear ferrous site. The biferrous site shows two different five-coordinate centers. After O2 oxidation and re-reduction, only the mononuclear ferrous signal is eliminated. The retention of the biferrous but not the mononuclear ferrous site upon O2 cycling supports a mechanism in which the binuclear site acts as a cofactor for the O2 reaction, while the mononuclear site binds the substrate Fe(II) that, after its oxidation to Fe(III), migrates to the mineral core.
Collapse
Affiliation(s)
- Yeonju Kwak
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Jennifer K Schwartz
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Victor W Huang
- Department of Chemistry, University of Texas at San Antonio , One UTSA Circle, San Antonio, Texas 78249, United States
| | - Emily Boice
- Department of Chemistry, University of Texas at San Antonio , One UTSA Circle, San Antonio, Texas 78249, United States
| | - Donald M Kurtz
- Department of Chemistry, University of Texas at San Antonio , One UTSA Circle, San Antonio, Texas 78249, United States
| | - Edward I Solomon
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| |
Collapse
|
44
|
Rajakovich LJ, Nørgaard H, Warui DM, Chang WC, Li N, Booker SJ, Krebs C, Bollinger JM, Pandelia ME. Rapid Reduction of the Diferric-Peroxyhemiacetal Intermediate in Aldehyde-Deformylating Oxygenase by a Cyanobacterial Ferredoxin: Evidence for a Free-Radical Mechanism. J Am Chem Soc 2015; 137:11695-709. [PMID: 26284355 DOI: 10.1021/jacs.5b06345] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Aldehyde-deformylating oxygenase (ADO) is a ferritin-like nonheme-diiron enzyme that catalyzes the last step in a pathway through which fatty acids are converted into hydrocarbons in cyanobacteria. ADO catalyzes conversion of a fatty aldehyde to the corresponding alk(a/e)ne and formate, consuming four electrons and one molecule of O2 per turnover and incorporating one atom from O2 into the formate coproduct. The source of the reducing equivalents in vivo has not been definitively established, but a cyanobacterial [2Fe-2S] ferredoxin (PetF), reduced by ferredoxin-NADP(+) reductase (FNR) using NADPH, has been implicated. We show that both the diferric form of Nostoc punctiforme ADO and its (putative) diferric-peroxyhemiacetal intermediate are reduced much more rapidly by Synechocystis sp. PCC6803 PetF than by the previously employed chemical reductant, 1-methoxy-5-methylphenazinium methyl sulfate. The yield of formate and alkane per reduced PetF approaches its theoretical upper limit when reduction of the intermediate is carried out in the presence of FNR. Reduction of the intermediate by either system leads to accumulation of a substrate-derived peroxyl radical as a result of off-pathway trapping of the C2-alkyl radical intermediate by excess O2, which consequently diminishes the yield of the hydrocarbon product. A sulfinyl radical located on residue Cys71 also accumulates with short-chain aldehydes. The detection of these radicals under turnover conditions provides the most direct evidence to date for a free-radical mechanism. Additionally, our results expose an inefficiency of the enzyme in processing its radical intermediate, presenting a target for optimization of bioprocesses exploiting this hydrocarbon-production pathway.
Collapse
Affiliation(s)
- Lauren J Rajakovich
- Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Hanne Nørgaard
- Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Douglas M Warui
- Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Wei-chen Chang
- Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Ning Li
- Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Squire J Booker
- Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - J Martin Bollinger
- Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Maria-Eirini Pandelia
- Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| |
Collapse
|
45
|
Shokri A, Que L. Conversion of Aldehyde to Alkane by a Peroxoiron(III) Complex: A Functional Model for the Cyanobacterial Aldehyde-Deformylating Oxygenase. J Am Chem Soc 2015; 137:7686-91. [PMID: 26030345 DOI: 10.1021/jacs.5b01053] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cyanobacterial aldehyde-deformylating oxygenase (cADO) converts long-chain fatty aldehydes to alkanes via a proposed diferric-peroxo intermediate that carries out the oxidative deformylation of the substrate. Herein, we report that the synthetic iron(III)-peroxo complex [Fe(III)(η(2)-O2)(TMC)](+) (TMC = tetramethylcyclam) causes a similar transformation in the presence of a suitable H atom donor, thus serving as a functional model for cADO. Mechanistic studies suggest that the H atom donor can intercept the incipient alkyl radical formed in the oxidative deformylation step in competition with the oxygen rebound step typically used by most oxygenases for forming C-O bonds.
Collapse
Affiliation(s)
- Alireza Shokri
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
46
|
Martinie RJ, Livada J, Chang WC, Green MT, Krebs C, Bollinger JM, Silakov A. Experimental Correlation of Substrate Position with Reaction Outcome in the Aliphatic Halogenase, SyrB2. J Am Chem Soc 2015; 137:6912-9. [PMID: 25965587 DOI: 10.1021/jacs.5b03370] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The iron(II)- and 2-(oxo)glutarate-dependent (Fe/2OG) oxygenases catalyze an array of challenging transformations, but how individual members of the enzyme family direct different outcomes is poorly understood. The Fe/2OG halogenase, SyrB2, chlorinates C4 of its native substrate, l-threonine appended to the carrier protein, SyrB1, but hydroxylates C5 of l-norvaline and, to a lesser extent, C4 of l-aminobutyric acid when SyrB1 presents these non-native amino acids. To test the hypothesis that positioning of the targeted carbon dictates the outcome, we defined the positions of these three substrates by measuring hyperfine couplings between substrate deuterium atoms and the stable, EPR-active iron-nitrosyl adduct, a surrogate for reaction intermediates. The Fe-(2)H distances and N-Fe-(2)H angles, which vary from 4.2 Å and 85° for threonine to 3.4 Å and 65° for norvaline, rationalize the trends in reactivity. This experimental correlation of position to outcome should aid in judging from structural data on other Fe/2OG enzymes whether they suppress hydroxylation or form hydroxylated intermediates on the pathways to other outcomes.
Collapse
Affiliation(s)
- Ryan J Martinie
- Departments of †Chemistry and of ‡Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Jovan Livada
- Departments of †Chemistry and of ‡Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Wei-chen Chang
- Departments of †Chemistry and of ‡Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Michael T Green
- Departments of †Chemistry and of ‡Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Departments of †Chemistry and of ‡Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - J Martin Bollinger
- Departments of †Chemistry and of ‡Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Alexey Silakov
- Departments of †Chemistry and of ‡Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| |
Collapse
|
47
|
Role of cysteine residues in the structure, stability, and alkane producing activity of cyanobacterial aldehyde deformylating oxygenase. PLoS One 2015; 10:e0122217. [PMID: 25837679 PMCID: PMC4383598 DOI: 10.1371/journal.pone.0122217] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 02/10/2015] [Indexed: 12/22/2022] Open
Abstract
Aldehyde deformylating oxygenase (AD) is a key enzyme for alkane biosynthesis in cyanobacteria, and it can be used as a catalyst for alkane production in vitro and in vivo. However, three free Cys residues in AD may impair its catalytic activity by undesired disulfide bond formation and oxidation. To develop Cys-deficient mutants of AD, we examined the roles of the Cys residues in the structure, stability, and alkane producing activity of AD from Nostoc punctiforme PCC 73102 by systematic Cys-to-Ala/Ser mutagenesis. The C71A/S mutations reduced the hydrocarbon producing activity of AD and facilitated the formation of a dimer, indicating that the conserved Cys71, which is located in close proximity to the substrate-binding site, plays crucial roles in maintaining the activity, structure, and stability of AD. On the other hand, mutations at Cys107 and Cys117 did not affect the hydrocarbon producing activity of AD. Therefore, we propose that the C107A/C117A double mutant is preferable to wild type AD for alkane production and that the double mutant may be used as a pseudo-wild type protein for further improvement of the alkane producing activity of AD.
Collapse
|
48
|
Frederick RE, Caranto JD, Masitas CA, Gebhardt LL, MacGowan CE, Limberger RJ, Kurtz DM. Dioxygen and nitric oxide scavenging by Treponema denticola flavodiiron protein: a mechanistic paradigm for catalysis. J Biol Inorg Chem 2015; 20:603-13. [PMID: 25700637 PMCID: PMC4768905 DOI: 10.1007/s00775-015-1248-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 02/13/2015] [Indexed: 10/24/2022]
Abstract
Flavodiiron proteins (FDPs) contain a unique active site consisting of a non-heme diiron carboxylate site proximal to a flavin mononucleotide (FMN). FDPs serve as the terminal components for reductive scavenging of dioxygen (to water) or nitric oxide (to nitrous oxide), which combats oxidative or nitrosative stress in many bacteria. Characterizations of FDPs from spirochetes or from any oral microbes have not been previously reported. Here, we report characterization of an FDP from the anaerobic spirochete, Treponema (T.) denticola, which is associated with chronic periodontitis. The isolated T. denticola FDP exhibited efficient four-electron dioxygen reductase activity and lower but significant anaerobic nitric oxide reductase activity. A mutant T. denticola strain containing the inactivated FDP-encoding gene was significantly more air-sensitive than the wild-type strain. Single turnover reactions of the four-electron-reduced FDP (FMNH2-Fe(II)Fe(II)) (FDPred) with O2 monitored on the milliseconds to seconds time scale indicated initial rapid formation of a spectral feature consistent with a cis-μ-1,2-peroxo-diferric intermediate, which triggered two-electron oxidation of FMNH2. Reaction of FDPred with NO showed apparent cooperativity between binding of the first and second NO to the diferrous site. The resulting diferrous dinitrosyl complex triggered two-electron oxidation of the FMNH2. Our cumulative results on this and other FDPs indicate that smooth two-electron FMNH2 oxidation triggered by the FDPred/substrate complex and overall four-electron oxidation of FDPred to FDPox constitutes a mechanistic paradigm for both dioxygen and nitric oxide reductase activities of FDPs. Four-electron reductive O2 scavenging by FDPs could contribute to oxidative stress protection in many other oral bacteria.
Collapse
Affiliation(s)
- Rosanne E. Frederick
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Jonathan D. Caranto
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Cesar A. Masitas
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Linda L. Gebhardt
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
| | - Charles E. MacGowan
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
| | - Ronald J. Limberger
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
| | - Donald M. Kurtz
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
| |
Collapse
|
49
|
Warui DM, Pandelia ME, Rajakovich LJ, Krebs C, Bollinger JM, Booker SJ. Efficient delivery of long-chain fatty aldehydes from the Nostoc punctiforme acyl-acyl carrier protein reductase to its cognate aldehyde-deformylating oxygenase. Biochemistry 2015; 54:1006-15. [PMID: 25496470 DOI: 10.1021/bi500847u] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A two-step pathway consisting of an acyl-acyl carrier protein (ACP) reductase (AAR) and an aldehyde-deformylating oxygenase (ADO) allows various cyanobacteria to convert long-chain fatty acids into hydrocarbons. AAR catalyzes the two-electron, NADPH-dependent reduction of a fatty acid attached to ACP via a thioester linkage to the corresponding fatty aldehyde, while ADO transforms the fatty aldehyde to a Cn-1 hydrocarbon and C1-derived formate. Considering that heptadec(a/e)ne is the most prevalent hydrocarbon produced by cyanobacterial ADOs, the insolubility of its precursor, octadec(a/e)nal, poses a conundrum with respect to its acquisition by ADO. Herein, we report that AAR from the cyanobacterium Nostoc punctiforme is activated almost 20-fold by potassium and other monovalent cations of similar ionic radius, and that AAR and ADO form a tight isolable complex with a Kd of 3 ± 0.3 μM. In addition, we show that when the aldehyde substrate is supplied to ADO by AAR, efficient in vitro turnover is observed in the absence of solubilizing agents. Similarly to studies by Lin et al. with AAR from Synechococcus elongatus [Lin et al. (2013) FEBS J. 280, 4773-4781], we show that catalysis by AAR proceeds via formation of a covalent intermediate involving a cysteine residue that we have identified as Cys294. Moreover, AAR specifically transfers the pro-R hydride of NADPH to the Cys294-thioester intermediate to afford its aldehyde product. Our results suggest that the interaction between AAR and ADO facilitates either direct transfer of the aldehyde product of AAR to ADO or formation of the aldehyde product in a microenvironment allowing for its efficient uptake by ADO.
Collapse
Affiliation(s)
- Douglas M Warui
- Department of Biochemistry and Molecular Biology, and ‡Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | | | | | | | | | | |
Collapse
|
50
|
Nawrocki WJ, Tourasse NJ, Taly A, Rappaport F, Wollman FA. The plastid terminal oxidase: its elusive function points to multiple contributions to plastid physiology. ANNUAL REVIEW OF PLANT BIOLOGY 2015; 66:49-74. [PMID: 25580838 DOI: 10.1146/annurev-arplant-043014-114744] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Plastids have retained from their cyanobacterial ancestor a fragment of the respiratory electron chain comprising an NADPH dehydrogenase and a diiron oxidase, which sustain the so-called chlororespiration pathway. Despite its very low turnover rates compared with photosynthetic electron flow, knocking out the plastid terminal oxidase (PTOX) in plants or microalgae leads to severe phenotypes that encompass developmental and growth defects together with increased photosensitivity. On the basis of a phylogenetic and structural analysis of the enzyme, we discuss its physiological contribution to chloroplast metabolism, with an emphasis on its critical function in setting the redox poise of the chloroplast stroma in darkness. The emerging picture of PTOX is that of an enzyme at the crossroads of a variety of metabolic processes, such as, among others, the regulation of cyclic electron transfer and carotenoid biosynthesis, which have in common their dependence on the redox state of the plastoquinone pool, set largely by the activity of PTOX in darkness.
Collapse
Affiliation(s)
- Wojciech J Nawrocki
- Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, UMR 7141, Centre National de la Recherche Scientifique-Université Pierre et Marie Curie
| | | | | | | | | |
Collapse
|