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Machovina MM, Ellis ES, Carney TJ, Brushett FR, DuBois JL. How a cofactor-free protein environment lowers the barrier to O 2 reactivity. J Biol Chem 2019; 294:3661-3669. [PMID: 30602564 DOI: 10.1074/jbc.ra118.006144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 01/01/2019] [Indexed: 11/06/2022] Open
Abstract
Molecular oxygen (O2)-utilizing enzymes are among the most important in biology. The abundance of O2, its thermodynamic power, and the benign nature of its end products have raised interest in oxidases and oxygenases for biotechnological applications. Although most O2-dependent enzymes have an absolute requirement for an O2-activating cofactor, several classes of oxidases and oxygenases accelerate direct reactions between substrate and O2 using only the protein environment. Nogalamycin monooxygenase (NMO) from Streptomyces nogalater is a cofactor-independent enzyme that catalyzes rate-limiting electron transfer between its substrate and O2 Here, using enzyme-kinetic, cyclic voltammetry, and mutagenesis methods, we demonstrate that NMO initially activates the substrate, lowering its pKa by 1.0 unit (ΔG* = 1.4 kcal mol-1). We found that the one-electron reduction potential, measured for the deprotonated substrate both inside and outside the protein environment, increases by 85 mV inside NMO, corresponding to a ΔΔG 0' of 2.0 kcal mol-1 (0.087 eV) and that the activation barrier, ΔG ‡, is lowered by 4.8 kcal mol-1 (0.21 eV). Applying the Marcus model, we observed that this suggests a sizable decrease of 28 kcal mol-1 (1.4 eV) in the reorganization energy (λ), which constitutes the major portion of the protein environment's effect in lowering the reaction barrier. A similar role for the protein has been proposed in several cofactor-dependent systems and may reflect a broader trend in O2-utilizing proteins. In summary, NMO's protein environment facilitates direct electron transfer, and NMO accelerates rate-limiting electron transfer by strongly lowering the reorganization energy.
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Affiliation(s)
- Melodie M Machovina
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715-3400 and
| | - Emerald S Ellis
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715-3400 and
| | | | - Fikile R Brushett
- Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307
| | - Jennifer L DuBois
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715-3400 and
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Machovina MM, Usselman RJ, DuBois JL. Monooxygenase Substrates Mimic Flavin to Catalyze Cofactorless Oxygenations. J Biol Chem 2016; 291:17816-28. [PMID: 27307041 DOI: 10.1074/jbc.m116.730051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Indexed: 01/16/2023] Open
Abstract
Members of the antibiotic biosynthesis monooxygenase family catalyze O2-dependent oxidations and oxygenations in the absence of any metallo- or organic cofactor. How these enzymes surmount the kinetic barrier to reactions between singlet substrates and triplet O2 is unclear, but the reactions have been proposed to occur via a flavin-like mechanism, where the substrate acts in lieu of a flavin cofactor. To test this model, we monitored the uncatalyzed and enzymatic reactions of dithranol, a substrate for the nogalamycin monooxygenase (NMO) from Streptomyces nogalater As with flavin, dithranol oxidation was faster at a higher pH, although the reaction did not appear to be base-catalyzed. Rather, conserved asparagines contributed to suppression of the substrate pKa The same residues were critical for enzymatic catalysis that, consistent with the flavoenzyme model, occurred via an O2-dependent slow step. Evidence for a superoxide/substrate radical pair intermediate came from detection of enzyme-bound superoxide during turnover. Small molecule and enzymatic superoxide traps suppressed formation of the oxygenation product under uncatalyzed conditions, whereas only the small molecule trap had an effect in the presence of NMO. This suggested that NMO both accelerated the formation and directed the recombination of a superoxide/dithranyl radical pair. These catalytic strategies are in some ways flavin-like and stand in contrast to the mechanisms of urate oxidase and (1H)-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase, both cofactor-independent enzymes that surmount the barriers to direct substrate/O2 reactivity via markedly different means.
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Affiliation(s)
- Melodie M Machovina
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715-3400
| | - Robert J Usselman
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715-3400
| | - Jennifer L DuBois
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715-3400
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Aoyama H, Saitoh S, Kuroiwa T, Nakamura S. Comparative analysis of zygospore transcripts during early germination in Chlamydomonas reinhardtii. JOURNAL OF PLANT PHYSIOLOGY 2014; 171:1685-1692. [PMID: 25209695 DOI: 10.1016/j.jplph.2014.07.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Revised: 07/31/2014] [Accepted: 07/31/2014] [Indexed: 06/03/2023]
Abstract
The unicellular green alga Chlamydomonas reinhardtii has a haplontic life cycle, and forms diploid zygotes for reproduction. The zygospore, a sporulating zygote, begins germination in response to light signals, generating haploid progenies and inducing several cell-biological events; e.g., DNA synthesis and meiotic division, successively. Their regulatory mechanisms remain largely unknown, so we focused on the early stages of germination and analyzed the dynamics of gene expression associated with the germination process. The gene expression levels of zygospores at 1 and 6h after light exposure were analyzed by a next-generation sequencing platform, the 454 GS Junior. At 6h, the photosynthesis pathway, including its antenna proteins and two methionine metabolism-related genes (methionine synthase and sulfite reductase), were up-regulated compared to 1h after light exposure. Meanwhile, three uncharacterized genes that contained an antibiotic biosynthesis monooxygenase domain and an HSP20/alpha crystallin family protein were specifically expressed at 1h after light exposure. These gene expressions were also verified by quantitative real-time PCR analysis. These results suggest that the photosynthesis and methionine synthesis pathways, both of which occur in the chloroplast, are activated in zygospores at around 6h after light exposure, and that some polyketides and/or a small heat shock protein may be related to the initiation of zygospore germination.
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Affiliation(s)
- Hiroaki Aoyama
- Center of Molecular Biosciences, Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa 903-0213; Laboratory of Cell and Functional Biology, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa 903-0213.
| | - Seikoh Saitoh
- Center of Molecular Biosciences, Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa 903-0213
| | - Tsuneyoshi Kuroiwa
- Initiative Research Unit, College of Science, Rikkyo University, Nishi-Ikebukuro, Tokyo, 171-8501
| | - Soichi Nakamura
- Laboratory of Cell and Functional Biology, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa 903-0213
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Sciara G, Kendrew SG, Miele AE, Marsh NG, Federici L, Malatesta F, Schimperna G, Savino C, Vallone B. The structure of ActVA-Orf6, a novel type of monooxygenase involved in actinorhodin biosynthesis. EMBO J 2003; 22:205-15. [PMID: 12514126 PMCID: PMC140106 DOI: 10.1093/emboj/cdg031] [Citation(s) in RCA: 135] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
ActVA-Orf6 monooxygenase from Streptomyces coelicolor that catalyses the oxidation of an aromatic intermediate of the actinorhodin biosynthetic pathway is a member of a class of small monooxygenases that carry out oxygenation without the assistance of any of the prosthetic groups, metal ions or cofactors normally associated with activation of molecular oxygen. The overall structure is a ferredoxin-like fold with a novel dimeric assembly, indicating that the widely represented ferredoxin fold may sustain yet another functionality. The resolution (1.3 A) of the enzyme structure and its complex with substrate and product analogues allows us to visualize the mechanism of binding and activation of the substrate for attack by molecular oxygen, and utilization of two gates for the reaction components including a proton gate and an O(2)/H(2)O gate with a putative protein channel. This is the first crystal structure of an enzyme involved in the tailoring of a type II aromatic polyketide and illustrates some of the enzyme-substrate recognition features that may apply to a range of other enzymes involved in modifying a polyketide core structure.
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Affiliation(s)
- Giuliano Sciara
- Dipartimento di Scienze Biochimiche and CNR, Centro di Studi sulla Biologia Molecolare, c/o Dipartimento di Scienze Biochimiche, Università di Roma ‘La Sapienza’, Piazzale A.Moro, 5, 00185 Roma, Dipartimento di Biologia di Base ed Applicata, Università di L’Aquila, 67100 L’Aquila, Istituto G.Donegani, 28100 Novara, Italy, Biotica Technology Ltd, 181A Huntingdon Road, Cambridge CB3 0DJ, UK and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA Corresponding author e-mail:
| | - Steven G. Kendrew
- Dipartimento di Scienze Biochimiche and CNR, Centro di Studi sulla Biologia Molecolare, c/o Dipartimento di Scienze Biochimiche, Università di Roma ‘La Sapienza’, Piazzale A.Moro, 5, 00185 Roma, Dipartimento di Biologia di Base ed Applicata, Università di L’Aquila, 67100 L’Aquila, Istituto G.Donegani, 28100 Novara, Italy, Biotica Technology Ltd, 181A Huntingdon Road, Cambridge CB3 0DJ, UK and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA Corresponding author e-mail:
| | - Adriana E. Miele
- Dipartimento di Scienze Biochimiche and CNR, Centro di Studi sulla Biologia Molecolare, c/o Dipartimento di Scienze Biochimiche, Università di Roma ‘La Sapienza’, Piazzale A.Moro, 5, 00185 Roma, Dipartimento di Biologia di Base ed Applicata, Università di L’Aquila, 67100 L’Aquila, Istituto G.Donegani, 28100 Novara, Italy, Biotica Technology Ltd, 181A Huntingdon Road, Cambridge CB3 0DJ, UK and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA Corresponding author e-mail:
| | - Neil G. Marsh
- Dipartimento di Scienze Biochimiche and CNR, Centro di Studi sulla Biologia Molecolare, c/o Dipartimento di Scienze Biochimiche, Università di Roma ‘La Sapienza’, Piazzale A.Moro, 5, 00185 Roma, Dipartimento di Biologia di Base ed Applicata, Università di L’Aquila, 67100 L’Aquila, Istituto G.Donegani, 28100 Novara, Italy, Biotica Technology Ltd, 181A Huntingdon Road, Cambridge CB3 0DJ, UK and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA Corresponding author e-mail:
| | - Luca Federici
- Dipartimento di Scienze Biochimiche and CNR, Centro di Studi sulla Biologia Molecolare, c/o Dipartimento di Scienze Biochimiche, Università di Roma ‘La Sapienza’, Piazzale A.Moro, 5, 00185 Roma, Dipartimento di Biologia di Base ed Applicata, Università di L’Aquila, 67100 L’Aquila, Istituto G.Donegani, 28100 Novara, Italy, Biotica Technology Ltd, 181A Huntingdon Road, Cambridge CB3 0DJ, UK and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA Corresponding author e-mail:
| | - Francesco Malatesta
- Dipartimento di Scienze Biochimiche and CNR, Centro di Studi sulla Biologia Molecolare, c/o Dipartimento di Scienze Biochimiche, Università di Roma ‘La Sapienza’, Piazzale A.Moro, 5, 00185 Roma, Dipartimento di Biologia di Base ed Applicata, Università di L’Aquila, 67100 L’Aquila, Istituto G.Donegani, 28100 Novara, Italy, Biotica Technology Ltd, 181A Huntingdon Road, Cambridge CB3 0DJ, UK and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA Corresponding author e-mail:
| | - Giuliana Schimperna
- Dipartimento di Scienze Biochimiche and CNR, Centro di Studi sulla Biologia Molecolare, c/o Dipartimento di Scienze Biochimiche, Università di Roma ‘La Sapienza’, Piazzale A.Moro, 5, 00185 Roma, Dipartimento di Biologia di Base ed Applicata, Università di L’Aquila, 67100 L’Aquila, Istituto G.Donegani, 28100 Novara, Italy, Biotica Technology Ltd, 181A Huntingdon Road, Cambridge CB3 0DJ, UK and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA Corresponding author e-mail:
| | - Carmelinda Savino
- Dipartimento di Scienze Biochimiche and CNR, Centro di Studi sulla Biologia Molecolare, c/o Dipartimento di Scienze Biochimiche, Università di Roma ‘La Sapienza’, Piazzale A.Moro, 5, 00185 Roma, Dipartimento di Biologia di Base ed Applicata, Università di L’Aquila, 67100 L’Aquila, Istituto G.Donegani, 28100 Novara, Italy, Biotica Technology Ltd, 181A Huntingdon Road, Cambridge CB3 0DJ, UK and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA Corresponding author e-mail:
| | - Beatrice Vallone
- Dipartimento di Scienze Biochimiche and CNR, Centro di Studi sulla Biologia Molecolare, c/o Dipartimento di Scienze Biochimiche, Università di Roma ‘La Sapienza’, Piazzale A.Moro, 5, 00185 Roma, Dipartimento di Biologia di Base ed Applicata, Università di L’Aquila, 67100 L’Aquila, Istituto G.Donegani, 28100 Novara, Italy, Biotica Technology Ltd, 181A Huntingdon Road, Cambridge CB3 0DJ, UK and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA Corresponding author e-mail:
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