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Nishiyama A, Tanaka Y, Mori S, Furuta H, Shimizu S. Oxidative nitration reaction of antiaromatic 5,15-dioxaporphyrin. J PORPHYR PHTHALOCYA 2020. [DOI: 10.1142/s108842461950113x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Upon oxidation of 20[Formula: see text]-electron antiaromatic 5,15-dioxaporphyrin (DOP) using nitrosonium ions as oxidants, a tetrakis-[Formula: see text]-nitrated compound was formed instead of the expected 18[Formula: see text]-electron aromatic dication species via an oxidative nitration reaction mechanism. Compared with the original DOP, this tetranitro DOP product exhibited a blue shift of absorption and downfield shifts of the [Formula: see text]-pyrrolic proton signals. The unique antiaromatic electronic structure of the tetranitro DOP was disclosed experimentally by electrochemistry and theoretically by DFT and NICS calculations.
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Affiliation(s)
- Akihide Nishiyama
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Yuki Tanaka
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Shigeki Mori
- Advanced Research Support Center (ADRES), Ehime University, Matsuyama 790-8577, Japan
| | - Hiroyuki Furuta
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
- Center for Molecular Systems (CMS), Kyushu University, Fukuoka 819-0395, Japan
| | - Soji Shimizu
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
- Center for Molecular Systems (CMS), Kyushu University, Fukuoka 819-0395, Japan
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Nishiyama A, Fukuda M, Mori S, Furukawa K, Fliegl H, Furuta H, Shimizu S. Rational Synthesis of Antiaromatic 5,15-Dioxaporphyrin and Oxidation into β,β-Linked Dimers. Angew Chem Int Ed Engl 2018; 57:9728-9733. [PMID: 29901249 DOI: 10.1002/anie.201804648] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 05/31/2018] [Indexed: 12/19/2022]
Abstract
5,15-Dioxaporphyrin was synthesized for the first time by a nucleophilic aromatic substitution reaction of a nickel bis(α,α'-dibromodipyrrin) complex with benzaldoxime, followed by an intramolecular annulation of the α-hydroxy-substituted intermediate. This unprecedented molecule is a 20π-electron antiaromatic system, in terms of Hückel's rule of aromaticity, because lone pair electrons of oxygen atoms are incorporated into the 18π-electron conjugated system of the porphyrin. A theoretical analysis based on the gauge-including magnetically induced current method confirmed its antiaromaticity and a dominant inner ring pathway for the ring current. The unique reactivity of 5,15-dioxaporphyrin forming a β,β-linked dimer upon oxidation was also revealed.
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Affiliation(s)
- Akihide Nishiyama
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka, 819-0395, Japan
| | - Masaya Fukuda
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka, 819-0395, Japan
| | - Shigeki Mori
- Advanced Research Support Center (ADRES), Ehime University, Matsuyama, 790-8577, Japan
| | - Ko Furukawa
- Center for Instrumental Analysis, Institute for Research Promotion, Niigata University, Niigata, 950-2181, Japan
| | - Heike Fliegl
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, 0315, Oslo, Norway
| | - Hiroyuki Furuta
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka, 819-0395, Japan.,Center for Molecular Systems (CMS), Kyushu University, Fukuoka, 819-0395, Japan
| | - Soji Shimizu
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka, 819-0395, Japan.,Center for Molecular Systems (CMS), Kyushu University, Fukuoka, 819-0395, Japan
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Nishiyama A, Fukuda M, Mori S, Furukawa K, Fliegl H, Furuta H, Shimizu S. Rational Synthesis of Antiaromatic 5,15-Dioxaporphyrin and Oxidation into β,β-Linked Dimers. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804648] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Akihide Nishiyama
- Department of Chemistry and Biochemistry; Graduate School of Engineering; Kyushu University; Fukuoka 819-0395 Japan
| | - Masaya Fukuda
- Department of Chemistry and Biochemistry; Graduate School of Engineering; Kyushu University; Fukuoka 819-0395 Japan
| | - Shigeki Mori
- Advanced Research Support Center (ADRES); Ehime University; Matsuyama 790-8577 Japan
| | - Ko Furukawa
- Center for Instrumental Analysis; Institute for Research Promotion; Niigata University; Niigata 950-2181 Japan
| | - Heike Fliegl
- Hylleraas Centre for Quantum Molecular Sciences; Department of Chemistry; University of Oslo; P.O. Box 1033 Blindern 0315 Oslo Norway
| | - Hiroyuki Furuta
- Department of Chemistry and Biochemistry; Graduate School of Engineering; Kyushu University; Fukuoka 819-0395 Japan
- Center for Molecular Systems (CMS); Kyushu University; Fukuoka 819-0395 Japan
| | - Soji Shimizu
- Department of Chemistry and Biochemistry; Graduate School of Engineering; Kyushu University; Fukuoka 819-0395 Japan
- Center for Molecular Systems (CMS); Kyushu University; Fukuoka 819-0395 Japan
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Soldano A, Klinke S, Otero LH, Rivera M, Catalano-Dupuy DL, Ceccarelli EA. Structural and mutational analyses of the Leptospira interrogans virulence-related heme oxygenase provide insights into its catalytic mechanism. PLoS One 2017; 12:e0182535. [PMID: 28771589 PMCID: PMC5542595 DOI: 10.1371/journal.pone.0182535] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/19/2017] [Indexed: 11/25/2022] Open
Abstract
Heme oxygenase from Leptospira interrogans is an important virulence factor. During catalysis, redox equivalents are provided to this enzyme by the plastidic-type ferredoxin-NADP+ reductase also found in L. interrogans. This process may have evolved to aid this bacterial pathogen to obtain heme-iron from their host and enable successful colonization. Herein we report the crystal structure of the heme oxygenase-heme complex at 1.73 Å resolution. The structure reveals several distinctive features related to its function. A hydrogen bonded network of structural water molecules that extends from the catalytic site to the protein surface was cleared observed. A depression on the surface appears to be the H+ network entrance from the aqueous environment to the catalytic site for O2 activation, a key step in the heme oxygenase reaction. We have performed a mutational analysis of the F157, located at the above-mentioned depression. The mutant enzymes were unable to carry out the complete degradation of heme to biliverdin since the reaction was arrested at the verdoheme stage. We also observed that the stability of the oxyferrous complex, the efficiency of heme hydroxylation and the subsequent conversion to verdoheme was adversely affected. These findings underscore a long-range communication between the outer fringes of the hydrogen-bonded network of structural waters and the heme active site during catalysis. Finally, by analyzing the crystal structures of ferredoxin-NADP+ reductase and heme oxygenase, we propose a model for the productive association of these proteins.
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Affiliation(s)
- Anabel Soldano
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Lisandro H. Otero
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Mario Rivera
- Department of Chemistry and Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, Kansas, United States of America
| | - Daniela L. Catalano-Dupuy
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Eduardo A. Ceccarelli
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- * E-mail:
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Affiliation(s)
- Yoshihiro Matano
- Department
of Chemistry,
Faculty of Science, Niigata University, Nishi-ku, Niigata 950-2181, Japan
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Ukpabi G, Takayama SIJ, Mauk AG, Murphy MEP. Inactivation of the heme degrading enzyme IsdI by an active site substitution that diminishes heme ruffling. J Biol Chem 2012; 287:34179-88. [PMID: 22891243 PMCID: PMC3464526 DOI: 10.1074/jbc.m112.393249] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
IsdG and IsdI are paralogous heme degrading enzymes from the bacterium Staphylococcus aureus. Heme bound by these enzymes is extensively ruffled such that the meso-carbons at the sites of oxidation are distorted toward bound oxygen. In contrast, the canonical heme oxygenase family degrades heme that is bound with minimal distortion. Trp-66 is a conserved heme pocket residue in IsdI implicated in heme ruffling. IsdI variants with Trp-66 replaced with residues having less bulky aromatic and alkyl side chains were characterized with respect to catalytic activity, heme ruffling, and electrochemical properties. The heme degradation activity of the W66Y and W66F variants was approximately half that of the wild-type enzyme, whereas the W66L and W66A variants were inactive. A crystal structure and NMR spectroscopic analysis of the W66Y variant reveals that heme binds to this enzyme with less heme ruffling than observed for wild-type IsdI. The reduction potential of this variant (-96 ± 7 mV versus standard hydrogen electrode) is similar to that of wild-type IsdI (-89 ± 7 mV), so we attribute the diminished activity of this variant to the diminished heme ruffling observed for heme bound to this enzyme and conclude that Trp-66 is required for optimal catalytic activity.
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Affiliation(s)
- Georgia Ukpabi
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3 Canada
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Crystallographic studies of heme oxygenase complexed with an unstable reaction intermediate, verdoheme. J Inorg Biochem 2012; 113:102-9. [PMID: 22673156 DOI: 10.1016/j.jinorgbio.2012.04.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 04/05/2012] [Accepted: 04/11/2012] [Indexed: 11/20/2022]
Abstract
This article discusses the accuracy of X-ray structural studies of heme oxygenase (HO) in complex with an unstable intermediate, verdoheme. Heme degradation by HO proceeds through three successive steps of O(2) activation. The mechanism of the third step, the ring opening of verdoheme, has been the least understood. Recent structural studies of the verdoheme-HO complex provide detailed information concerning this mechanism. Due to X-ray-induced photoreduction and the instability of verdoheme, it has been difficult to obtain an accurate structure for the ferrous verdoheme-HO complex. Therefore, accurate structural studies, including analysis of the electronic state of the verdoheme-HO complex, are needed to elucidate the proper reaction mechanism.
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Electronic properties of the highly ruffled heme bound to the heme degrading enzyme IsdI. Proc Natl Acad Sci U S A 2011; 108:13071-6. [PMID: 21788475 DOI: 10.1073/pnas.1101459108] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
IsdI, a heme-degrading protein from Staphylococcus aureus, binds heme in a manner that distorts the normally planar heme prosthetic group to an extent greater than that observed so far for any other heme-binding protein. To understand better the relationship between this distinct structural characteristic and the functional properties of IsdI, spectroscopic, electrochemical, and crystallographic results are reported that provide evidence that this heme ruffling is essential to the catalytic activity of the protein and eliminates the need for the water cluster in the distal heme pocket that is essential for the activity of classical heme oxygenases. The lack of heme orientational disorder in (1)H-NMR spectra of the protein argues that the catalytic formation of β- and δ-biliverdin in nearly equal yield results from the ability of the protein to attack opposite sides of the heme ring rather than from binding of the heme substrate in two alternative orientations.
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Sato H, Higashimoto Y, Sakamoto H, Sugishima M, Shimokawa C, Harada J, Palmer G, Noguchi M. Reduction of oxaporphyrin ring of CO-bound α-verdoheme complexed with heme oxygenase-1 by NADPH-cytochrome P450 reductase. J Inorg Biochem 2010; 105:289-96. [PMID: 21194630 DOI: 10.1016/j.jinorgbio.2010.11.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 11/05/2010] [Accepted: 11/10/2010] [Indexed: 11/18/2022]
Abstract
Heme oxygenase (HO) catalyses the degradation of heme to biliverdin, carbon monoxide (CO) and ferrous iron via three successive monooxygenase reactions, using electrons provided by NADPH-cytochrome P450 reductase (CPR) and oxygen molecules. For cleavage of the oxaporphyrin ring of ferrous α-verdoheme, an intermediate in the HO reaction, involvement of a verdoheme π-neutral radical has been proposed. To explore this hypothetical mechanism, we performed electrochemical reduction of ferrous α-verdoheme-rat HO-1 complex under anaerobic conditions. Upon binding of CO, an O(2) surrogate, the midpoint potential for one-electron reduction of the oxaporphyrin ring of ferrous α-verdoheme was increased from -0.465 to -0.392 V vs the normal hydrogen electrode. Because the latter potential is close to that of the semiquinone/reduced redox couple of FAD in CPR, the one-electron reduction of the oxaporphyrin ring of CO-bound verdoheme complexed with HO-1 is considered to be a thermodynamically likely process. Indeed the one-electron reduced species, [Fe(II)(verdoheme•)], was observed spectroscopically in the presence of CO in both NADPH/wild-type and FMN-depleted CPR systems under anaerobic conditions. Under physiological conditions, therefore, it is possible that O(2) initially binds to the ferrous iron of α-verdoheme in its complex with HO-1 and an electron is subsequently transferred from CPR, probably via FAD, to the oxaporphyrin ring.
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Affiliation(s)
- Hideaki Sato
- Department of Medical Biochemistry, Kurume University School of Medicine, 67 Asahi-machi, Kurume 830-0011, Japan.
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Crystal structure of rat haem oxygenase-1 in complex with ferrous verdohaem: presence of a hydrogen-bond network on the distal side. Biochem J 2009; 419:339-45. [PMID: 19154182 DOI: 10.1042/bj20082279] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
HO (haem oxygenase) catalyses the degradation of haem to biliverdin, CO and ferrous iron via three successive oxygenation reactions, i.e. haem to alpha-hydroxyhaem, alpha-hydroxyhaem to alpha-verdohaem and alpha-verdohaem to ferric biliverdin-iron chelate. In the present study, we determined the crystal structure of ferrous alpha-verdohaem-rat HO-1 complex at 2.2 A (1 A=0.1 nm) resolution. The overall structure of the verdohaem complex was similar to that of the haem complex. Water or OH- was co-ordinated to the verdohaem iron as a distal ligand. A hydrogen-bond network consisting of water molecules and several amino acid residues was observed at the distal side of verdohaem. Such a hydrogen-bond network was conserved in the structures of rat HO-1 complexes with haem and with the ferric biliverdin-iron chelate. This hydrogen-bond network may act as a proton donor to form an activated oxygen intermediate, probably a ferric hydroperoxide species, in the degradation of alpha-verdohaem to ferric biliverdin-iron chelate similar to that seen in the first oxygenation step.
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