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Gong L, Chen J, Hu Y, He K, Bylaska EJ, Tratnyek PG, He F. Degradation of Chloroform by Zerovalent Iron: Effects of Mechanochemical Sulfidation and Nitridation on the Kinetics and Mechanism. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37339398 DOI: 10.1021/acs.est.3c02039] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Chloroform (CF) is a widely used chemical reagent and disinfectant and a probable human carcinogen. The extensive literature on halocarbon reduction with zerovalent iron (ZVI) shows that transformation of CF is slow, even with nano, bimetallic, sulfidated, and other modified forms of ZVI. In this study, an alternative method of ZVI modification─involving simultaneous sulfidation and nitridation through mechanochemical ball milling─was developed and shown to give improved degradation of CF (i.e., higher degradation rate and inhibited H2 evolution reaction). The composite material (denoted as S-N(C)-ZVI) gave synergistic effects of nitridation and sulfidation on CF degradation. A complete chemical reaction network (CRN) analysis of CF degradation suggests that O-nucleophile-mediated transformation pathways may be the main route for the formation of the terminal nonchlorinated products (formate, CO, and glycolic polymers) that have been used to explain the undetected products needed for mass balance. Material characterizations of the ZVI recovered after batch experiments showed that sulfidation and nitridation promoted the formation of Fe3O4 on the S-N(C)-ZVI particles, and the effect of aging on CF degradation rates was minor for S-N(C)-ZVI. The synergistic benefits of sulfidation and nitridation on CF degradation were also observed in experiments performed with groundwater.
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Affiliation(s)
- Li Gong
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jingting Chen
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yao Hu
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Kai He
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Eric J Bylaska
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99354, United States
| | - Paul G Tratnyek
- OHSU-PSU School of Public Health, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Feng He
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
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2
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Singh N, Bhatla SC. Heme oxygenase-nitric oxide crosstalk-mediated iron homeostasis in plants under oxidative stress. Free Radic Biol Med 2022; 182:192-205. [PMID: 35247570 DOI: 10.1016/j.freeradbiomed.2022.02.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 12/22/2022]
Abstract
Plant growth under abiotic stress conditions significantly enhances intracellular generation of reactive oxygen species (ROS). Oxidative status of plant cells is directly affected by the modulation of iron homeostasis. Among mammals and plants, heme oxygenase-1 (HO-1) is a well-known antioxidant enzyme. It catalyzes oxygenation of heme, thereby producing Fe2+, CO and biliverdin as byproducts. The antioxidant potential of HO-1 is primarily due to its catalytic reaction byproducts. Biliverdin and bilirubin possess conjugated π-electrons which escalate the ability of these biomolecules to scavenge free radicals. CO also enhances the ROS scavenging ability of plants cells by upregulating catalase and peroxidase activity. Enhanced expression of HO-1 in plants under oxidative stress accompanies sequestration of iron in specialized iron storage proteins localized in plastids and mitochondria, namely ferritin for Fe3+ storage and frataxin for storage of Fe-S clusters, respectively. Nitric oxide (NO) crosstalks with HO-1 at multiple levels, more so in plants under oxidative stress, in order to maintain intracellular iron status. Formation of dinitrosyl-iron complexes (DNICs) significantly prevents Fenton reaction during oxidative stress. DNICs also release NO upon dissociation in target cells over long distance in plants. They also function as antioxidants against superoxide anions and lipidic free radicals. A number of NO-modulated transcription factors also facilitate iron homeostasis in plant cells. Plants facing oxidative stress exhibit modulation of lateral root formation by HO-1 through NO and auxin-dependent pathways. The present review provides an in-depth analysis of the structure-function relationship of HO-1 in plants and mammals, correlating them with their adaptive mechanisms of survival under stress.
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Affiliation(s)
- Neha Singh
- Department of Botany, Gargi College, University of Delhi, India.
| | - Satish C Bhatla
- Laboratory of Plant Physiology and Biochemistry, Department of Botany, University of Delhi, Delhi, 110007, India.
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Gong L, Qiu X, Cheng D, Hu Y, Zhang Z, Yuan Q, Yang D, Liu C, Liang L, He F. Coincorporation of N and S into Zero-Valent Iron to Enhance TCE Dechlorination: Kinetics, Electron Efficiency, and Dechlorination Capacity. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:16088-16098. [PMID: 34787396 DOI: 10.1021/acs.est.1c03784] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Sulfidated zero-valent iron (S-ZVI) enhances the degradation of chlorinated hydrocarbon (CHC) in contaminated groundwater. Despite numerous studies of S-ZVI, a versatile strategy to improve its dechlorination kinetics, electron efficiency (εe), and dechlorination capacity is still needed. Here, we used heteroatom incorporation of N(C) and S by ball-milling of microscale ZVI with melamine and sulfur via nitridation and sulfidation to synthesize S-N(C)-mZVIbm particles that contain reactive Fe-NX(C) and FeS species. Sulfidation and nitridation synergistically increased the trichloroethene (TCE) dechlorination rate, with reaction constants kSA of 2.98 × 10-2 L·h-1·m-2 by S-N(C)-mZVIbm, compared to 1.77 × 10-3 and 8.15 × 10-5 L·h-1·m-2 by S-mZVIbm and N(C)-mZVIbm, respectively. Data show that sulfidation suppressed the reductive dissociation of N(C) from S-N(C)-mZVIbm, which stabilized the reactive Fe-NX(C) and reserved electrons for TCE dechlorination. In addition to lowering H2 production, S-N(C)-mZVIbm dechlorinated TCE to less reduced products (e.g., acetylene), contributing to the material's higher εe and dechlorination capacity. This synergistic effect on TCE degradation can be extended to other recalcitrant CHCs (e.g., chloroform) in both deionized and groundwater. This multiheteroatom incorporation approach to optimize ZVI for groundwater remediation provides a basis for further advances in reactive material synthesis.
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Affiliation(s)
- Li Gong
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xiaojiang Qiu
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Dong Cheng
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yao Hu
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Zaizhi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Qunsen Yuan
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Dezhi Yang
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Chengshuai Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Liyuan Liang
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Feng He
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
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4
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Gong L, Qiu X, Tratnyek PG, Liu C, He F. FeN X(C)-Coated Microscale Zero-Valent Iron for Fast and Stable Trichloroethylene Dechlorination in both Acidic and Basic pH Conditions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:5393-5402. [PMID: 33729752 DOI: 10.1021/acs.est.0c08176] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
FeNX in Fe single-atom catalysts can be the active site for adsorption and activation of reactants. In addition, FeNX species have been shown to facilitate electron transfer between Fe and the carbon supports used in newly developed metal-air batteries. We hypothesized that the combination of FeNX species with granular zero-valent iron (ZVI) might result in catalyzed reductive decontamination of groundwater contaminants such as trichloroethylene (TCE). Here, such materials synthesized by ball milling microscale ZVI with melamine and the resulting N species were mainly in the form of pyridinic, pyrrolic, and graphitic N. This new material (abbreviated as N-C-mZVIbm) dechlorinated TCE at higher rates than bare mZVIbm (about 3.5-fold) due to facilitated electron transfer through (or around) the surface layer of iron oxides by the newly formed Fe-NX(C). N-C-mZVIbm gave higher kTCE (0.4-1.14 day-1) than mZVIbm (0-0.4 day-1) over a wide range of pH values (4-11). Unlike most ZVI systems, kTCE for N-C-mZVIbm increased with increasing pH values. This is because the oxide layer that passivates Fe0 at a high pH is disrupted by Fe-NX(C) formed on N-C-mZVIbm, thereby allowing TCE dechlorination and HER under basic conditions. Serial respike experiments gave no evidence of decreased performance of N-C-mZVIbm, showing that the advantages of this material might remain under field applications.
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Affiliation(s)
- Li Gong
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xiaojiang Qiu
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Paul G Tratnyek
- OHSU-PSU School of Public Health, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Chengshuai Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Feng He
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
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Brewitz HH, Hagelueken G, Imhof D. Structural and functional diversity of transient heme binding to bacterial proteins. Biochim Biophys Acta Gen Subj 2017; 1861:683-697. [DOI: 10.1016/j.bbagen.2016.12.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 12/15/2016] [Accepted: 12/20/2016] [Indexed: 11/27/2022]
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6
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Sigala PA, Morante K, Tsumoto K, Caaveiro JMM, Goldberg DE. In-Cell Enzymology To Probe His-Heme Ligation in Heme Oxygenase Catalysis. Biochemistry 2016; 55:4836-49. [PMID: 27490825 DOI: 10.1021/acs.biochem.6b00562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Heme oxygenase (HO) is a ubiquitous enzyme with key roles in inflammation, cell signaling, heme disposal, and iron acquisition. HO catalyzes the oxidative conversion of heme to biliverdin (BV) using a conserved histidine to coordinate the iron atom of bound heme. This His-heme interaction has been regarded as being essential for enzyme activity, because His-to-Ala mutants fail to convert heme to biliverdin in vitro. We probed a panel of proximal His mutants of cyanobacterial, human, and plant HO enzymes using a live-cell activity assay based on heterologous co-expression in Escherichia coli of each HO mutant and a fluorescent biliverdin biosensor. In contrast to in vitro studies with purified proteins, we observed that multiple HO mutants retained significant activity within the intracellular environment of bacteria. X-ray crystallographic structures of human HO1 H25R with bound heme and additional functional studies suggest that HO mutant activity inside these cells does not involve heme ligation by a proximal amino acid. Our study reveals unexpected plasticity in the active site binding interactions with heme that can support HO activity within cells, suggests important contributions by the surrounding active site environment to HO catalysis, and can guide efforts to understand the evolution and divergence of HO function.
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Affiliation(s)
- Paul A Sigala
- Departments of Medicine and Molecular Microbiology, Washington University School of Medicine , St. Louis, Missouri 63110, United States
| | - Koldo Morante
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo , Bunkyo-ku, Tokyo 113-8654, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo , Bunkyo-ku, Tokyo 113-8654, Japan.,Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo , Minato-ku, Tokyo 108-8639, Japan
| | - Jose M M Caaveiro
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo , Bunkyo-ku, Tokyo 113-8654, Japan
| | - Daniel E Goldberg
- Departments of Medicine and Molecular Microbiology, Washington University School of Medicine , St. Louis, Missouri 63110, United States
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7
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Sheldon JR, Heinrichs DE. Recent developments in understanding the iron acquisition strategies of gram positive pathogens. FEMS Microbiol Rev 2015; 39:592-630. [DOI: 10.1093/femsre/fuv009] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2015] [Indexed: 12/26/2022] Open
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8
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Identification of essential histidine residues involved in heme binding and Hemozoin formation in heme detoxification protein from Plasmodium falciparum. Sci Rep 2014; 4:6137. [PMID: 25138161 PMCID: PMC4138515 DOI: 10.1038/srep06137] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 07/31/2014] [Indexed: 12/22/2022] Open
Abstract
Malaria parasites digest hemoglobin within a food vacuole to supply amino acids, releasing the toxic product heme. During the detoxification, toxic free heme is converted into an insoluble crystalline form called hemozoin (Hz). Heme detoxification protein (HDP) in Plasmodium falciparum is one of the most potent of the hemozoin-producing enzymes. However, the reaction mechanisms of HDP are poorly understood. We identified the active site residues in HDP using a combination of Hz formation assay and spectroscopic characterization of mutant proteins. Replacement of the critical histidine residues His122, His172, His175, and His197 resulted in a reduction in the Hz formation activity to approximately 50% of the wild-type protein. Spectroscopic characterization of histidine-substituted mutants revealed that His122 binds heme and that His172 and His175 form a part of another heme-binding site. Our results show that the histidine residues could be present in the individual active sites and could be ligated to each heme. The interaction between heme and the histidine residues would serve as a molecular tether, allowing the proper positioning of two hemes to enable heme dimer formation. The heme dimer would act as a seed for the crystal growth of Hz in P. falciparum.
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9
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SHEN XH, HU YL, WANG DC. A Novel Substitution of The Heme-binding Residue Histidine-245 by Histidine-249 in Heme Oxygenase HugZ*. PROG BIOCHEM BIOPHYS 2012. [DOI: 10.3724/sp.j.1206.2011.00513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Hu Y, Jiang F, Guo Y, Shen X, Zhang Y, Zhang R, Guo G, Mao X, Zou Q, Wang DC. Crystal structure of HugZ, a novel heme oxygenase from Helicobacter pylori. J Biol Chem 2010; 286:1537-44. [PMID: 21030596 DOI: 10.1074/jbc.m110.172007] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The crystal structure of a heme oxygenase (HO) HugZ from Helicobacter pylori complexed with heme has been solved and refined at 1.8 Å resolution. HugZ is part of the iron acquisition mechanism of H. pylori, a major pathogen of human gastroenteric diseases. It is required for the adaptive colonization of H. pylori in hosts. Here, we report that HugZ is distinct from all other characterized HOs. It exists as a dimer in solution and in crystals, and the dimer adopts a split-barrel fold that is often found in FMN-binding proteins but has not been observed in hemoproteins. The heme is located at the intermonomer interface and is bound by both monomers. The heme iron is coordinated by the side chain of His(245) and an azide molecule when it is present in crystallization conditions. Experiments show that Arg(166), which is involved in azide binding, is essential for HugZ enzymatic activity, whereas His(245), surprisingly, is not, implying that HugZ has an enzymatic mechanism distinct from other HOs. The placement of the azide corroborates the observed γ-meso specificity for the heme degradation reaction, in contrast to most known HOs that have α-meso specificity. We demonstrate through sequence and structural comparisons that HugZ belongs to a new heme-binding protein family with a split-barrel fold. Members of this family are widespread in pathogenic bacteria and may play important roles in the iron acquisition of these bacteria.
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Affiliation(s)
- Yonglin Hu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
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Du Z, Unno M, Matsui T, Ikeda-Saito M, La Mar GN. Solution 1H NMR characterization of substrate-free C. diphtheriae heme oxygenase: pertinence for determining magnetic axes in paramagnetic substrate complexes. J Inorg Biochem 2010; 104:1063-70. [PMID: 20655112 DOI: 10.1016/j.jinorgbio.2010.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Revised: 06/03/2010] [Accepted: 06/16/2010] [Indexed: 11/28/2022]
Abstract
Proton 2D NMR was used to confirm in solution a highly conserved portion of the molecular structure upon substrate loss for the heme oxygenase from the pathogenic bacterium Corynebacterium diphtheriae, HmuO. The chemical shifts for the conserved portion of the structure are assessed as references for the dipolar shifts needed to determine the orientation of the paramagnetic susceptibility tensor, chi, in paramagnetic substrate complexes of HmuO. It is shown that the chemical shifts for the structurally conserved portion of substrate-free HmuO serve as excellent references for residues with only small to moderate sized dipolar shifts in the cyanide-inhibited substrate complex of HmuO, yielding an orientation of chi that is essentially the same as conventionally obtained from large dipolar shifts based on empirical estimates of the diamagnetic reference. The implications of these diamagnetic chemical shifts for characterizing the hydrogen bonding in the physiologically relevant, resting-state, high-spin aquo complex are discussed. The pattern of labile proton exchange in the distal H-bond network of substrate-free HmuO allowed comparison of changes in dynamic stability of tertiary contacts in the substrate-free and substrate-bound HmuO and with the same complexes of human heme oxygenase.
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Affiliation(s)
- Zhenming Du
- Department of Chemistry, University of California, Davis, CA 95616, USA.
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12
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Shekhawat GS, Verma K. Haem oxygenase (HO): an overlooked enzyme of plant metabolism and defence. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:2255-70. [PMID: 20378668 DOI: 10.1093/jxb/erq074] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Haem oxygenase (HO) degrades free haem released from haem proteins with the generation of ferrous iron (Fe2+), biliverdin-IXalpha (BV-IXalpha), and carbon monoxide (CO). The mechanism of haem cleavage has been conserved between plants and other organisms even though the function, subcellular localization, and cofactor requirements of HO differ substantially. The crystal structure of HO1, a monomeric protein, has been extensively reported in mammals, pathogenic bacteria, and cyanobacteria, but no such reports are available for higher plant HOs except a predicted model for pea HO1. Along with haem degradation, HO performs various cellular processes including iron acquisition/mobilization, phytochrome chromophore synthesis, cell protection, and stomatal regulation. To date, four HO genes (HO1, HO2, HO3, and HO4) have been reported in plants. HO1 has been well explored in cell metabolism; however, the divergent roles of the other three HOs is less known. The transcriptional up-regulation of HO1 in plants responds to many agents, such as light, UV, iron deprivation, reactive oxygen species (ROS), abscisic acid (ABA), and haematin. Recently the HO1/CO system has gained more attention due to its physiological cytoprotective role in plants. This review focuses on the recent advances made in plant HO research involving its role in environmental stresses. Moreover, the review emphasizes physiological, biochemical, and molecular aspects of this enzyme in plants.
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Affiliation(s)
- G S Shekhawat
- Department of Bioscience and Biotechnology, Banasthali University, Banasthali-304022, Rajasthan, India.
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Badyal SK, Eaton G, Mistry S, Pipirou Z, Basran J, Metcalfe CL, Gumiero A, Handa S, Moody PCE, Raven EL. Evidence for heme oxygenase activity in a heme peroxidase. Biochemistry 2009; 48:4738-46. [PMID: 19309109 DOI: 10.1021/bi900118j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The heme peroxidase and heme oxygenase enzymes share a common heme prosthetic group but catalyze fundamentally different reactions, the first being H(2)O(2)-dependent oxidation of substrate using an oxidized Compound I intermediate, and the second O(2)-dependent degradation of heme. It has been proposed that these enzymes utilize a common reaction intermediate, a ferric hydroperoxide species, that sits at a crossroads in the mechanism and beyond which there are two mutually exclusive mechanistic pathways. Here, we present evidence to support this proposal in a heme peroxidase. Hence, we describe kinetic data for a variant of ascorbate peroxidase (W41A) which reacts slowly with tert-butyl hydroperoxide and does not form the usual peroxidase Compound I intermediate; instead, structural data show that a product is formed in which the heme has been cleaved at the alpha-meso position, analogous to the heme oxygenase mechanism. We interpret this to mean that the Compound I (peroxidase) pathway is shut down, so that instead the reaction intermediate diverts through the alternative (heme oxygenase) route. A mechanism for formation of the product is proposed and discussed in the light of what is known about the heme oxygenase reaction mechanism.
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Affiliation(s)
- Sandip K Badyal
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, UK
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14
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Chen H, Moreau Y, Derat E, Shaik S. Quantum Mechanical/Molecular Mechanical Study of Mechanisms of Heme Degradation by the Enzyme Heme Oxygenase: The Strategic Function of the Water Cluster. J Am Chem Soc 2008; 130:1953-65. [DOI: 10.1021/ja076679p] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Hui Chen
- Department of Organic Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
| | - Yohann Moreau
- Department of Organic Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
| | - Etienne Derat
- Department of Organic Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
| | - Sason Shaik
- Department of Organic Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
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15
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Unno M, Matsui T, Ikeda-Saito M. Structure and catalytic mechanism of heme oxygenase. Nat Prod Rep 2007; 24:553-70. [PMID: 17534530 DOI: 10.1039/b604180a] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Masaki Unno
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba, Sendai 980-8577, Japan
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16
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Gohya T, Zhang X, Yoshida T, Migita CT. Spectroscopic characterization of a higher plant heme oxygenase isoform-1 from Glycine max (soybean)--coordination structure of the heme complex and catabolism of heme. FEBS J 2006; 273:5384-99. [PMID: 17076701 DOI: 10.1111/j.1742-4658.2006.05531.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Heme oxygenase converts heme into biliverdin, CO, and free iron. In plants, as well as in cyanobacteria, heme oxygenase plays a particular role in the biosynthesis of photoreceptive pigments, such as phytochromobilins and phycobilins, supplying biliverdin IX(alpha) as a direct synthetic resource. In this study, a higher plant heme oxygenase, GmHO-1, of Glycine max (soybean), was prepared to evaluate the molecular features of its heme complex, the enzymatic activity, and the mechanism of heme conversion. The similarity in the amino acid sequence between GmHO-1 and heme oxygenases from other biological species is low, and GmHO-1 binds heme with 1 : 1 stoichiometry at His30; this position does not correspond to the proximal histidine of other heme oxygenases in their sequence alignments. The heme bound to GmHO-1, in the ferric high-spin state, exhibits an acid-base transition and is converted to biliverdin IX(alpha) in the presence of NADPH/ferredoxin reductase/ferredoxin, or ascorbate. During the heme conversion, an intermediate with an absorption maximum different from that of typical verdoheme-heme oxygenase or CO-verdoheme-heme oxygenase complexes was observed and was extracted as a bis-imidazole complex; it was identified as verdoheme. A myoglobin mutant, H64L, with high CO affinity trapped CO produced during the heme degradation. Thus, the mechanism of heme degradation by GmHO-1 appears to be similar to that of known heme oxygenases, despite the low sequence homology. The heme conversion by GmHO-1 is as fast as that by SynHO-1 in the presence of NADPH/ferredoxin reductase/ferredoxin, thereby suggesting that the latter is the physiologic electron-donating system.
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Affiliation(s)
- Tomohiko Gohya
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Japan
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17
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Silvernail NJ, Noll BC, Schulz CE, Scheidt WR. Coordination of diatomic ligands to heme: simply CO. Inorg Chem 2006; 45:7050-2. [PMID: 16933901 PMCID: PMC1586066 DOI: 10.1021/ic0613356] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The synthesis and molecular structures of three iron(II) porphyrinates with only CO as the axial ligand(s) are reported. Two five-coordinate [Fe(OEP)(CO)] derivatives have Fe-C = 1.7077(13) and 1.7140(10) A, much shorter than those of six-coordinate [Fe(OEP)(Im)(CO)], although nu(C-O) is 1944-1948 cm(-1). The six-coordinate species [Fe(OEP)(CO)2] has also been studied. The competition for pi-back-bonding of two CO ligands leads to Fe-C distance of 1.8558(10) A and nu(C-O) being increased to 2021 cm(-1). The Mössbauer spectrum has a quadrupole splitting constant of 0 mm/s at 4.2 K, indicating high electronic symmetry.
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Zhang W, Olson JS, Phillips GN. Biophysical and kinetic characterization of HemAT, an aerotaxis receptor from Bacillus subtilis. Biophys J 2005; 88:2801-14. [PMID: 15653746 PMCID: PMC1305375 DOI: 10.1529/biophysj.104.047936] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2004] [Accepted: 11/24/2004] [Indexed: 11/18/2022] Open
Abstract
HemAT from Bacillus subtilis is a new type of heme protein responsible for sensing oxygen. The structural and functional properties of the full-length HemAT protein, the sensor domain (1-178), and Tyr-70 mutants have been characterized. Kinetic and equilibrium measurements reveal that both full-length HemAT and the sensor domain show two distinct O(2) binding components. The high-affinity component has a K(dissociation) approximately 1-2 microM and a normal O(2) dissociation rate constant, k(O2) = 50-80 s(-1). The low-affinity component has a K(dissociation) approximately 50-100 microM and a large O(2) dissociation rate constant equal to approximately 2000 s(-1). The low n-value and biphasic character of the equilibrium curve indicate that O(2) binding to HemAT involves either independent binding to high- and low-affinity subunits in the dimer or negative cooperativity. Replacement of Tyr-70(B10) with Phe, Leu, or Trp in the sensor domain causes dramatic increases in k(O2) for both the high- and low-affinity components. In contrast, the rates and affinity for CO binding are little affected by loss of the Tyr-70 hydroxyl group. These results suggest highly dynamic behavior for the Tyr-70 side chain and the fraction of the "up" versus "down" conformation is strongly influenced by the nature of the iron-ligand complex. As a result of having both high- and low-affinity components, HemAT can respond to oxygen concentration gradients under both hypoxic (0-10 microM) and aerobic (50-250 microM) conditions, a property which could, in principle, be important for a robust sensing system. The unusual ligand-binding properties of HemAT suggest that asymmetry and apparent negative cooperativity play an important role in the signal transduction pathway.
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Affiliation(s)
- Wei Zhang
- Department of Biochemistry and Cell Biology, W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005, USA
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19
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Hirotsu S, Chu GC, Unno M, Lee DS, Yoshida T, Park SY, Shiro Y, Ikeda-Saito M. The crystal structures of the ferric and ferrous forms of the heme complex of HmuO, a heme oxygenase of Corynebacterium diphtheriae. J Biol Chem 2003; 279:11937-47. [PMID: 14645223 DOI: 10.1074/jbc.m311631200] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Crystal structures of the ferric and ferrous heme complexes of HmuO, a 24-kDa heme oxygenase of Corynebacterium diphtheriae, have been refined to 1.4 and 1.5 A resolution, respectively. The HmuO structures show that the heme group is closely sandwiched between the proximal and distal helices. The imidazole group of His-20 is the proximal heme ligand, which closely eclipses the beta- and delta-meso axis of the porphyrin ring. A long range hydrogen bonding network is present, connecting the iron-bound water ligand to the solvent water molecule. This enables proton transfer from the solvent to the catalytic site, where the oxygen activation occurs. In comparison to the ferric complex, the proximal and distal helices move closer to the heme plane in the ferrous complex. Together with the kinked distal helix, this movement leaves only the alpha-meso carbon atom accessible to the iron-bound dioxygen. The heme pocket architecture is responsible for stabilization of the ferric hydroperoxo-active intermediate by preventing premature heterolytic O-O bond cleavage. This allows the enzyme to oxygenate selectively at the alpha-meso carbon in HmuO catalysis.
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Affiliation(s)
- Shoko Hirotsu
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba, Sendai 980-8577, Japan
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20
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Skaar EP, Gaspar AH, Schneewind O. IsdG and IsdI, heme-degrading enzymes in the cytoplasm of Staphylococcus aureus. J Biol Chem 2003; 279:436-43. [PMID: 14570922 DOI: 10.1074/jbc.m307952200] [Citation(s) in RCA: 206] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Staphylococcus aureus requires iron for growth and utilizes heme as a source of iron during infection. Staphylococcal surface proteins capture hemoglobin, release heme from hemoglobin and transport this compound across the cell wall envelope and plasma membrane into the bacterial cytoplasm. Here we show that Staphylococcus aureus isdG and isdI encode cytoplasmic proteins with heme binding properties. IsdG and IsdI cleave the tetrapyrrol ring structure of heme in the presence of NADPH cytochrome P450 reductase, thereby releasing iron. Further, IsdI complements the heme utilization deficiency of a Corynebacterium ulcerans heme oxygenase mutant, demonstrating in vivo activity of this enzyme. Although Staphylococcus epidermidis, Listeria monocytogenes, and Bacillus anthracis encode homologues of IsdG and IsdI, these proteins are not found in other bacteria or mammals. Thus, it appears that bacterial pathogens evolved different strategies to retrieve iron from scavenged heme molecules and that staphylococcal IsdG and IsdI represent examples of bacterial heme-oxygenases.
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Affiliation(s)
- Eric P Skaar
- Committee on Microbiology, University of Chicago, Chicago, Illinois 60637, USA
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21
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Colas C, Ortiz de Montellano PR. Autocatalytic radical reactions in physiological prosthetic heme modification. Chem Rev 2003; 103:2305-32. [PMID: 12797831 DOI: 10.1021/cr0204303] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Christophe Colas
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, California 94143-0446, USA
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22
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Auclair K, Huang HW, Moënne-Loccoz P, Ortiz de Montellano PR. Cloning and expression of a heme binding protein from the genome of Saccharomyces cerevisiae. Protein Expr Purif 2003; 28:340-9. [PMID: 12699699 DOI: 10.1016/s1046-5928(02)00699-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The YLR205c gene of Saccharomyces cerevisiae does not show significant sequence identity to any known gene, except for heme oxygenase (22% to human HO-1). The YLR205 ORF was cloned and overexpressed in both Escherichia coli and S. cerevisiae. Both expression systems yielded proteins that bound heme tightly. The isolated YLR205c protein underwent reduction in the presence of either NADPH-cytochrome P450 reductase or NADH-putidaredoxin-putidaredoxin reductase but did not exhibit heme oxygenase activity. The protein exhibited modest H(2)O(2)-dependent peroxidase activities with guaiacol, potassium iodide, and 2,2(')-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid (ABTS). Thus, YLR205c codes for a hemoprotein of unknown physiological function that exhibits peroxidase activity.
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Affiliation(s)
- Karine Auclair
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 2K6.
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23
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Makino R, Obayashi E, Homma N, Shiro Y, Hori H. YC-1 facilitates release of the proximal His residue in the NO and CO complexes of soluble guanylate cyclase. J Biol Chem 2003; 278:11130-7. [PMID: 12540839 DOI: 10.1074/jbc.m209026200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The benzylindazole compound YC-1 has been shown to activate soluble guanylate cyclase by increasing the sensitivity toward NO and CO. Here we report the action of YC-1 on the coordination of CO- and NO-hemes in the enzyme and correlate the events with the activation of enzyme catalysis. A single YC-1-binding site on the heterodimeric enzyme was identified by equilibrium dialysis. To explore the affect of YC-1 on the NO-heme coordination, the six-coordinate NO complex of the enzyme was stabilized by dibromodeuteroheme substitution. Using the dibromodeuteroheme enzyme, YC-1 converted the six-coordinate NO-heme to a five-coordinate NO-heme with a characteristic EPR signal that differed from that in the absence of YC-1. These results revealed that YC-1 facilitated cleavage of the proximal His-iron bond and caused geometrical distortion of the five-coordinate NO-heme. Resonance Raman studies demonstrated the presence of two iron-CO stretch modes at 488 and 521 cm(-1) specific to the YC-1-bound CO complex of the native enzyme. Together with the infrared C-O stretching measurements, we assigned the 488-cm(-1) band to the iron-CO stretch of a six-coordinate CO-heme and the 521-cm(-1) band to the iron-CO stretch of a five-coordinate CO-heme. These results indicate that YC-1 stimulates enzyme activity by weakening or cleaving the proximal His-iron bond in the CO complex as well as the NO complex.
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Affiliation(s)
- Ryu Makino
- Department of Life Science, College of Science, Rikkyo University, Nishi-ikebukuro 3-34-1, Toshima-ku, Tokyo 171-8501, Japan.
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24
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Li Y, Syvitski RT, Chu GC, Ikeda-Saito M, Mar GNL. Solution 1H NMR investigation of the active site molecular and electronic structures of substrate-bound, cyanide-inhibited HmuO, a bacterial heme oxygenase from Corynebacterium diphtheriae. J Biol Chem 2003; 278:6651-63. [PMID: 12480929 DOI: 10.1074/jbc.m211249200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The molecular structure and dynamic properties of the active site environment of HmuO, a heme oxygenase (HO) from the pathogenic bacterium Corynebacterium diphtheriae, have been investigated by (1)H NMR spectroscopy using the human HO (hHO) complex as a homology model. It is demonstrated that not only the spatial contacts among residues and between residues and heme, but the magnetic axes that can be related to the direction and magnitude of the steric tilt of the FeCN unit are strongly conserved in the two HO complexes. The results indicate that very similar contributions of steric blockage of several meso positions and steric tilt of the attacking ligand are operative. A distal H-bond network that involves numerous very strong H-bonds and immobilized water molecules is identified in HmuO that is analogous to that previously identified in hHO (Li, Y., Syvitski, R. T., Auclair, K., Wilks, A., Ortiz de Montellano, P. R., and La Mar, G. N. (2002) J. Biol. Chem. 277, 33018-33031). The NMR results are completely consistent with the very recent crystal structure of the HmuO.substrate complex. The H-bond network/ordered water molecules are proposed to orient the distal water molecule near the catalytically key Asp(136) (Asp(140) in hHO) that stabilizes the hydroperoxy intermediate. The dynamic stability of this H-bond network in HmuO is significantly greater than in hHO and may account for the slower catalytic rate in bacterial HO compared with mammalian HO.
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Affiliation(s)
- Yiming Li
- Department of Chemistry, University of California, Davis, California 95616, USA
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Migita CT, Zhang X, Yoshida T. Expression and characterization of cyanobacterium heme oxygenase, a key enzyme in the phycobilin synthesis. Properties of the heme complex of recombinant active enzyme. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:687-98. [PMID: 12581208 DOI: 10.1046/j.1432-1033.2003.03421.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
An efficient bacterial expression system of cyanobacterium Synechocystis sp. PCC 6803 heme oxygenase gene, ho-1, has been constructed, using a synthetic gene. A soluble protein was expressed at high levels and was highly purified, for the first time. The protein binds equimolar free hemin to catabolize the bound hemin to ferric-biliverdin IX alpha in the presence of oxygen and reducing equivalents, showing the heme oxygenase activity. During the reaction, verdoheme intermediate is formed with the evolution of carbon monoxide. Though both ascorbate and NADPH-cytochrome P450 reductase serve as an electron donor, the heme catabolism assisted by ascorbate is considerably slow and the reaction with NADPH-cytochrome P450 reductase is greatly retarded after the oxy-heme complex formation. The optical absorption spectra of the heme-enzyme complexes are similar to those of the known heme oxygenase complexes but have some distinct features, exhibiting the Soret band slightly blue-shifted and relatively strong CT bands of the high-spin component in the ferric form spectrum. The heme-enzyme complex shows the acid-base transition, where two alkaline species are generated. EPR of the nitrosyl heme complex has established the nitrogenous proximal ligand, presumably histidine 17 and the obtained EPR parameters are discriminated from those of the rat heme oxygenase-1 complex. The spectroscopic characters as well as the catabolic activities strongly suggest that, in spite of very high conservation of the primary structure, the heme pocket structure of Synechocystis heme oxygenase isoform-1 is different from that of rat heme oxygenase isoform-1, rather resembling that of bacterial heme oxygenase, H mu O.
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Affiliation(s)
- Catharina T Migita
- Department of Biological Chemistry, Faculty of Agriculture, Yoshida, Yamaguchi University, Japan.
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