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Yao Y, Li QX. Efficient, fast and robust degradation of chlortetracycline in wastewater catalyzed by recombinant Arthromyces ramosus peroxidase. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159872. [PMID: 36461571 DOI: 10.1016/j.scitotenv.2022.159872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/27/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
Chlortetracycline (CTC), a widely used antibiotic, is recalcitrant and ubiquitous in the environment. Enzymatic degradation of CTC is an economical and efficient bioremediation method. In this work, recombinant Arthromyces ramosus peroxidase (rARP) at a concentration of 3.13 × 10-9 M was used to catalyze rapid degradation of CTC in water. The second-order rate constants of rARP showed up to 62-fold catalytic efficiency of horseradish peroxidase (HRP) toward CTC. The degradation half-life of CTC at the concentrations of 2 and 40 mg L-1 in wastewater under the rARP catalysis was, respectively, 5.3 and 5.7 min at 25 °C, and 2.7 and 3.1 min at 40 °C, which were up to 15-fold and 111-fold faster than HRP and laccase, respectively, but use of 3 % the amount of rARP as HRP. rARP catalyzed degradation of CTC at 2-40 mg L-1 in wastewater completed in 20-24 min, and its catalytic efficiency varied within only 2-fold at 25-40 °C. rARP showed only 2-3-fold discrepancy of catalytic efficiency among pH 5.0, 7.5 and 9.0. CTC under rARP catalysis underwent demethylation and oxidation to form nontoxic N-dedimethyl-9-hydroxy-CTC. The high catalytic efficiency of rARP agreed with a short distance between rARP's δN-His56 and CTC's dimethylamine N as indicated by docking simulation. rARP is a useful enzyme for CTC bioremediation.
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Affiliation(s)
- Yuqun Yao
- School of Medicine, Guangxi University of Science and Technology, Liushi Road 257, Liuzhou 545025, China; Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, 1955 East-West Road, Honolulu, HI 96822, USA
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, 1955 East-West Road, Honolulu, HI 96822, USA.
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2
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Zhang B, Lewis JA, Kovacs F, Sattler SE, Sarath G, Kang C. Activity of Cytosolic Ascorbate Peroxidase (APX) from Panicum virgatum against Ascorbate and Phenylpropanoids. Int J Mol Sci 2023; 24:1778. [PMID: 36675291 PMCID: PMC9864165 DOI: 10.3390/ijms24021778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
APX is a key antioxidant enzyme in higher plants, scavenging H2O2 with ascorbate in several cellular compartments. Here, we report the crystal structures of cytosolic ascorbate peroxidase from switchgrass (Panicum virgatum L., Pvi), a strategic feedstock plant with several end uses. The overall structure of PviAPX was similar to the structures of other APX family members, with a bound ascorbate molecule at the ɣ-heme edge pocket as in other APXs. Our results indicated that the H2O2-dependent oxidation of ascorbate displayed positive cooperativity. Significantly, our study suggested that PviAPX can oxidize a broad range of phenylpropanoids with δ-meso site in a rather similar efficiency, which reflects its role in the fortification of cell walls in response to insect feeding. Based on detailed structural and kinetic analyses and molecular docking, as well as that of closely related APX enzymes, the critical residues in each substrate-binding site of PviAPX are proposed. Taken together, these observations shed new light on the function and catalysis of PviAPX, and potentially benefit efforts improve plant health and biomass quality in bioenergy and forage crops.
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Affiliation(s)
- Bixia Zhang
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Jacob A. Lewis
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Frank Kovacs
- Chemistry Department, University of Nebraska-Kearney, Kearney, NE 68849, USA
| | - Scott E. Sattler
- Wheat, Sorghum and Forage Research Unit, U.S. Department of Agriculture—Agricultural Research Service, Lincoln, NE 68583, USA
| | - Gautam Sarath
- Wheat, Sorghum and Forage Research Unit, U.S. Department of Agriculture—Agricultural Research Service, Lincoln, NE 68583, USA
| | - ChulHee Kang
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA
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Song J, Wang Z, Zhang S, Wang Y, Liang Y, Dai Q, Huo Z, Xu K. The Toxicity of Salicylhydroxamic Acid and Its Effect on the Sensitivity of Ustilaginoidea virens to Azoxystrobin and Pyraclostrobin. J Fungi (Basel) 2022; 8:jof8111231. [PMID: 36422052 PMCID: PMC9692728 DOI: 10.3390/jof8111231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/17/2022] [Accepted: 11/19/2022] [Indexed: 11/24/2022] Open
Abstract
Rice false smut (RFS) caused by Ustilaginoidea virens has been one of the most severe rice diseases. Fungicide-based chemical control is a significant measure to control RFS. In the sensitivity determination of quinone outside inhibitor (QoI) fungicide in vitro, salicylhydroxamic acid (SHAM) has been commonly added to artificial culture media in order to inhibit alternative oxidase of phytopathogenic fungi. However, some studies showed that artificial media should not include SHAM due to its toxicity. Whether SHAM should be added in the assay of U. virens sensitivity to QoI fungicide remains unknown. In this study, two appropriate media, potato sucrose agar (PSA) and minimal medium (MM), were selected to test SHAM toxicity and sensitivity of U. virens to azoxystrobin and pyraclostrobin. The mycelial growth and sensitivity to azoxystrobin and pyraclostrobin had no significant difference between on PSA and MM. SHAM could significantly inhibit mycelial growth, conidial germination, peroxidase (POD) and esterase activity of U. virens. Average effective concentration for inhibiting 50% (EC50) values of SHAM against mycelial growth of ten U. virens were 27.41 and 12.75 μg/mL on PSA and MM, respectively. The EC50 values of SHAM against conidial germination of isolates HWD and JS60 were 70.36 and 44.69 μg/mL, respectively. SHAM at 30 μg/mL significantly inhibited POD and esterase activity of isolates HWD and JS60, and even SHAM at 10 μg/mL significantly inhibited POD activity of isolate HWD. In addition, SHAM significantly reduced EC50 values and EC90 values of azoxystrobin and pyraclostrobin on both PSA and MM. Even in the presence of SHAM at 10 μg/mL, average EC50 values of ten U. virens isolates for azoxystrobin decreased 1.7-fold on PSA and 4.8-fold on MM, and for pyraclostrobin that decreased 2.8-fold on PSA and 4.8-fold on MM. Therefore, these results suggest that SHAM should not be included in artificial media in the assay of U. virens sensitivity to QoI fungicides.
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Song JH, Zhang SJ, Wang Y, Chen YT, Luo JF, Liang Y, Zhang HC, Dai QG, Xu K, Huo ZY. Baseline Sensitivity and Control Efficacy of Two Quinone Outside Inhibitor Fungicides, Azoxystrobin and Pyraclostrobin, Against Ustilaginoidea virens. PLANT DISEASE 2022; 106:2967-2973. [PMID: 35306849 DOI: 10.1094/pdis-12-21-2850-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Rice false smut caused by the filamentous fungus Ustilaginoidea virens is a devastating grain disease in rice. Fungicides have been an important measure for the control of this disease. In this study, baseline sensitivities of 179 isolates of U. virens to the quinone outside inhibitor (QoI) fungicides azoxystrobin and pyraclostrobin were established. The distribution of the 50% effective concentration (EC50) values of each fungicide was unimodal. The frequency distribution of logarithmically transformed EC50 values fit or fit closer to a normal distribution. The ranges of EC50 values for azoxystrobin and pyraclostrobin were 0.001 to 0.864 and 0.001 to 0.569 μg/ml, with means and standard errors of the mean values of 0.203 ± 0.012 and 0.079 ± 0.006 μg/ml, respectively. There was a statistically significant and moderately positive correlation (n = 100, r = 0.469, P = 0.001) in sensitivity between these two fungicides. No cross-resistance was found between azoxystrobin, pyraclostrobin, and carbendazim or sterol demethylation inhibitor fungicides. Each fungicide had a significantly higher mean preventive efficacy compared with its curative efficacy. Field assays showed that the control efficacy of pyraclostrobin against rice false smut was greater than that of azoxystrobin. Pyraclostrobin had the best control of rice false smut in three rice varieties, with the control efficacy ranging from 81.5 to 95.5%, whereas azoxystrobin decreased the disease index by 64.1 to 69.2% under the same conditions. These results provide us a reference point in the management of U. virens and future QoI fungicide resistance monitoring programs.
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Affiliation(s)
- Jie-Hui Song
- Jiangsu Key Laboratory of Crop Genetics and Physiology & Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Si-Jie Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology & Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Yan Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology & Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Yun-Tong Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology & Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Jun-Fei Luo
- Jiangsu Key Laboratory of Crop Genetics and Physiology & Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - You Liang
- Jiangsu Key Laboratory of Crop Genetics and Physiology & Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Hong-Cheng Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology & Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Qi-Gen Dai
- Jiangsu Key Laboratory of Crop Genetics and Physiology & Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Ke Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology & Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Zhong-Yang Huo
- Jiangsu Key Laboratory of Crop Genetics and Physiology & Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu 225009, China
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Matsuzaki Y, Uda Y, Kurahashi M, Iwahashi F. Microtiter plate test using liquid medium is an alternative method for monitoring metyltetraprole sensitivity in Cercospora beticola. PEST MANAGEMENT SCIENCE 2021; 77:1226-1234. [PMID: 33051963 PMCID: PMC7894156 DOI: 10.1002/ps.6133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/14/2020] [Accepted: 10/13/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Metyltetraprole is a new quinone outside inhibitor (QoI) fungicide showing potent activity against QoI-resistant fungi that possess the G143A cytochrome b mutation, which confers resistance to existing QoIs such as trifloxystrobin. For its sustainable use, monitoring of metyltetraprole sensitivity is necessary and the establishment of appropriate methodology is important in each pathogen species. RESULTS In Cercospora beticola, the causal agent of sugar beet leaf spot, some isolates were less sensitive to metyltetraprole (EC50 > 1 mg L-1 , higher than the saturated concentration) using the common agar plate method, even with 100 mg L-1 salicylhydroxamic acid, an alternative oxidase inhibitor. However, microtiter tests (EC50 < 0.01 mg L-1 ), conidial germination tests (EC50 < 0.01 mg L-1 ) and in planta tests (>80% control at 75 mg L-1 run-off spraying) confirmed that all tested isolates were highly sensitive to metyltetraprole. For trifloxystrobin, G143A mutants were clearly resistant upon microtiter plate tests (median EC50 > 2 mg L-1 ) and distinct from wild-type isolates (median EC50 < 0.01 mg L-1 ). Notably, mycelium fragments were usable for the microtiter plate tests and the test was applicable for isolates that do not form sufficient conidia. Our monitoring study by microtiter plate tests did not indicate the presence of metyltetraprole-resistant C. beticola isolates in populations in Hokkaido, Japan. CONCLUSION The microtiter tests were revealed to be useful for monitoring the sensitivity of C. beticola to metyltetraprole and trifloxystrobin. © 2020 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Yuichi Matsuzaki
- Health and Crop Sciences Research LaboratorySumitomo Chemical Co., LtdTakarazukaJapan
| | - Yukie Uda
- Health and Crop Sciences Research LaboratorySumitomo Chemical Co., LtdTakarazukaJapan
| | - Makoto Kurahashi
- Makabe Experimental FarmSumitomo Chemical Co., LtdSakuragawaJapan
| | - Fukumatsu Iwahashi
- Health and Crop Sciences Research LaboratorySumitomo Chemical Co., LtdTakarazukaJapan
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Liang H, Li J, Luo C, Li J, Zhu FX. Effects of SHAM on the Sensitivity of Sclerotinia sclerotiorum and Botrytis cinerea to QoI Fungicides. PLANT DISEASE 2019; 103:1884-1888. [PMID: 31161931 DOI: 10.1094/pdis-12-18-2142-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
It is a common practice to add salicylhydroxamic acid (SHAM) into artificial medium in the in vitro sensitivity assay of fungal phytopathogens to the quinone outside inhibitor (QoI) fungicides. The rationale for adding SHAM is to inhibit fungal alternative oxidase, which is presumed to be inhibited by secondary metabolites of plants. Therefore, the ideal characteristics of SHAM should be almost nontoxic to phytopathogens and have no significant effect on control efficacy of fungicides. However, this study showed that the average effective concentration for 50% inhibition (EC50) of mycelial growth values of SHAM were 97.5 and 401.4 μg/ml for Sclerotinia sclerotiorum and Botrytis cinerea, respectively. EC50 values of the three QoI fungicides azoxystrobin, kresoxim-methyl, and trifloxystrobin in the presence of SHAM at 20 and 80 μg/ml for S. sclerotiorum and B. cinerea, respectively, declined by 52.7 to 78.1% compared with those without SHAM. For the dicarboximide fungicide dimethachlone, the average EC50 values in the presence of SHAM declined by 18.2% (P = 0.008) for S. sclerotiorum and 35.9% (P = 0.012) for B. cinerea. Pot experiments showed that SHAM increased control efficacy of the three QoI fungicides against the two pathogens by 43 to 83%. For dimethachlone, SHAM increased control efficacy by 134% for S. sclerotiorum and 86% for B. cinerea. Biochemical studies showed that SHAM significantly inhibited peroxidase activity (P = 0.024) of B. cinerea and esterase activity (P = 0.015) of S. sclerotiorum. The strong inhibitions of SHAM per se on mycelial growth of B. cinerea and S. sclerotiorum and significant influences on the sensitivity of the two pathogens to both the QoI fungicides and dimethachlone as well as inhibitions on peroxidase and esterase indicate that SHAM should not be added in the in vitro assay of sensitivity to the QoI fungicides.
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Affiliation(s)
- Hongjie Liang
- 1College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- 2Potato Research Institute, Gansu Academy of Agricultural Sciences, Gansu 730070, China
| | - Jinli Li
- 1College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chaoxi Luo
- 1College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianhong Li
- 1College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Fu-Xing Zhu
- 1College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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7
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The role of Ala134 in controlling substrate binding and reactivity in ascorbate peroxidase. J Inorg Biochem 2017; 180:230-234. [PMID: 29317104 DOI: 10.1016/j.jinorgbio.2017.12.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 12/06/2017] [Accepted: 12/24/2017] [Indexed: 11/21/2022]
Abstract
Ascorbate peroxidase (APX) is a class I heme peroxidase. It has two sites for binding of substrates. One is close to the γ-heme edge and is used for oxidation of ascorbate; the other is at the δ-heme edge and is used for binding of aromatic substrates [Gumiero et al., (2010) Arch. Biochem. Biophys. 500, 13-20]. In this work, we have examined the structural factors that control binding at the δ-heme edge by replacement of Ala134 in APX with a proline residue that is more commonly found in other class II and III peroxidases. Kinetic data indicate that replacement of Ala134 by proline has only a small effect on the catalytic mechanism, or the oxidation of ascorbate or guaiacol. Chemical modification with phenylhydrazine indicates that heme accessibility close to the δ-heme edge is only minorly affected by the substitution. We conclude that the A134P mutation alone is not enough to substantially affect the reactivity of APX towards aromatic substrates bound at the δ-heme edge. The data are relevant to the recent application of APX (APEX) in cellular imaging.
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Gupta SP. QSAR Studies on Hydroxamic Acids: A Fascinating Family of Chemicals with a Wide Spectrum of Activities. Chem Rev 2015; 115:6427-90. [DOI: 10.1021/cr500483r] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Satya P. Gupta
- Department of Applied Sciences, National Institute of Technical Teachers’ Training and Research, Shamla
Hills, Bhopal-462002, India
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Liang HJ, Di YL, Li JL, You H, Zhu FX. Baseline Sensitivity of Pyraclostrobin and Toxicity of SHAM to Sclerotinia sclerotiorum. PLANT DISEASE 2015; 99:267-273. [PMID: 30699559 DOI: 10.1094/pdis-06-14-0633-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Sclerotinia sclerotiorum is a cosmopolitan plant pathogen notable for its wide host range. The quinone outside inhibitor (QoI) fungicide pyraclostrobin has not been registered for control of S. sclerotiorum in China. In this study, baseline sensitivity of pyraclostrobin was established based on effective concentration for 50% inhibition of mycelial growth (EC50) values of 153 isolates of S. sclerotiorum collected from five provinces of China and toxicity of alternative oxidase inhibitor salicylhydroxamic acid (SHAM) to S. sclerotiorum was determined. Results showed that the frequency distribution of EC50 values of the 153 isolates was unimodal but with a right-hand tail. The mean EC50 value was 0.1027 μg/ml and the range of EC50 values was 0.0124 to 0.6324 μg/ml. Applied as a preventive fungicide in pot experiments, pyraclostrobin at 5, 15, and 45 μg/ml provided control efficacies of 61, 77, and 100%, respectively. There was no positive cross-resistance between pyraclostrobin and carbendazim or dimethachlon. EC50 values for SHAM against four isolates of S. sclerotiorum were 44.4, 51.8, 54.4, and 68.7 μg/ml. SHAM at 20 μg/ml could significantly increase not only the inhibitory effect of pyraclostrobin on mycelial growth on potato dextrose agar media but also the control efficacy in planta. These results indicated that SHAM should not be added into artificial media in in vitro assay of S. sclerotiorum sensitivity to pyraclostrobin. This has broad implications for assay of sensitivity of fungal pathogen to QoI fungicides.
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Affiliation(s)
- Hong-Jie Liang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ya-Li Di
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jin-Li Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hong You
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fu-Xing Zhu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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Kamachi S, Hirabayashi K, Tamoi M, Shigeoka S, Tada T, Wada K. Crystal structure of the catalase-peroxidase KatG W78F mutant from Synechococcus elongatus PCC7942 in complex with the antitubercular pro-drug isoniazid. FEBS Lett 2014; 589:131-7. [PMID: 25479089 DOI: 10.1016/j.febslet.2014.11.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 11/21/2014] [Accepted: 11/23/2014] [Indexed: 10/24/2022]
Abstract
Isoniazid (INH) is a pro-drug that has been extensively used to treat tuberculosis. INH is activated by the heme enzyme catalase-peroxidase (KatG), but the mechanism of the activation is poorly understood, in part because the INH binding site has not been clearly established. Here, we observed that a single-residue mutation of KatG from Synechococcus elongatus PCC7942 (SeKatG), W78F, enhances INH activation. The crystal structure of INH-bound KatG-W78F revealed that INH binds to the heme pocket. The results of a thermal-shift assay implied that the flexibility of the SeKatG molecule is increased by the W78F mutation, allowing the INH molecule to easily invade the heme pocket through the access channel on the γ-edge side of the heme.
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Affiliation(s)
- Saori Kamachi
- Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Kei Hirabayashi
- Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki 889-1692, Japan; Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Masahiro Tamoi
- Faculty of Agriculture, Kinki University, Nakamachi, Nara 631-8505, Japan
| | - Shigeru Shigeoka
- Faculty of Agriculture, Kinki University, Nakamachi, Nara 631-8505, Japan
| | - Toshiji Tada
- Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan.
| | - Kei Wada
- Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki 889-1692, Japan.
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11
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Pandey VP, Singh S, Jaiswal N, Awasthi M, Pandey B, Dwivedi UN. Papaya fruit ripening: ROS metabolism, gene cloning, characterization and molecular docking of peroxidase. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2013.10.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Diorganotin(IV) derivatives of N-methyl p-fluorobenzo-hydroxamic acid: preparation, spectral characterization, X-ray diffraction studies and antitumor activity. Molecules 2013; 18:8696-711. [PMID: 23881054 PMCID: PMC6270222 DOI: 10.3390/molecules18078696] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 07/15/2013] [Accepted: 07/16/2013] [Indexed: 11/16/2022] Open
Abstract
Three diorganotin(IV) complexes of the general formula R2Sn[RcC(O)N(RN)O] (Rc = aryl, RN = Alkyl) have been synthesized by refluxing in toluene the corresponding diorganotin(IV) oxides with the free ligand N-methyl p-fluorobenzohydroxamic acid, using a Dean and Stark water separator. The ligand was derived from the reaction of the corresponding p-fluorobenzoyl chloride and N-methylhydroxylamine hydrochloride in the presence of sodium hydrogen carbonate. The isolated free ligand and its respective diorganotin compounds have been characterized by elemental analysis, IR and 1H-, 13C-, 119Sn-NMR spectroscopies. The crystal structures of the diorganotin complexes have been confirmed by single crystal X-ray diffraction methods. The investigations carried out on the diorganotin(IV) complexes of N-methyl p-fluorobenzohydroxamic acid confirmed a 1:2 stoichiometry. The complex formation took place through the O,O-coordination via the carbonyl oxygen and subsequent deprotonated hydroxyl group to the tin atom. The crystal structures of three diorganotin complexes were determined and were found to adopt six coordination geometries at the tin centre with coordination to two ligand moieties.
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Singh S, Pandey VP, Naaz H, Dwivedi UN. Phylogenetic analysis, molecular modeling, substrate-inhibitor specificity, and active site comparison of bacterial, fungal, and plant heme peroxidases. Biotechnol Appl Biochem 2012; 59:283-94. [DOI: 10.1002/bab.1025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 06/05/2012] [Indexed: 11/07/2022]
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14
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Murphy EJ, Metcalfe CL, Nnamchi C, Moody PCE, Raven EL. Crystal structure of guaiacol and phenol bound to a heme peroxidase. FEBS J 2011; 279:1632-9. [PMID: 22093282 DOI: 10.1111/j.1742-4658.2011.08425.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Guaiacol is a universal substrate for all peroxidases, and its use in a simple colorimetric assay has wide applications. However, its exact binding location has never been defined. Here we report the crystal structures of guaiacol bound to cytochrome c peroxidase (CcP). A related structure with phenol bound is also presented. The CcP-guaiacol and CcP-phenol crystal structures show that both guaiacol and phenol bind at sites distinct from the cytochrome c binding site and from the δ-heme edge, which is known to be the binding site for other substrates. Although neither guaiacol nor phenol is seen bound at the δ-heme edge in the crystal structures, inhibition data and mutagenesis strongly suggest that the catalytic binding site for aromatic compounds is the δ-heme edge in CcP. The functional implications of these observations are discussed in terms of our existing understanding of substrate binding in peroxidases [Gumiero A et al. (2010) Arch Biochem Biophys 500, 13-20].
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Affiliation(s)
- Emma J Murphy
- Department of Chemistry, University of Leicester, Leicester, UK
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15
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Yin H, Dong L, Hong M, Cui J. Structural diversity of organotin(IV) complexes self-assembled from hydroxamic acid and mono- or dialkyltin salts. J Organomet Chem 2011. [DOI: 10.1016/j.jorganchem.2011.02.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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16
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Metal complexes of cyclic hydroxamates. Synthesis and crystal structures of 3-hydroxy-2-methyl-3H-quinazolin-4-one (ChaH) and of its Fe(III), Co(II), Ni(II), Cu(II) and Zn(II) complexes. Inorganica Chim Acta 2011. [DOI: 10.1016/j.ica.2010.12.047] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Gumiero A, Murphy EJ, Metcalfe CL, Moody PC, Raven EL. An analysis of substrate binding interactions in the heme peroxidase enzymes: A structural perspective. Arch Biochem Biophys 2010; 500:13-20. [DOI: 10.1016/j.abb.2010.02.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Revised: 02/23/2010] [Accepted: 02/27/2010] [Indexed: 11/29/2022]
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18
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Singh AK, Kumar RP, Pandey N, Singh N, Sinha M, Bhushan A, Kaur P, Sharma S, Singh TP. Mode of binding of the tuberculosis prodrug isoniazid to heme peroxidases: binding studies and crystal structure of bovine lactoperoxidase with isoniazid at 2.7 A resolution. J Biol Chem 2009; 285:1569-76. [PMID: 19907057 DOI: 10.1074/jbc.m109.060327] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Isoniazid (INH) is an anti-tuberculosis prodrug that is activated by mammalian lactoperoxidase and Mycobacterium tuberculosis catalase peroxidase (MtCP). We report here binding studies, an enzyme assay involving INH, and the crystal structure of the complex of bovine lactoperoxidase (LPO) with INH to illuminate binding properties and INH activation as well as the mode of diffusion and interactions together with a detailed structural and functional comparison with MtCP. The structure determination shows that isoniazid binds to LPO at the substrate binding site on the distal heme side. The substrate binding site is connected to the protein surface through a long hydrophobic channel. The acyl hydrazide moiety of isoniazid interacts with Phe(422) O, Gln(423) O(epsilon1), and Phe(254) O. In this arrangement, pyridinyl nitrogen forms a hydrogen bond with a water molecule, W-1, which in turn forms three hydrogen bonds with Fe(3+), His(109) N(epsilon2), and Gln(105) N(epsilon2). The remaining two sides of isoniazid form hydrophobic interactions with the atoms of heme pyrrole ring A, C(beta) and C(gamma) atoms of Glu(258), and C(gamma) and C(delta) atoms of Arg(255). The binding studies indicate that INH binds to LPO with a value of 0.9 x 10(-6) m for the dissociation constant. The nitro blue tetrazolium reduction assay shows that INH is activated by the reaction of LPO-H(2)O(2) with INH. This suggests that LPO can be used for INH activation. It also indicates that the conversion of INH into isonicotinoyl radical by LPO may be the cause of INH toxicity.
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Affiliation(s)
- Amit K Singh
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110 029, India
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Singh AK, Singh N, Sinha M, Bhushan A, Kaur P, Srinivasan A, Sharma S, Singh TP. Binding modes of aromatic ligands to mammalian heme peroxidases with associated functional implications: crystal structures of lactoperoxidase complexes with acetylsalicylic acid, salicylhydroxamic acid, and benzylhydroxamic acid. J Biol Chem 2009; 284:20311-8. [PMID: 19465478 PMCID: PMC2740456 DOI: 10.1074/jbc.m109.010280] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2009] [Indexed: 11/06/2022] Open
Abstract
The binding and structural studies of bovine lactoperoxidase with three aromatic ligands, acetylsalicylic acid (ASA), salicylhydoxamic acid (SHA), and benzylhydroxamic acid (BHA) show that all the three compounds bind to lactoperoxidase at the substrate binding site on the distal heme side. The binding of ASA occurs without perturbing the position of conserved heme water molecule W-1, whereas both SHA and BHA displace it by the hydroxyl group of their hydroxamic acid moieties. The acetyl group carbonyl oxygen atom of ASA forms a hydrogen bond with W-1, which in turn makes three other hydrogen-bonds, one each with heme iron, His-109 N(epsilon2), and Gln-105 N(epsilon2). In contrast, in the complexes of SHA and BHA, the OH group of hydroxamic acid moiety in both complexes interacts with heme iron directly with Fe-OH distances of 3.0 and 3.2A respectively. The OH is also hydrogen bonded to His-109 N(epsilon2) and Gln-105N(epsilon2). The plane of benzene ring of ASA is inclined at 70.7 degrees from the plane of heme moiety, whereas the aromatic planes of SHA and BHA are nearly parallel to the heme plane with inclinations of 15.7 and 6.2 degrees , respectively. The mode of ASA binding provides the information about the mechanism of action of aromatic substrates, whereas the binding characteristics of SHA and BHA indicate the mode of inhibitor binding.
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Affiliation(s)
- Amit K. Singh
- From the Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110 029, India
| | - Nagendra Singh
- From the Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110 029, India
| | - Mau Sinha
- From the Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110 029, India
| | - Asha Bhushan
- From the Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110 029, India
| | - Punit Kaur
- From the Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110 029, India
| | - Alagiri Srinivasan
- From the Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110 029, India
| | - Sujata Sharma
- From the Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110 029, India
| | - Tej P. Singh
- From the Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110 029, India
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20
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Ruiz-Dueñas FJ, Morales M, García E, Miki Y, Martínez MJ, Martínez AT. Substrate oxidation sites in versatile peroxidase and other basidiomycete peroxidases. JOURNAL OF EXPERIMENTAL BOTANY 2009; 60:441-52. [PMID: 18987391 DOI: 10.1093/jxb/ern261] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Versatile peroxidase (VP) is defined by its capabilities to oxidize the typical substrates of other basidiomycete peroxidases: (i) Mn(2+), the manganese peroxidase (MnP) substrate (Mn(3+) being able to oxidize phenols and initiate lipid peroxidation reactions); (ii) veratryl alcohol (VA), the typical lignin peroxidase (LiP) substrate; and (iii) simple phenols, which are the substrates of Coprinopsis cinerea peroxidase (CIP). Crystallographic, spectroscopic, directed mutagenesis, and kinetic studies showed that these 'hybrid' properties are due to the coexistence in a single protein of different catalytic sites reminiscent of those present in the other basidiomycete peroxidase families. Crystal structures of wild and recombinant VP, and kinetics of mutated variants, revealed certain differences in its Mn-oxidation site compared with MnP. These result in efficient Mn(2+) oxidation in the presence of only two of the three acidic residues forming its binding site. On the other hand, a solvent-exposed tryptophan is the catalytically-active residue in VA oxidation, initiating an electron transfer pathway to haem (two other putative pathways were discarded by mutagenesis). Formation of a tryptophanyl radical after VP activation by peroxide was detected using electron paramagnetic resonance. This was the first time that a protein radical was directly demonstrated in a ligninolytic peroxidase. In contrast with LiP, the VP catalytic tryptophan is not beta-hydroxylated under hydrogen peroxide excess. It was also shown that the tryptophan environment affected catalysis, its modification introducing some LiP properties in VP. Moreover, some phenols and dyes are oxidized by VP at the edge of the main haem access channel, as found in CIP. Finally, the biotechnological interest of VP is discussed.
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Murphy EJ, Metcalfe CL, Basran J, Moody PCE, Raven EL. Engineering the Substrate Specificity and Reactivity of a Heme Protein: Creation of an Ascorbate Binding Site in Cytochrome c Peroxidase. Biochemistry 2008; 47:13933-41. [DOI: 10.1021/bi801480r] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Emma J. Murphy
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester, LE1 9HN, England U.K., and Department of Biochemistry and Henry Wellcome Laboratories for Structural Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester, LE1 9HN, England U.K
| | - Clive L. Metcalfe
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester, LE1 9HN, England U.K., and Department of Biochemistry and Henry Wellcome Laboratories for Structural Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester, LE1 9HN, England U.K
| | - Jaswir Basran
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester, LE1 9HN, England U.K., and Department of Biochemistry and Henry Wellcome Laboratories for Structural Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester, LE1 9HN, England U.K
| | - Peter C. E. Moody
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester, LE1 9HN, England U.K., and Department of Biochemistry and Henry Wellcome Laboratories for Structural Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester, LE1 9HN, England U.K
| | - Emma Lloyd Raven
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester, LE1 9HN, England U.K., and Department of Biochemistry and Henry Wellcome Laboratories for Structural Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester, LE1 9HN, England U.K
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22
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Kulys J, Dapkunas Z, Stupak R. Intensification of Biocatalytical Processes by Synergistic Substrate Conversion. Fungal Peroxidase Catalyzed N-Hydroxy Derivative Oxidation in Presence of 10-Propyl Sulfonic Acid Phenoxazine. Appl Biochem Biotechnol 2008; 158:445-56. [DOI: 10.1007/s12010-008-8415-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Accepted: 10/27/2008] [Indexed: 11/24/2022]
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23
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Purification, characterization, and gene cloning of Ceriporiopsis sp. strain MD-1 peroxidases that decolorize human hair melanin. Appl Environ Microbiol 2008; 74:5106-12. [PMID: 18586974 DOI: 10.1128/aem.00253-08] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ceriporiopsis sp. strain MD-1, isolated from forest soil, produced several extracellular enzymes that decolorized human hair melanin. Among them, three enzymes (E1, E2-1, and E2-2) were purified to homogeneity and characterized. The enzymes required hydrogen peroxide in their enzyme reactions and, typical of other fungal peroxidases, oxidized various phenol compounds such as guaiacol, but not 3,4-dimethoxybenzyl alcohol. The spectra of the three enzymes showed an absorption maximum at 406 nm, indicating that they were heme proteins. However, the A(406)/A(280) values of the enzymes were below 0.4, which was lower than those of other peroxidases. E2-1 and E2-2 were similar to each other in their molecular and catalytic properties, and they possibly represent products of posttranslational modifications and/or allelic variants of the same gene, mdcA. The corresponding cDNA was cloned and sequenced; the deduced amino acid sequence showed high identities to the manganese peroxidases from other microorganisms. The specific activities and K(m) values of E2-1 and E2-2 for synthetic and human hair melanins were much higher than those of Phanerochaete chrysosporium manganese peroxidase and lignin peroxidase.
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Metcalfe C, Macdonald IK, Murphy EJ, Brown KA, Raven EL, Moody PC. The Tuberculosis Prodrug Isoniazid Bound to Activating Peroxidases. J Biol Chem 2008; 283:6193-200. [DOI: 10.1074/jbc.m707412200] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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25
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Shang X, Wu J, Li Q. New Coordination Modes of Substituted Benzohydroxamic Acid with Dialkyltin(IV): Structural Diversity through Ligand Isomerization. Eur J Inorg Chem 2006. [DOI: 10.1002/ejic.200600546] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xian‐mei Shang
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan 030001, P. R. China
- School of Pharmaceutical Science, Tongji Medical College,Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, P. R. China
| | - Ji‐zhou Wu
- School of Pharmaceutical Science, Tongji Medical College,Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, P. R. China
| | - Qing‐shan Li
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan 030001, P. R. China
- School of Pharmaceutical Science, Tongji Medical College,Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, P. R. China
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26
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Kirton SB, Murray CW, Verdonk ML, Taylor RD. Prediction of binding modes for ligands in the cytochromes P450 and other heme-containing proteins. Proteins 2006; 58:836-44. [PMID: 15651036 DOI: 10.1002/prot.20389] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The cytochromes P450 (P450s) are a family of heme-containing monooxygenase enzymes involved in a variety of functions, including the metabolism of endogenous and exogenous substances in the human body. During lead optimization, and in drug development, many potential drug candidates are rejected because of the affinity they display for drug-metabolising P450s. Recently, crystal structures of human enzymes involved in drug metabolism have been determined, significantly augmenting the prospect of using structure-based design to modulate the binding and metabolizing properties of compounds against P450 proteins. An important step in the application of structure-based metabolic optimization is the accurate prediction of docking modes in heme binding proteins. In this paper we assess the performance of the docking program GOLD at predicting the binding mode of 45 heme-containing complexes. We achieved success rates of 64% and 57% for Chemscore and Goldscore respectively; these success rates are significantly lower than the value of 79% observed with both scoring functions for the full GOLD validation set. Re-parameterization of metal-acceptor interactions and lipophilicity of planar nitrogen atoms in the scoring functions resulted in a significant increase in the percentage of successful dockings against the heme binding proteins (Chemscore 73%, Goldscore 65%). The modified scoring functions will be useful in docking applications on P450 enzymes and other heme binding proteins.
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27
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Larrondo L, Gonzalez A, Perez Acle T, Cullen D, Vicuña R. The nop gene from Phanerochaete chrysosporium encodes a peroxidase with novel structural features. Biophys Chem 2005; 116:167-73. [PMID: 15950829 DOI: 10.1016/j.bpc.2005.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2005] [Accepted: 03/05/2005] [Indexed: 10/25/2022]
Abstract
Inspection of the genome of the ligninolytic basidiomycete Phanerochaete chrysosporium revealed an unusual peroxidase_like sequence. The corresponding full length cDNA was sequenced and an archetypal secretion signal predicted. The deduced mature protein (NoP, novel peroxidase) contains 295 aa residues and is therefore considerably shorter than other Class II (fungal) peroxidases, such as lignin peroxidases and manganese peroxidases. Comparative modeling of NoP was conducted using the crystal structures of Coprinus cinereus and Arthromyces ramosus peroxidases as templates. The model was validated by molecular dynamics and showed several novel structural features. In particular, NoP has only three disulfide bridges and tryptophan replaces the distal phenylalanine within the heme pocket.
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Affiliation(s)
- Luisf Larrondo
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia, Universidad Católica de Chile, Santiago, Chile and Instituto Milenio de Biología Fundamental y Aplicada, Alameda 340, Santiago, Chile
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28
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Bertrand T, Eady NAJ, Jones JN, Nagy JM, Jamart-Grégoire B, Raven EL, Brown KA. Crystal Structure of Mycobacterium tuberculosis Catalase-Peroxidase. J Biol Chem 2004; 279:38991-9. [PMID: 15231843 DOI: 10.1074/jbc.m402382200] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Mycobacterium tuberculosis catalase-peroxidase is a multifunctional heme-dependent enzyme that activates the core anti-tuberculosis drug isoniazid. Numerous studies have been undertaken to elucidate the enzyme-dependent mechanism of isoniazid activation, and it is well documented that mutations that reduce activity or inactivate the catalase-peroxidase lead to increased levels of isoniazid resistance in M. tuberculosis. Interpretation of the catalytic activities and the effects of mutations upon the action of the enzyme to date have been limited due to the lack of a three-dimensional structure for this enzyme. In order to provide a more accurate model of the three-dimensional structure of the M. tuberculosis catalase-peroxidase, we have crystallized the enzyme and now report its crystal structure refined to 2.4-A resolution. The structure reveals new information about dimer assembly and provides information about the location of residues that may play a role in catalysis including candidates for protein-based radical formation. Modeling and computational studies suggest that the binding site for isoniazid is located near the delta-meso heme edge rather than in a surface loop structure as currently proposed. The availability of a crystal structure for the M. tuberculosis catalase-peroxidase also permits structural and functional effects of mutations implicated in causing elevated levels of isoniazid resistance in clinical isolates to be interpreted with improved confidence.
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Affiliation(s)
- Thomas Bertrand
- Department of Biological Sciences, Centre for Molecular Microbiology and Infection, Flowers Building, Imperial College London, London SW7 2AZ, United Kingdom
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29
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Pierattelli R, Banci L, Eady NAJ, Bodiguel J, Jones JN, Moody PCE, Raven EL, Jamart-Grégoire B, Brown KA. Enzyme-catalyzed Mechanism of Isoniazid Activation in Class I and Class III Peroxidases. J Biol Chem 2004; 279:39000-9. [PMID: 15231844 DOI: 10.1074/jbc.m402384200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
There is an urgent need to understand the mechanism of activation of the frontline anti-tuberculosis drug isoniazid by the Mycobacterium tuberculosis catalase-peroxidase. To address this, a combination of NMR spectroscopic, biochemical, and computational methods have been used to obtain a model of the frontline anti-tuberculosis drug isoniazid bound to the active site of the class III peroxidase, horseradish peroxidase C. This information has been used in combination with the new crystal structure of the M. tuberculosis catalase-peroxidase to predict the mode of INH binding across the class I heme peroxidase family. An enzyme-catalyzed mechanism for INH activation is proposed that brings together structural, functional, and spectroscopic data from a variety of sources. Collectively, the information not only provides a molecular basis for understanding INH activation by the M. tuberculosis catalase-peroxidase but also establishes a new conceptual framework for testing hypotheses regarding the enzyme-catalyzed turnover of this compound in a number of heme peroxidases.
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Affiliation(s)
- Roberta Pierattelli
- Dipartimento di Chimica e Centro Risonanze Magnetiche, Universitá di Firenze, Polo Scientifico, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
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30
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Marmion C, Griffith D, Nolan K. Hydroxamic Acids − An Intriguing Family of Enzyme Inhibitors and Biomedical Ligands. Eur J Inorg Chem 2004. [DOI: 10.1002/ejic.200400221] [Citation(s) in RCA: 149] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Celine J. Marmion
- Centre for Synthesis and Chemical Biology, Department of Pharmaceutical & Medicinal Chemistry, Royal College of Surgeons in Ireland, 123 St. Stephen’s Green, Dublin 2, Ireland, Fax: (internat.) + 353‐1‐4022168
| | - Darren Griffith
- Centre for Synthesis and Chemical Biology, Department of Pharmaceutical & Medicinal Chemistry, Royal College of Surgeons in Ireland, 123 St. Stephen’s Green, Dublin 2, Ireland, Fax: (internat.) + 353‐1‐4022168
| | - Kevin B. Nolan
- Centre for Synthesis and Chemical Biology, Department of Pharmaceutical & Medicinal Chemistry, Royal College of Surgeons in Ireland, 123 St. Stephen’s Green, Dublin 2, Ireland, Fax: (internat.) + 353‐1‐4022168
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31
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Gupta K, Selinsky BS, Kaub CJ, Katz AK, Loll PJ. The 2.0 A resolution crystal structure of prostaglandin H2 synthase-1: structural insights into an unusual peroxidase. J Mol Biol 2004; 335:503-18. [PMID: 14672659 DOI: 10.1016/j.jmb.2003.10.073] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Prostaglandin H2 synthase (EC 1.14.99.1) is an integral membrane enzyme containing a cyclooxygenase site, which is the target for the non-steroidal anti-inflammatory drugs, and a spatially distinct peroxidase site. Previous crystallographic studies of this clinically important drug target have been hindered by low resolution. We present here the 2.0 A resolution X-ray crystal structure of ovine prostaglandin H2 synthase-1 in complex with alpha-methyl-4-biphenylacetic acid, a defluorinated analog of the non-steroidal anti-inflammatory drug flurbiprofen. Detergent molecules are seen to bind to the protein's membrane-binding domain, and their positions suggest the depth to which this domain is likely to penetrate into the lipid bilayer. The relation of the enzyme's proximal heme ligand His388 to the heme iron is atypical for a peroxidase; the iron-histidine bond is unusually long and a substantial tilt angle is observed between the heme and imidazole planes. A molecule of glycerol, used as a cryoprotectant during diffraction experiments, is seen to bind in the peroxidase site, offering the first view of any ligand in this active site. Insights gained from glycerol binding may prove useful in the design of a peroxidase-specific ligand.
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Affiliation(s)
- Kushol Gupta
- Department of Biochemistry, Drexel University College of Medicine, 245 N 15th Street, Mailstop 497, Philadelphia, PA 19102-1192, USA
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Tegoni M, Dallavalle F, Belosi B, Remelli M. Unexpected formation of a copper(ii) 12-metallacrown-4 with (S)-glutamic-γ-hydroxamic acid: a thermodynamic and spectroscopic study in aqueous solution. Dalton Trans 2004:1329-33. [PMID: 15252625 DOI: 10.1039/b316607d] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The equilibria of copper(II) with (S)-glutamic-gamma-hydroxamic acid (H2L) were investigated in aqueous solution by different techniques: glass electrode potentiometry; calorimetry; VIS and CD spectrophotometry; and ES-MS. An unexpected pentacopper(II) 12-metallacrown-4 [Cu5L4H(-4)](2-) was detected, analogous to those well known formed by alpha- and beta-aminohydroxamic acids, but of lower stability. Another five species were found: [CuLH]+; [CuL2H2]; [Cu2L2]; [CuL2H]-; and [CuL2]2-. Their structures are proposed based on both spectroscopic and calorimetric data.
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Affiliation(s)
- Matteo Tegoni
- Dipartimento di Chimica Generale ed Inorganica, Chimica Analitica, Chimica Fisica, Universita di Parma, Parco Area delle Scienze, 17A, 43100 Parma, Italy
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33
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Martı́nez AT. Molecular biology and structure-function of lignin-degrading heme peroxidases. Enzyme Microb Technol 2002. [DOI: 10.1016/s0141-0229(01)00521-x] [Citation(s) in RCA: 321] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kulys J, Deussen HJ, Krikstopaitis K, Lolck R, Schneider P, Ziemys A. N-Arylhydroxamic Acids as Novel Oxidoreductase Substrates. European J Org Chem 2001. [DOI: 10.1002/1099-0690(200109)2001:18<3475::aid-ejoc3475>3.0.co;2-k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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35
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Wariishi H, Nonaka D, Johjima T, Nakamura N, Naruta Y, Kubo S, Fukuyama K. Direct binding of hydroxylamine to the heme iron of Arthromyces ramosus peroxidase. Substrate analogue that inhibits compound I formation in a competetive manner. J Biol Chem 2000; 275:32919-24. [PMID: 10915789 DOI: 10.1074/jbc.m004223200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The interaction of hydroxylamine (HA) with Arthromyces ramosus peroxidase (ARP) was investigated by kinetic, spectroscopic, and x-ray crystallographic techniques. HA inhibited the reaction of native ARP with H(2)O(2) in a competitive manner. Electron absorption and resonance Raman spectroscopic studies indicated that pentacoordinate high spin species of native ARP are converted to hexacoordinate low spin species upon the addition of HA, strongly suggesting the occurrence of a direct interaction of HA with ARP heme iron. Kinetic analysis exhibited that the apparent dissociation constant is 6.2 mm at pH 7.0 and that only one HA molecule likely binds to the vicinity of the heme. pH dependence of HA binding suggested that the nitrogen atom of HA could be involved in the interaction with the heme iron. X-ray crystallographic analysis of ARP in complex with HA at 2.0 A resolution revealed that the electron density ascribed to HA is located in the distal pocket between the heme iron and the distal His(56). HA seems to directly interact with the heme iron but is too far away to interact with Arg(52). In HA, it is likely that the nitrogen atom is coordinated to the heme iron and that hydroxyl group is hydrogen bonded to the distal His(56).
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Affiliation(s)
- H Wariishi
- Department of Forest Products and the Institute for Fundamental Research of Organic Chemistry, Kyushu University, Fukuoka 812-8581, Japan
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