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Liang J, Cheng ZY, Shan F, Cao Y, Xia QR. Serum indoleamine 2, 3-dioxygenase and tryptophan-2, 3-dioxygenase: potential biomarkers for the diagnosis of major depressive disorder. Psychopharmacology (Berl) 2024; 241:1093-1099. [PMID: 38286858 DOI: 10.1007/s00213-024-06542-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 01/22/2024] [Indexed: 01/31/2024]
Abstract
OBJECTIVE The objective of this study was to observe the changes in the levels of indoleamine 2, 3-dioxygenase (IDO) and tryptophan-2, 3-dioxygenase (TDO) in patients with major depressive disorder (MDD) and investigate their potential role as novel biomarkers for diagnosing MDD. METHODS A total of 55 MDD patients and 55 healthy controls (HC) were enrolled in the study. The severity of MDD was assessed using the 24-item Hamilton Depression Rating Scale (HAMD-24) before and after treatment. The serum concentrations of IDO and TDO were measured at baseline and after treatment. The correlations between the serum levels of IDO and TDO and HAMD-24 scores were evaluated using Pearson's correlation test. Receiver operating characteristic (ROC) curve analysis was used to evaluate the area under the curve (AUC) of serum levels of IDO and TDO for discriminating MDD patients from HC. RESULTS The serum IDO and TDO concentrations were significantly higher in patients with MDD at baseline than in healthy controls, and decreased significantly after 2 weeks or 1 month of treatment. The levels of IDO and TDO were significantly positively correlated with HAMD-24 scores. Furthermore, the AUC values for IDO and TDO were 0.999 and 0.966, respectively. CONCLUSION The study suggests that serum IDO and TDO may serve as novel biomarkers for diagnosing MDD. These findings may lead to a better understanding of the pathogenesis of MDD and the development of new therapeutic targets.
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Affiliation(s)
- Jun Liang
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, China
- Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, China
- Psychopharmacology Research Laboratory, Anhui Mental Health Center, Hefei, China
- Anhui Clinical Research Center for Mental Disorders, Hefei, China
| | - Zhuo-Yu Cheng
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, China
- Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, China
- Psychopharmacology Research Laboratory, Anhui Mental Health Center, Hefei, China
- Anhui Clinical Research Center for Mental Disorders, Hefei, China
| | - Feng Shan
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, China
- Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, China
- Psychopharmacology Research Laboratory, Anhui Mental Health Center, Hefei, China
- Anhui Clinical Research Center for Mental Disorders, Hefei, China
| | - Yin Cao
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, China
- Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, China
- Psychopharmacology Research Laboratory, Anhui Mental Health Center, Hefei, China
- Anhui Clinical Research Center for Mental Disorders, Hefei, China
| | - Qing-Rong Xia
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, China.
- Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, China.
- Psychopharmacology Research Laboratory, Anhui Mental Health Center, Hefei, China.
- Anhui Clinical Research Center for Mental Disorders, Hefei, China.
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2
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Nolan K, Wang Y. Combined spectroscopic and structural approaches to explore the mechanism of histidine-ligated heme-dependent aromatic oxygenases. Methods Enzymol 2023; 685:405-432. [PMID: 37245909 PMCID: PMC11057917 DOI: 10.1016/bs.mie.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The emergence of histidine-ligated heme-dependent aromatic oxygenases (HDAOs) has greatly enriched heme chemistry, and more studies are required to appreciate the diversity found in His-ligated heme proteins. This chapter describes recent methods in probing the HDAO mechanisms in detail, along with the discussion on how they can benefit structure-function studies of other heme systems. The experimental details are centered on studies of TyrHs, followed by explanation of how the results obtained would advance the understanding of the specific enzyme and also HDAOs. Spectroscopic methods, namely, electronic absorption and EPR spectroscopies, and X-ray crystallography are valuable techniques commonly used to characterize the properties of the heme center and the nature of heme-based intermediate. Herein, we show that the combination of these tools are extremely powerful, not only because one can acquire electronic, magnetic, and conformational information from different phases, but also because of the advantages brought by spectroscopic characterization on crystal samples.
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Affiliation(s)
- Katie Nolan
- Department of Chemistry, University of Georgia, Athens, GA, United States
| | - Yifan Wang
- Department of Chemistry, University of Georgia, Athens, GA, United States.
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3
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Wu X, Ma X, Zhong Y, Chen W, Xu M, Zhang H, Wang L, Tu X, Han Z, Zhao W, Wu Z, Moschos SJ, Li Z. Development of [ 18F]F-5-OMe-Tryptophans through Photoredox Radiofluorination: A New Method to Access Tryptophan-Based PET Agents. J Med Chem 2023; 66:3262-3272. [PMID: 36826835 PMCID: PMC10463268 DOI: 10.1021/acs.jmedchem.2c01544] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Although various radiolabeled tryptophan analogs have been developed to monitor tryptophan metabolism using positron emission tomography (PET) for various human diseases including melanoma and other cancers, their application can be limited due to the complicated synthesis process. In this study, we demonstrated that photoredox radiofluorination represents a simple method to access novel tryptophan-based PET agents. In brief, 4-F-5-OMe-tryptophans (l/d-T13) and 6-F-5-OMe-tryptophans (l/d-T18) were easily synthesized. The 18F-labeled analogs were produced by photoredox radiofluorination with radiochemical yields ranging from 2.6 ± 0.5% to 32.4 ± 4.1% (3 ≤ n ≤ 5, enantiomeric excess ≥ 99.0%) and over 98.0% radiochemical purity. Small animal imaging showed that l-[18F]T13 achieved 9.58 ± 0.26%ID/g tumor uptake and good contrast in B16F10 tumor-bearing mice (n = 3). Clearly, l-[18F]T13 exhibited prominent tumor uptake, warranting future evaluations of its potential usage in precise immunotherapy monitoring.
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Affiliation(s)
- Xuedan Wu
- Department of Radiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Biomedical Research Imaging Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xinrui Ma
- Department of Radiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Biomedical Research Imaging Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yaofeng Zhong
- Department of Radiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Biomedical Research Imaging Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Wei Chen
- Department of Radiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Biomedical Research Imaging Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Muyun Xu
- Department of Radiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Biomedical Research Imaging Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - He Zhang
- Department of Radiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Biomedical Research Imaging Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Li Wang
- Department of Radiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Biomedical Research Imaging Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xianshuang Tu
- Department of Radiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Biomedical Research Imaging Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Zhaoguo Han
- Department of Radiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Biomedical Research Imaging Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Weiling Zhao
- Department of Radiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Biomedical Research Imaging Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Zhanhong Wu
- Department of Radiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Biomedical Research Imaging Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA
| | - Stergios J. Moschos
- Lineberger Comprehensive Cancer Center, The University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA
- Departments of Medicine, Division of Medical Oncology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Zibo Li
- Department of Radiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Biomedical Research Imaging Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA
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4
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Emamian S, Ireland KA, Purohit V, McWhorter KL, Maximova O, Allen W, Jensen S, Casa DM, Pushkar Y, Davis KM. X-ray Emission Spectroscopy of Single Protein Crystals Yields Insights into Heme Enzyme Intermediates. J Phys Chem Lett 2023; 14:41-48. [PMID: 36566390 PMCID: PMC9990082 DOI: 10.1021/acs.jpclett.2c03018] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Enzyme reactivity is often enhanced by changes in oxidation state, spin state, and metal-ligand covalency of associated metallocofactors. The development of spectroscopic methods for studying these processes coincidentally with structural rearrangements is essential for elucidating metalloenzyme mechanisms. Herein, we demonstrate the feasibility of collecting X-ray emission spectra of metalloenzyme crystals at a third-generation synchrotron source. In particular, we report the development of a von Hamos spectrometer for the collection of Fe Kβ emission optimized for analysis of dilute biological samples. We further showcase its application in crystals of the immunosuppressive heme-dependent enzyme indoleamine 2,3-dioxygenase. Spectra from protein crystals in different states were compared with relevant reference compounds. Complementary density functional calculations assessing covalency support our spectroscopic analysis and identify active site conformations that correlate to high- and low-spin states. These experiments validate the suitability of an X-ray emission approach for determining spin states of previously uncharacterized metalloenzyme reaction intermediates.
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Affiliation(s)
- Sahand Emamian
- Department of Physics, Emory University, Atlanta, GA 30322, USA
| | | | - Vatsal Purohit
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | | | - Olga Maximova
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Winter Allen
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Scott Jensen
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Diego M. Casa
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Yulia Pushkar
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
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5
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Zheng Y, Deng W, Liu D, Li Y, Peng K, Lorimer GH, Wang J. Redox and spectroscopic properties of mammalian nitrite reductase-like hemoproteins. J Inorg Biochem 2022; 237:111982. [PMID: 36116154 DOI: 10.1016/j.jinorgbio.2022.111982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 01/18/2023]
Abstract
Besides the canonical pathway of L-arginine oxidation to produce nitric oxide (NO) in vivo, the nitrate-nitrite-NO pathway has been widely accepted as another source for circulating NO in mammals, especially under hypoxia. To date, there have been at least ten heme-containing nitrite reductase-like proteins discovered in mammals with activities mainly identified in vitro, including four globins (hemoglobin, myoglobin, neuroglobin (Ngb), cytoglobin (Cygb)), three mitochondrial respiratory chain enzymes (cytochrome c oxidase, cytochrome bc1, cytochrome c), and three other heme proteins (endothelial nitric oxide synthase, cytochrome P450 and indoleamine 2,3-dioxygenase 1 (IDO1)). The pathophysiological functions of these proteins are closely related to their redox and spectroscopic properties, as well as their protein structure, although the physiological roles of Ngb, Cygb and IDO1 remain unclear. So far, comprehensive summaries of the redox and spectroscopic properties of these nitrite reductase-like hemoproteins are still lacking. In this review, we have mainly summarized the published data on the application of ultraviolet-visible, electron paramagnetic resonance, circular dichroism and resonance Raman spectroscopies, and X-ray crystallography in studying nitrite reductase-like activity of these 10 proteins, in order to sort out the relationships among enzymatic function, structure and spectroscopic characterization, which might help in understanding their roles in redox biology and medicine.
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Affiliation(s)
- Yunlong Zheng
- Hubei University of Technology Autism & Depression Diagnosis and Intervention Institute, Hubei University of Technology, Wuhan, Hubei, China; International Joint Research Center for General Health, Precision Medicine & Nutrition, Hubei University of Technology, Wuhan, Hubei, China; Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, Hubei, China
| | - Wenwen Deng
- Hubei University of Technology Autism & Depression Diagnosis and Intervention Institute, Hubei University of Technology, Wuhan, Hubei, China; International Joint Research Center for General Health, Precision Medicine & Nutrition, Hubei University of Technology, Wuhan, Hubei, China; Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, Hubei, China
| | - Di Liu
- Hubei University of Technology Autism & Depression Diagnosis and Intervention Institute, Hubei University of Technology, Wuhan, Hubei, China; International Joint Research Center for General Health, Precision Medicine & Nutrition, Hubei University of Technology, Wuhan, Hubei, China; Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, Hubei, China
| | - Youheng Li
- Hubei University of Technology Autism & Depression Diagnosis and Intervention Institute, Hubei University of Technology, Wuhan, Hubei, China; International Joint Research Center for General Health, Precision Medicine & Nutrition, Hubei University of Technology, Wuhan, Hubei, China; Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, Hubei, China
| | - Kang Peng
- Hubei University of Technology Autism & Depression Diagnosis and Intervention Institute, Hubei University of Technology, Wuhan, Hubei, China; International Joint Research Center for General Health, Precision Medicine & Nutrition, Hubei University of Technology, Wuhan, Hubei, China; Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, Hubei, China
| | | | - Jun Wang
- Hubei University of Technology Autism & Depression Diagnosis and Intervention Institute, Hubei University of Technology, Wuhan, Hubei, China; International Joint Research Center for General Health, Precision Medicine & Nutrition, Hubei University of Technology, Wuhan, Hubei, China; Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, Hubei, China.
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6
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Pallotta MT, Rossini S, Suvieri C, Coletti A, Orabona C, Macchiarulo A, Volpi C, Grohmann U. Indoleamine 2,3-dioxygenase 1 (IDO1): an up-to-date overview of an eclectic immunoregulatory enzyme. FEBS J 2022; 289:6099-6118. [PMID: 34145969 PMCID: PMC9786828 DOI: 10.1111/febs.16086] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/04/2021] [Accepted: 06/18/2021] [Indexed: 12/30/2022]
Abstract
Indoleamine 2,3-dioxygenase 1 (IDO1) catalyzes the initial rate-limiting step in the degradation of the essential amino acid tryptophan along the kynurenine pathway. When discovered more than 50 years ago, IDO1 was thought to be an effector molecule capable of mediating a survival strategy based on the deprivation of bacteria and tumor cells of the essential amino acid tryptophan. Since 1998, when tryptophan catabolism was discovered to be crucially involved in the maintenance of maternal T-cell tolerance, IDO1 has become the focus of several laboratories around the world. Indeed, IDO1 is now considered as an authentic immune regulator not only in pregnancy, but also in autoimmune diseases, chronic inflammation, and tumor immunity. However, in the last years, a bulk of new information-including structural, biological, and functional evidence-on IDO1 has come to light. For instance, we now know that IDO1 has a peculiar conformational plasticity and, in addition to a complex and highly regulated catalytic activity, is capable of performing a nonenzymic function that reprograms the expression profile of immune cells toward a highly immunoregulatory phenotype. With this state-of-the-art review, we aimed at gathering the most recent information obtained for this eclectic protein as well as at highlighting the major unresolved questions.
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Affiliation(s)
| | - Sofia Rossini
- Department of Medicine and SurgeryUniversity of PerugiaItaly
| | - Chiara Suvieri
- Department of Medicine and SurgeryUniversity of PerugiaItaly
| | - Alice Coletti
- Department of Pharmaceutical SciencesUniversity of PerugiaItaly
| | - Ciriana Orabona
- Department of Medicine and SurgeryUniversity of PerugiaItaly
| | | | - Claudia Volpi
- Department of Medicine and SurgeryUniversity of PerugiaItaly
| | - Ursula Grohmann
- Department of Medicine and SurgeryUniversity of PerugiaItaly
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7
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Yuasa HJ. Inhibitory effect of ascorbate on tryptophan 2,3-dioxygenase. J Biochem 2022; 171:653-661. [PMID: 35244712 DOI: 10.1093/jb/mvac024] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/02/2022] [Indexed: 11/13/2022] Open
Abstract
Tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) catalyze the same reaction, oxidative cleavage of L-tryptophan (L-Trp) to N-formyl-kynurenine. In both enzymes, the ferric (FeIII) form is inactive, and ascorbate (Asc) is frequently used as a reductant in in vitro assays to activate the enzymes by reducing the heme iron. Recently, it has been reported that Asc activates IDO2 by acting as a reductant, however, it is also a competitive inhibitor of the enzyme. Here, the effect of Asc on human TDO (hTDO) is investigated. Similar to its interaction with IDO2, Asc acts as both a reductant and a competitive inhibitor of hTDO in the absence of catalase, and its inhibitory effect was enhanced by the addition of H2O2. Interestingly, however, no inhibitory effect of Asc was observed in the presence of catalase. TDO is known to be activated by H2O2 and a ferryl-oxo (FeIV=O) intermediate (Compound II) is generated during the activation process. The observation that Asc acts as a competitive inhibitor of hTDO only in the absence of catalase can be explained by assuming that the target of Asc is Compound II. Asc seems to compete with L-Trp in an unusual manner.
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Affiliation(s)
- Hajime Julie Yuasa
- Laboratory of Biochemistry, Department of Chemistry and Biotechnology, Faculty of Science and Technology, National University Corporation Kochi University, Kochi 780-8520, Japan
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8
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Mammoli A, Riccio A, Bianconi E, Coletti A, Camaioni E, Macchiarulo A. One Key and Multiple Locks: Substrate Binding in Structures of Tryptophan Dioxygenases and Hydroxylases. ChemMedChem 2021; 16:2732-2743. [PMID: 34137184 PMCID: PMC8518741 DOI: 10.1002/cmdc.202100312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 06/14/2021] [Indexed: 12/18/2022]
Abstract
Since its discovery at the beginning of the past century, the essential nutrient l-Tryptophan (l-Trp) and its catabolic pathways have acquired an increasing interest in an ever wider scientific community for their pivotal roles in underlying many important physiological functions and associated pathological conditions. As a consequence, enzymes catalyzing rate limiting steps along l-Trp catabolic pathways - including IDO1, TDO, TPH1 and TPH2 - have turned to be interesting drug targets for the design and development of novel therapeutic agents for different disorders such as carcinoid syndrome, cancer and autoimmune diseases. This article provides a fresh comparative overview on the most recent advancements that crystallographic studies, biophysical and computational works have brought on structural aspects and molecular recognition patterns of these enzymes toward l-Trp. Finally, a conformational analysis of l-Trp is also discussed as part of the molecular recognition process governing the binding of a substrate to its cognate enzymes.
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Affiliation(s)
- Andrea Mammoli
- Department of Pharmaceutical SciencesUniversity of PerugiaVia del Liceo N. 106123PerugiaItaly
| | - Alessandra Riccio
- Department of Pharmaceutical SciencesUniversity of PerugiaVia del Liceo N. 106123PerugiaItaly
| | - Elisa Bianconi
- Department of Pharmaceutical SciencesUniversity of PerugiaVia del Liceo N. 106123PerugiaItaly
| | - Alice Coletti
- Department of Medicine and SurgeryUniversity of PerugiaP. le Gambuli06132PerugiaItaly
| | - Emidio Camaioni
- Department of Pharmaceutical SciencesUniversity of PerugiaVia del Liceo N. 106123PerugiaItaly
| | - Antonio Macchiarulo
- Department of Pharmaceutical SciencesUniversity of PerugiaVia del Liceo N. 106123PerugiaItaly
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9
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Yuasa HJ, Stocker R. Methylene blue and ascorbate interfere with the accurate determination of the kinetic properties of IDO2. FEBS J 2021; 288:4892-4904. [PMID: 33686747 DOI: 10.1111/febs.15806] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/16/2021] [Accepted: 03/08/2021] [Indexed: 11/30/2022]
Abstract
Indoleamine 2,3-dioxygenases (IDOs) catalyze the oxidative cleavage of L-tryptophan (Trp) to N-formylkynurenine. Two IDOs, IDO1 and IDO2, are present in vertebrates. IDO1 is a high-affinity Trp-degrading enzyme involved in several physiological processes. By comparison, IDO2 generally has been reported to have low affinity (high Km -value) for Trp, and the enzyme's in vivo function remains unclear. Using IDOs from different species, we show that compared with ferrous-oxy (Fe2+ -O2 ) IDO1, Fe2+ -O2 IDO2 is substantially more stable and engages in multiple turnovers of the reaction in the absence of a reductant. Without reductant, Fe2+ -O2 IDO2 showed Km -values in the range of 80-356 μM, that is, values substantially lower than reported previously and close to the physiological concentrations of Trp. Methylene blue and ascorbate (Asc), used commonly as the reducing system for IDO activity determination, significantly affected the enzymatic activity of IDO2: In combination, the two reductants increased the apparent Km - and kcat -values 8- to 117-fold and 2-fold, respectively. Asc alone both activated and inhibited IDO2 by acting as a source of electrons and as a weak competitive inhibitor, respectively. In addition, ferric (Fe3+ ) IDO1 and IDO2 exhibited weak dioxygenase activity, similar to tryptophan 2,3-dioxygenase. Our results shed new light in the enzymatic activity of IDO2, and they support the view that this isoform of IDO also participates in the metabolism of Trp in vivo.
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Affiliation(s)
- Hajime J Yuasa
- Laboratory of Biochemistry, Department of Chemistry and Biotechnology, Faculty of Science and Technology, National University Corporation Kochi University, Japan
| | - Roland Stocker
- Arterial Inflammation and Redox Biology Group, Heart Research Institute, Newtown, NSW, Australia
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10
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Greco FA, Albini E, Coletti A, Dolciami D, Carotti A, Orabona C, Grohmann U, Macchiarulo A. Tracking Hidden Binding Pockets Along the Molecular Recognition Path ofl‐Trp to Indoleamine 2,3‐Dioxygenase 1. ChemMedChem 2019; 14:2084-2092. [DOI: 10.1002/cmdc.201900529] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/17/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Francesco A. Greco
- Department of Pharmaceutical SciencesUniversity of Perugia via del liceo n.1 06123 Perugia Italy
| | - Elisa Albini
- Department of Experimental MedicineUniversity of Perugia P.le Gambuli 06132 Perugia Italy
| | - Alice Coletti
- Department of Pharmaceutical SciencesUniversity of Perugia via del liceo n.1 06123 Perugia Italy
| | - Daniela Dolciami
- Department of Pharmaceutical SciencesUniversity of Perugia via del liceo n.1 06123 Perugia Italy
| | - Andrea Carotti
- Department of Pharmaceutical SciencesUniversity of Perugia via del liceo n.1 06123 Perugia Italy
| | - Ciriana Orabona
- Department of Experimental MedicineUniversity of Perugia P.le Gambuli 06132 Perugia Italy
| | - Ursula Grohmann
- Department of Experimental MedicineUniversity of Perugia P.le Gambuli 06132 Perugia Italy
| | - Antonio Macchiarulo
- Department of Pharmaceutical SciencesUniversity of Perugia via del liceo n.1 06123 Perugia Italy
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11
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Nelp MT, Zheng V, Davis KM, Stiefel KJE, Groves JT. Potent Activation of Indoleamine 2,3-Dioxygenase by Polysulfides. J Am Chem Soc 2019; 141:15288-15300. [PMID: 31436417 DOI: 10.1021/jacs.9b07338] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Indoleamine 2,3-dioxygenase (IDO1) is a heme enzyme that catalyzes the oxygenation of the indole ring of tryptophan to afford N-formylkynurenine. This activity significantly suppresses the immune response, mediating inflammation and autoimmune reactions. These consequential effects are regulated through redox changes in the heme cofactor of IDO1, which autoxidizes to the inactive ferric state during turnover. This change in redox status increases the lability of the heme cofactor leading to further suppression of activity. The cell can thus regulate IDO1 activity through the supply of heme and reducing agents. We show here that polysulfides bind to inactive ferric IDO1 and reduce it to the oxygen-binding ferrous state, thus activating IDO1 to maximal turnover even at low, physiologically significant concentrations. The on-rate for hydrogen disulfide binding to ferric IDO1 was found to be >106 M-1 s-1 at pH 7 using stopped-flow spectrometry. Fe K-edge XANES and EPR spectroscopy indicated initial formation of a low-spin ferric sulfur-bound species followed by reduction to the ferrous state. The μM affinity of polysulfides for IDO1 implicates these polysulfides as important signaling factors in immune regulation through the kynurenine pathway. Tryptophan significantly enhanced the relatively lower-affinity binding of hydrogen sulfide to IDO1, inspiring the use of the small molecule 3-mercaptoindole (3MI), which selectively binds to and activates ferric IDO1. 3MI sustains turnover by catalytically transferring reducing equivalents from glutathione to IDO1, representing a novel strategy of upregulating innate immunosuppression for treatment of autoimmune disorders. Reactive sulfur species are thus likely unrecognized immune-mediators with potential as therapeutic agents through these interactions with IDO1.
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Affiliation(s)
- Micah T Nelp
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
| | - Vincent Zheng
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
| | - Katherine M Davis
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
| | - Katherine J E Stiefel
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
| | - John T Groves
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
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12
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Yuasa HJ. A comprehensive comparison of the metazoan tryptophan degrading enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1868:140247. [PMID: 31276825 DOI: 10.1016/j.bbapap.2019.06.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/28/2019] [Accepted: 06/30/2019] [Indexed: 01/15/2023]
Abstract
Tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) have an independent origin; however, they have distinctly evolved to catalyze the same reaction. In general, TDO is a single-copy gene in each metazoan species, and TDO enzymes demonstrate similar enzyme activity regardless of their biological origin. In contrast, multiple IDO paralogues are observed in many species, and they display various enzymatic properties. Similar to vertebrate IDO2, invertebrate IDOs generally show low affinity/catalytic efficiency for L-Trp. Meanwhile, two IDO isoforms from scallop (IDO-I and -III) and sponge IDOs show high L-Trp catalytic activity, which is comparable to vertebrate IDO1. Site-directed mutagenesis experiments have revealed that primarily two residues, Tyr located at the 2nd residue on the F-helix (F2nd) and His located at the 9th residue on the G-helix (G9th), are crucial for the high affinity/catalytic efficiency of these 'high performance' invertebrate IDOs. Conversely, those two amino acid substitutions (F2nd/Tyr and G9th/His) resulted in high affinity and catalytic activity in other molluscan 'low performance' IDOs. In human IDO1, G9th is Ser167, whereas the counterpart residue of G9th in human TDO is His76. Previous studies have shown that Ser167 could not be substituted by His because the human IDO1 Ser167His variant showed significantly low catalytic activity. However, this may be specific for human IDO1 because G9th/His was demonstrated to be very effective in increasing the L-Trp affinity even in vertebrate IDOs. Therefore, these findings indicate that the active sites of TDO and IDO are more similar to each other than previously expected.
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Affiliation(s)
- Hajime Julie Yuasa
- Laboratory of Biochemistry, Department of Applied Science, Faculty of Science and Technology, National University Corporation Kochi University, Kochi 780-8520, Japan.
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13
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Wang Y, Davis I, Shin I, Wherritt DJ, Griffith WP, Dornevil K, Colabroy KL, Liu A. Biocatalytic Carbon-Hydrogen and Carbon-Fluorine Bond Cleavage through Hydroxylation Promoted by a Histidyl-Ligated Heme Enzyme. ACS Catal 2019; 9:4764-4776. [PMID: 31355048 DOI: 10.1021/acscatal.9b00231] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
LmbB2 is a peroxygenase-like enzyme that hydroxylates L-tyrosine to L-3,4-dihydroxyphenylalanine (DOPA) in the presence of hydrogen peroxide. However, its heme cofactor is ligated by a proximal histidine, not cysteine. We show that LmbB2 can oxidize L-tyrosine analogs with ring-deactivated substituents such as 3-nitro-, fluoro-, chloro-, iodo-L-tyrosine. We also found that the 4-hydroxyl group of the substrate is essential for reacting with the heme-based oxidant and activating the aromatic C-H bond. The most interesting observation of this study was obtained with 3-fluoro-L-tyrosine as a substrate and mechanistic probe. The LmbB2-mediated catalytic reaction yielded two hydroxylated products with comparable populations, i.e., oxidative C-H bond cleavage at C5 to generate 3-fluoro-5-hydroxyl-L-tyrosine and oxygenation at C3 concomitant with a carbon-fluorine bond cleavage to yield DOPA and fluoride. An iron protein-mediated hydroxylation on both C-H and C-F bonds with multiple turnovers is unprecedented. Thus, this finding reveals a significant potential of biocatalysis in C-H/C-X bond (X = halogen) cleavage. Further 18O-labeling results suggest that the source of oxygen for hydroxylation is a peroxide, and that a commonly expected oxidation by a high-valent iron intermediate followed by hydrolysis is not supported for the C-F bond cleavage. Instead, the C-F bond cleavage is proposed to be initiated by a nucleophilic aromatic substitution mediated by the iron-hydroperoxo species. Based on the experimental results, two mechanisms are proposed to explain how LmbB2 hydroxylates the substrate and cleaves C-H/C-F bond. This study broadens the understanding of heme enzyme catalysis and sheds light on enzymatic applications in medicinal and environmental fields.
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Affiliation(s)
- Yifan Wang
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
| | - Ian Davis
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
| | - Inchul Shin
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
| | - Daniel J. Wherritt
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
| | - Wendell P. Griffith
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
| | - Kednerlin Dornevil
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
| | - Keri L. Colabroy
- Department of Chemistry, Muhlenberg College, Allentown, Pennsylvania 18104, United States
| | - Aimin Liu
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
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14
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Miyanokoshi M, Yokosawa T, Wakasugi K. Tryptophanyl-tRNA synthetase mediates high-affinity tryptophan uptake into human cells. J Biol Chem 2018; 293:8428-8438. [PMID: 29666190 DOI: 10.1074/jbc.ra117.001247] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 04/03/2018] [Indexed: 01/08/2023] Open
Abstract
The tryptophan (Trp) transport system has a high affinity and selectivity toward Trp, and has been reported to exist in both human and mouse macrophages. Although this system is highly expressed in interferon-γ (IFN-γ)-treated cells and indoleamine 2,3-dioxygenase 1 (IDO1)-expressing cells, its identity remains incompletely understood. Tryptophanyl-tRNA synthetase (TrpRS) is also highly expressed in IFN-γ-treated cells and also has high affinity and selectivity for Trp. Here, we investigated the effects of human TrpRS expression on Trp uptake into IFN-γ-treated human THP-1 monocytes or HeLa cells. Inhibition of human TrpRS expression by TrpRS-specific siRNAs decreased and overexpression of TrpRS increased Trp uptake into the cells. Of note, the TrpRS-mediated uptake system had more than hundred-fold higher affinity for Trp than the known System L amino acid transporter, promoted uptake of low Trp concentrations, and had very high Trp selectivity. Moreover, site-directed mutagenesis experiments indicated that Trp- and ATP-binding sites, but not tRNA-binding sites, in TrpRS are essential for TrpRS-mediated Trp uptake into the human cells. We further demonstrate that the addition of purified TrpRS to cell culture medium increases Trp uptake into cells. Taken together, our results reveal that TrpRS plays an important role in high-affinity Trp uptake into human cells.
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Affiliation(s)
- Miki Miyanokoshi
- From the Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan and
| | - Takumi Yokosawa
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Keisuke Wakasugi
- From the Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan and .,Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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15
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A single amino acid residue regulates the substrate affinity and specificity of indoleamine 2,3-dioxygenase. Arch Biochem Biophys 2017; 640:1-9. [PMID: 29288638 DOI: 10.1016/j.abb.2017.12.019] [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: 09/26/2017] [Revised: 12/21/2017] [Accepted: 12/23/2017] [Indexed: 11/20/2022]
Abstract
Indoleamine 2,3-dioxygenase (IDO) is a heme-containing enzyme that catalyses the oxidative cleavage of L-Trp. The ciliate Blepharisma stoltei has four IDO genes (IDO-I, -II, -III and -IV), which seem to have evolved via two sequential gene duplication events. Each IDO enzyme has a distinct enzymatic property, where IDO-III has a high affinity for L-Trp, whereas the affinity of the other three isoforms for L-Trp is low. IDO-I also exhibits a significant catalytic activity with another indole compound: 5-hydroxy-l-tryptophan (5-HTP). IDO-I is considered to be an enzyme that is involved in the biosynthesis of the 5-HTP-derived mating pheromone, gamone 2. By analysing a series of chimeric enzymes based on extant and predicted ancestral enzymes, we identified Asn131 in IDO-I and Glu132 in IDO-III as the key residues responsible for their high affinity for each specific substrate. These two residues were aligned in an identical position as the substrate-determining residue (SDR). Thus, the substrate affinity and specificity are regulated mostly by a single amino acid residue in the Blepharisma IDO-I and IDO-III enzymes.
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16
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Sugiura M, Yuasa HJ, Harumoto T. Novel Specificity of IDO Enzyme Involved in the Biosynthesis of Mating Pheromone in the Ciliate Blepharisma stoltei. Protist 2017; 168:686-696. [DOI: 10.1016/j.protis.2017.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 08/24/2017] [Accepted: 09/09/2017] [Indexed: 01/12/2023]
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17
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Coletti A, Greco FA, Dolciami D, Camaioni E, Sardella R, Pallotta MT, Volpi C, Orabona C, Grohmann U, Macchiarulo A. Advances in indoleamine 2,3-dioxygenase 1 medicinal chemistry. MEDCHEMCOMM 2017; 8:1378-1392. [PMID: 30108849 PMCID: PMC6072487 DOI: 10.1039/c7md00109f] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/11/2017] [Indexed: 12/11/2022]
Abstract
Indoleamine 2,3-dioxygenase 1 (IDO1) mediates multiple immunoregulatory processes including the induction of regulatory T cell differentiation and activation, suppression of T cell immune responses and inhibition of dendritic cell function, which impair immune recognition of cancer cells and promote tumor growth. On this basis, this enzyme is widely recognized as a valuable drug target for the development of immunotherapeutic small molecules in oncology. Although medicinal chemistry has made a substantial contribution to the discovery of numerous chemical classes of potent IDO1 inhibitors in the past 20 years, only very few compounds have progressed in clinical trials. In this review, we provide an overview of the current understanding of structure-function relationships of the enzyme, and discuss structure-activity relationships of selected classes of inhibitors that have shaped the hitherto few successes of IDO1 medicinal chemistry. An outlook opinion is also given on trends in the design of next generation inhibitors of the enzyme.
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Affiliation(s)
- Alice Coletti
- Department of Pharmaceutical Sciences , University of Perugia , via del Liceo 1 , 06123 Perugia , Italy . ; ; Tel: +39 075 585 5160
| | - Francesco Antonio Greco
- Department of Pharmaceutical Sciences , University of Perugia , via del Liceo 1 , 06123 Perugia , Italy . ; ; Tel: +39 075 585 5160
| | - Daniela Dolciami
- Department of Pharmaceutical Sciences , University of Perugia , via del Liceo 1 , 06123 Perugia , Italy . ; ; Tel: +39 075 585 5160
| | - Emidio Camaioni
- Department of Pharmaceutical Sciences , University of Perugia , via del Liceo 1 , 06123 Perugia , Italy . ; ; Tel: +39 075 585 5160
| | - Roccaldo Sardella
- Department of Pharmaceutical Sciences , University of Perugia , via del Liceo 1 , 06123 Perugia , Italy . ; ; Tel: +39 075 585 5160
| | - Maria Teresa Pallotta
- Department of Experimental Medicine , University of Perugia , P.le Gambuli , 06132 Perugia , Italy
| | - Claudia Volpi
- Department of Experimental Medicine , University of Perugia , P.le Gambuli , 06132 Perugia , Italy
| | - Ciriana Orabona
- Department of Experimental Medicine , University of Perugia , P.le Gambuli , 06132 Perugia , Italy
| | - Ursula Grohmann
- Department of Experimental Medicine , University of Perugia , P.le Gambuli , 06132 Perugia , Italy
| | - Antonio Macchiarulo
- Department of Pharmaceutical Sciences , University of Perugia , via del Liceo 1 , 06123 Perugia , Italy . ; ; Tel: +39 075 585 5160
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18
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Raven EL. A short history of heme dioxygenases: rise, fall and rise again. J Biol Inorg Chem 2016; 22:175-183. [PMID: 27909919 PMCID: PMC5350241 DOI: 10.1007/s00775-016-1412-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/10/2016] [Indexed: 01/20/2023]
Abstract
It is well established that there are two different classes of enzymes—tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO)—that catalyse the O2-dependent oxidation of l-tryptophan to N-formylkynurenine. But it was not always so. This perspective presents a short history of the early TDO and IDO literature, the people that were involved in creating it, and the legacy that this left for the future.
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Affiliation(s)
- Emma L Raven
- Department of Chemistry, University of Leicester, University Road, Leicester, LE1 7RH, UK.
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19
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Yuasa HJ. Highl-Trp affinity of indoleamine 2,3-dioxygenase 1 is attributed to two residues located in the distal heme pocket. FEBS J 2016; 283:3651-3661. [DOI: 10.1111/febs.13834] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 05/31/2016] [Accepted: 08/12/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Hajime J. Yuasa
- Laboratory of Biochemistry; Department of Applied Science; Faculty of Science; National University Corporation Kochi University; Japan
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20
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Álvarez L, Lewis-Ballester A, Roitberg A, Estrin DA, Yeh SR, Marti MA, Capece L. Structural Study of a Flexible Active Site Loop in Human Indoleamine 2,3-Dioxygenase and Its Functional Implications. Biochemistry 2016; 55:2785-93. [PMID: 27112409 DOI: 10.1021/acs.biochem.6b00077] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Human indoleamine 2,3-dioxygenase catalyzes the oxidative cleavage of tryptophan to N-formyl kynurenine, the initial and rate-limiting step in the kynurenine pathway. Additionally, this enzyme has been identified as a possible target for cancer therapy. A 20-amino acid protein segment (the JK loop), which connects the J and K helices, was not resolved in the reported hIDO crystal structure. Previous studies have shown that this loop undergoes structural rearrangement upon substrate binding. In this work, we apply a combination of replica exchange molecular dynamics simulations and site-directed mutagenesis experiments to characterize the structure and dynamics of this protein region. Our simulations show that the JK loop can be divided into two regions: the first region (JK loop(C)) displays specific and well-defined conformations and is within hydrogen bonding distance of the substrate, while the second region (JK loop(N)) is highly disordered and exposed to the solvent. The peculiar flexible nature of JK loop(N) suggests that it may function as a target for post-translational modifications and/or a mediator for protein-protein interactions. In contrast, hydrogen bonding interactions are observed between the substrate and Thr379 in the highly conserved "GTGG" motif of JK loop(C), thereby anchoring JK loop(C) in a closed conformation, which secures the appropriate substrate binding mode for catalysis. Site-directed mutagenesis experiments confirm the key role of this residue, highlighting the importance of the JK loop(C) conformation in regulating the enzymatic activity. Furthermore, the existence of the partially and totally open conformations in the substrate-free form suggests a role of JK loop(C) in controlling substrate and product dynamics.
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Affiliation(s)
- Lucía Álvarez
- Dto. de Química Inorgánica, Analítica y Química Física, Fac. de Ciencias Exactas y Naturales, Universidad de Buenos Aires , Buenos Aires C1428EGA, Argentina.,INQUIMAE-CONICET , Buenos Aires C1428EGA, Argentina
| | - Ariel Lewis-Ballester
- Department of Physiology and Biophysics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, New York, New York 10461, United States
| | - Adrián Roitberg
- Department of Chemistry, University of Florida , 440 Leigh Hall, Gainesville, Florida 32611-7200, United States
| | - Darío A Estrin
- Dto. de Química Inorgánica, Analítica y Química Física, Fac. de Ciencias Exactas y Naturales, Universidad de Buenos Aires , Buenos Aires C1428EGA, Argentina.,INQUIMAE-CONICET , Buenos Aires C1428EGA, Argentina
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, New York, New York 10461, United States
| | - Marcelo A Marti
- Dto. de Química Biologica Fac. de Ciencias Exactas y Naturales, Universidad de Buenos Aires , Buenos Aires C1428EGA, Argentina.,IQUIBICEN-CONICET , Buenos Aires C1428EGA, Argentina
| | - Luciana Capece
- Dto. de Química Inorgánica, Analítica y Química Física, Fac. de Ciencias Exactas y Naturales, Universidad de Buenos Aires , Buenos Aires C1428EGA, Argentina.,INQUIMAE-CONICET , Buenos Aires C1428EGA, Argentina
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21
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Wirthgen E, Hoeflich A. Endotoxin-Induced Tryptophan Degradation along the Kynurenine Pathway: The Role of Indolamine 2,3-Dioxygenase and Aryl Hydrocarbon Receptor-Mediated Immunosuppressive Effects in Endotoxin Tolerance and Cancer and Its Implications for Immunoparalysis. JOURNAL OF AMINO ACIDS 2015; 2015:973548. [PMID: 26881062 PMCID: PMC4736209 DOI: 10.1155/2015/973548] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 10/28/2015] [Accepted: 12/06/2015] [Indexed: 12/16/2022]
Abstract
The degradation of tryptophan (TRP) along the kynurenine pathway plays a crucial role as a neuro- and immunomodulatory mechanism in response to inflammatory stimuli, such as lipopolysaccharides (LPS). In endotoxemia or sepsis, an enhanced activation of the rate-limiting enzyme indoleamine 2,3-dioxygenase (IDO) is associated with a higher mortality risk. It is assumed that IDO induced immunosuppressive effects provoke the development of a protracted compensatory hypoinflammatory phase up to a complete paralysis of the immune system, which is characterized by an endotoxin tolerance. However, the role of IDO activation in the development of life-threatening immunoparalysis is still poorly understood. Recent reports described the impact of inflammatory IDO activation and aryl hydrocarbon receptor- (AhR-) mediated pathways on the development of LPS tolerance and immune escape of cancer cells. These immunosuppressive mechanisms offer new insights for a better understanding of the development of cellular dysfunctions in immunoparalysis. This review provides a comprehensive update of significant biological functions of TRP metabolites along the kynurenine pathway and the complex regulation of LPS-induced IDO activation. In addition, the review focuses on the role of IDO-AhR-mediated immunosuppressive pathways in endotoxin tolerance and carcinogenesis revealing the significance of enhanced IDO activity for the establishment of life-threatening immunoparalysis in sepsis.
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Affiliation(s)
- Elisa Wirthgen
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Germany
| | - Andreas Hoeflich
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Germany
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22
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Booth ES, Basran J, Lee M, Handa S, Raven EL. Substrate Oxidation by Indoleamine 2,3-Dioxygenase: EVIDENCE FOR A COMMON REACTION MECHANISM. J Biol Chem 2015; 290:30924-30. [PMID: 26511316 PMCID: PMC4692220 DOI: 10.1074/jbc.m115.695684] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Indexed: 11/06/2022] Open
Abstract
The kynurenine pathway is the major route of l-tryptophan (l-Trp) catabolism in biology, leading ultimately to the formation of NAD+. The initial and rate-limiting step of the kynurenine pathway involves oxidation of l-Trp to N-formylkynurenine. This is an O2-dependent process and catalyzed by indoleamine 2,3-dioxygenase and tryptophan 2,3-dioxygenase. More than 60 years after these dioxygenase enzymes were first isolated (Kotake, Y., and Masayama, I. (1936) Z. Physiol. Chem. 243, 237–244), the mechanism of the reaction is not established. We examined the mechanism of substrate oxidation for a series of substituted tryptophan analogues by indoleamine 2,3-dioxygenase. We observed formation of a transient intermediate, assigned as a Compound II (ferryl) species, during oxidation of l-Trp, 1-methyl-l-Trp, and a number of other substrate analogues. The data are consistent with a common reaction mechanism for indoleamine 2,3-dioxygenase-catalyzed oxidation of tryptophan and other tryptophan analogues.
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Affiliation(s)
- Elizabeth S Booth
- From the Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, Great Britain, United Kingdom and
| | - Jaswir Basran
- Department of Molecular and Cellular Biology and Henry Wellcome Laboratories for Structural Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, Great Britain, United Kingdom
| | - Michael Lee
- From the Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, Great Britain, United Kingdom and
| | - Sandeep Handa
- From the Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, Great Britain, United Kingdom and
| | - Emma L Raven
- From the Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, Great Britain, United Kingdom and
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23
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Hargrove TY, Wawrzak Z, Lamb DC, Guengerich FP, Lepesheva GI. Structure-Functional Characterization of Cytochrome P450 Sterol 14α-Demethylase (CYP51B) from Aspergillus fumigatus and Molecular Basis for the Development of Antifungal Drugs. J Biol Chem 2015; 290:23916-34. [PMID: 26269599 DOI: 10.1074/jbc.m115.677310] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Indexed: 01/18/2023] Open
Abstract
Aspergillus fumigatus is the opportunistic fungal pathogen that predominantly affects the immunocompromised population and causes 600,000 deaths/year. The cytochrome P450 51 (CYP51) inhibitor voriconazole is currently the drug of choice, yet the treatment efficiency remains low, calling for rational development of more efficient agents. A. fumigatus has two CYP51 genes, CYP51A and CYP51B, which share 59% amino acid sequence identity. CYP51B is expressed constitutively, whereas gene CYP51A is reported to be inducible. We expressed, purified, and characterized A. fumigatus CYP51B, including determination of its substrate preferences, catalytic parameters, inhibition, and x-ray structure in complexes with voriconazole and the experimental inhibitor (R)-N-(1-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl)ethyl)-4-(5-phenyl-1,3,4-oxadiazol-2-yl)benzamide (VNI). The enzyme demethylated its natural substrate eburicol and the plant CYP51 substrate obtusifoliol at steady-state rates of 17 and 16 min(-1), respectively, but did not metabolize lanosterol, and the topical antifungal drug miconazole was the strongest inhibitor that we identified. The x-ray crystal structures displayed high overall similarity of A. fumigatus CYP51B to CYP51 orthologs from other biological kingdoms but revealed phylum-specific differences relevant to enzyme catalysis and inhibition. The complex with voriconazole provides an explanation for the potency of this relatively small molecule, whereas the complex with VNI outlines a direction for further enhancement of the efficiency of this new inhibitory scaffold to treat humans afflicted with filamentous fungal infections.
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Affiliation(s)
- Tatiana Y Hargrove
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Zdzislaw Wawrzak
- the Synchrotron Research Center, Life Science Collaborative Access Team, Northwestern University, Argonne, Illinois 60439
| | - David C Lamb
- Swansea University, Swansea, Wales SA2 8PP, United Kingdom, and
| | - F Peter Guengerich
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Galina I Lepesheva
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, the Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232
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24
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Abstract
IDO1 (indoleamine 2,3-dioxygenase 1) is a member of a unique class of mammalian haem dioxygenases that catalyse the oxidative catabolism of the least-abundant essential amino acid, L-Trp (L-tryptophan), along the kynurenine pathway. Significant increases in knowledge have been recently gained with respect to understanding the fundamental biochemistry of IDO1 including its catalytic reaction mechanism, the scope of enzyme reactions it catalyses, the biochemical mechanisms controlling IDO1 expression and enzyme activity, and the discovery of enzyme inhibitors. Major advances in understanding the roles of IDO1 in physiology and disease have also been realised. IDO1 is recognised as a prominent immune regulatory enzyme capable of modulating immune cell activation status and phenotype via several molecular mechanisms including enzyme-dependent deprivation of L-Trp and its conversion into the aryl hydrocarbon receptor ligand kynurenine and other bioactive kynurenine pathway metabolites, or non-enzymatic cell signalling actions involving tyrosine phosphorylation of IDO1. Through these different modes of biochemical signalling, IDO1 regulates certain physiological functions (e.g. pregnancy) and modulates the pathogenesis and severity of diverse conditions including chronic inflammation, infectious disease, allergic and autoimmune disorders, transplantation, neuropathology and cancer. In the present review, we detail the current understanding of IDO1’s catalytic actions and the biochemical mechanisms regulating IDO1 expression and activity. We also discuss the biological functions of IDO1 with a focus on the enzyme's immune-modulatory function, its medical implications in diverse pathological settings and its utility as a therapeutic target.
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25
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Makino R, Obayashi E, Hori H, Iizuka T, Mashima K, Shiro Y, Ishimura Y. Initial O2 Insertion Step of the Tryptophan Dioxygenase Reaction Proposed by a Heme-Modification Study. Biochemistry 2015; 54:3604-16. [DOI: 10.1021/acs.biochem.5b00048] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ryu Makino
- Department
of Life Science, College of Science, Rikkyo University, Nishi-ikebukuro
3-34-1, Toshima-ku, Tokyo 171-8501, Japan
| | - Eiji Obayashi
- Department
of Biochemistry, Shimane University School of Medicine, Izumo, Shimane 693-8501, Japan
| | - Hiroshi Hori
- Center
for Quantum Science and Technology under Extreme Conditions, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Tetsutaro Iizuka
- RIKEN Harima Institute/Spring 8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Keisuke Mashima
- Department
of Life Science, College of Science, Rikkyo University, Nishi-ikebukuro
3-34-1, Toshima-ku, Tokyo 171-8501, Japan
| | - Yoshitsugu Shiro
- RIKEN Harima Institute/Spring 8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yuzuru Ishimura
- Department
of Biochemistry, School of Medicine, Keio University, 35 Shinanomachi,
Shinjuku-ku, Tokyo 160-8582, Japan
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26
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Yuasa HJ, Mizuno K, Ball HJ. Low efficiency IDO2 enzymes are conserved in lower vertebrates, whereas higher efficiency IDO1 enzymes are dispensable. FEBS J 2015; 282:2735-45. [PMID: 25950090 DOI: 10.1111/febs.13316] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 04/01/2015] [Accepted: 04/30/2015] [Indexed: 12/16/2022]
Abstract
Indoleamine 2,3-dioxygenase (IDO) is a Trp-degrading enzyme that catalyzes the first step in the kynurenine pathway. Two IDO genes, IDO1 and IDO2, are found in vertebrates and the timing of the gene duplication giving rise to the genes has been controversial. In the present study, we report that several fishes and two turtles also have both IDO1 and IDO2. This represents definitive evidence for the gene duplication occurring before the divergence of vertebrates, with IDO1 having been lost in a number of lower vertebrate lineages. IDO2 enzymes have a relatively low affinity for l-Trp; however, Anolis carolinensis (lizard) IDO2 has an affinity for l-Trp comparable to mammalian IDO1 enzymes. We identified a Ser residue located in the distal heme pocket of IDO1 (distal-Ser) (corresponding to Ser167 of human IDO1) that is conserved in all IDO1 enzymes and the lizard IDO2. This residue is conserved as Thr (distal-Thr) in other IDO2 enzymes. Biochemical analyses, using IDO variants with either Ser or Thr substitutions, suggest that the distal-Ser change was crucial for the improvement in affinity for l-Trp in ancient IDO1. The ancestral IDO1 likely had a 'moderate' enzymatic efficiency for l-Trp, clearly higher than IDO2 but lower than mammalian IDO1. The distal-Ser of lizard IDO2 bestows a high affinity for l-Trp, however, this unique IDO2 has a low enzymatic efficiency because of its very low catalytic velocity. Thus, low efficiency IDO2 enzymes have been conserved throughout vertebrate evolution, whereas higher efficiency IDO1 enzymes are dispensable in many lower vertebrate lineages.
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Affiliation(s)
- Hajime J Yuasa
- Laboratory of Biochemistry, Department of Applied Science, Faculty of Science, National University Corporation Kochi University, Japan
| | - Keiko Mizuno
- Laboratory of Biochemistry, Department of Applied Science, Faculty of Science, National University Corporation Kochi University, Japan
| | - Helen J Ball
- Molecular Immunopathology Unit, Discipline of Pathology, School of Medical Sciences and Bosch Institute, University of Sydney, Australia
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Kolawole AO, Hixon BP, Dameron LS, Chrisman IM, Smirnov VV. Catalytic activity of human indoleamine 2,3-dioxygenase (hIDO1) at low oxygen. Arch Biochem Biophys 2015; 570:47-57. [PMID: 25712221 PMCID: PMC4412315 DOI: 10.1016/j.abb.2015.02.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 02/12/2015] [Accepted: 02/15/2015] [Indexed: 11/30/2022]
Abstract
A cytokine-inducible extrahepatic human indoleamine 2,3-dioxygenase (hIDO1) catalyzes the first step of the kynurenine pathway. Immunosuppressive activity of hIDO1 in tumor cells weakens host T-cell immunity, contributing to the progression of cancer. Here we report on enzyme kinetics and catalytic mechanism of hIDO1, studied at varied levels of dioxygen (O2) and L-tryptophan (L-Trp). Using a cytochrome b5-based activating system, we measured the initial rates of O2 decay with a Clark-type oxygen electrode at physiologically-relevant levels of both substrates. Kinetics was also studied in the presence of two substrate analogs: 1-methyl-L-tryptophan and norharmane. Quantitative analysis supports a steady-state rather than a rapid equilibrium kinetic mechanism, where the rates of individual pathways, leading to a ternary complex, are significantly different, and the overall rate of catalysis depends on contributions of both routes. One path, where O2 binds to ferrous hIDO1 first, is faster than the second route, which starts with the binding of L-Trp. However, L-Trp complexation with free ferrous hIDO1 is more rapid than that of O2. As the level of L-Trp increases, the slower route becomes a significant contributor to the overall rate, resulting in observed substrate inhibition.
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Affiliation(s)
- Ayodele O Kolawole
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, United States
| | - Brian P Hixon
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, United States
| | - Laura S Dameron
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, United States
| | - Ian M Chrisman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, United States
| | - Valeriy V Smirnov
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, United States.
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Yuasa HJ, Ball HJ. Efficient tryptophan-catabolizing activity is consistently conserved through evolution of TDO enzymes, but not IDO enzymes. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 324:128-40. [DOI: 10.1002/jez.b.22608] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 10/27/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Hajime J. Yuasa
- Laboratory of Biochemistry; Department of Applied Science; Faculty of Science; National University Corporation Kochi University; Kochi Japan
| | - Helen J. Ball
- Molecular Immunopathology Unit; Discipline of Pathology; School of Medical Sciences; and Bosch Institute; University of Sydney; NSW Australia
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29
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Human indoleamine 2,3-dioxygenase-2 has substrate specificity and inhibition characteristics distinct from those of indoleamine 2,3-dioxygenase-1. Amino Acids 2014; 46:2155-63. [DOI: 10.1007/s00726-014-1766-3] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 05/14/2014] [Indexed: 02/07/2023]
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Efimov I, Parkin G, Millett ES, Glenday J, Chan CK, Weedon H, Randhawa H, Basran J, Raven EL. A simple method for the determination of reduction potentials in heme proteins. FEBS Lett 2014; 588:701-4. [PMID: 24440354 PMCID: PMC3999514 DOI: 10.1016/j.febslet.2013.12.030] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 12/20/2013] [Accepted: 12/24/2013] [Indexed: 11/28/2022]
Abstract
A simple method for determination of heme protein reduction potentials is described. We use the method to determine reduction potentials for human NPAS2 and human CLOCK. The method can be easily applied to other heme proteins.
We describe a simple method for the determination of heme protein reduction potentials. We use the method to determine the reduction potentials for the PAS-A domains of the regulatory heme proteins human NPAS2 (Em = −115 mV ± 2 mV, pH 7.0) and human CLOCK (Em = −111 mV ± 2 mV, pH 7.0). We suggest that the method can be easily and routinely applied to the determination of reduction potentials across the family of heme proteins.
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Affiliation(s)
- Igor Efimov
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Gary Parkin
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Elizabeth S Millett
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Jennifer Glenday
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Cheuk K Chan
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Holly Weedon
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Harpreet Randhawa
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Jaswir Basran
- Department of Biochemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 9HN, United Kingdom
| | - Emma L Raven
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom.
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31
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Yanagisawa S, Hara M, Sugimoto H, Shiro Y, Ogura T. Resonance Raman study on indoleamine 2,3-dioxygenase: Control of reactivity by substrate-binding. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.02.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Yuasa HJ, Ball HJ. Indoleamine 2,3-dioxygenases with very low catalytic activity are well conserved across kingdoms: IDOs of Basidiomycota. Fungal Genet Biol 2013; 56:98-106. [PMID: 23548750 DOI: 10.1016/j.fgb.2013.03.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 03/03/2013] [Accepted: 03/14/2013] [Indexed: 11/15/2022]
Abstract
Indoleamine 2,3-dioxygenase (IDO) is a tryptophan-degrading enzyme and is found in animals, fungi and bacteria. In fungi, its primary role is to supply nicotinamide adenine dinucleotide (NAD(+)) via the kynurenine pathway. A number of organisms possess more than one IDO gene, for example, mammals have IDO1 and IDO2 genes. We previously reported that the Pezizomycotina fungi commonly possess three types of IDO genes, IDOα, IDOβ and IDOγ. In this study, we surveyed the nature of IDO genes from Basidiomycota fungi, which are categorized into three subphyla (Agaricomycotina, Pucciniomycotina and Ustilaginomycotina). The Agaricomycotina fungi generally have three types of IDO genes (IDOa, IDOb and IDOc), which are distinct from Pezizomycotina three isozymes. Pucciniomycotina and Ustilaginomycotina species possess two types of IDO; one forms a monophyletic clade with Agaricomycotina IDOs in the phylogenetic tree, these IDOs are referred to as "typical Basidiomycota IDOs". The other is IDOγ, which showed more than 40% identity with Pezizomycotina and ciliate IDOγ. We previously demonstrated that IDO2 in mammals and IDOγ in Perzizomycotina fungi have much lower catalytic efficiencies in an in vitro assay, compared with the other IDO isoforms found in the respective species. We have developed a functional assay to determine whether particular IDO enzymes have sufficient enzymatic activity to rescue a yeast strain where IDO-deletion has rendered it auxotrophic for nicotinic acid. IDOα and IDOβ showed comparable catalytic efficiency, both of them could function in the Pezizomycotina fungal L-Trp metabolism. The catalytic efficiency and functional capacity of the Basidiomycota IDOa and IDOb were similar to Pezizomycotina IDOα/IDOβ. We found that Basidiomycota IDOc could not rescue the nicotinic acid auxotroph, similar to other IDO enzymes with low catalytic efficiency (mammalian IDO2 and most fungal IDOγ). Our study suggests that some fungal IDO enzymes function in tryptophan metabolism and NAD(+) supply. In contrast, other IDO enzymes do not possess sufficient Trp-metabolising capacity to supply NAD(+). Although the role of these low catalytic efficiency IDOs is not clear, it is interesting to note that IDO enzymes possessing these characteristics have evolved across different kingdoms.
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Affiliation(s)
- Hajime J Yuasa
- Laboratory of Biochemistry, Department of Applied Science, Faculty of Science, National University Corporation Kochi University, Kochi 780-8520, Japan.
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33
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Freewan M, Rees MD, Plaza TSS, Glaros E, Lim YJ, Wang XS, Yeung AWS, Witting PK, Terentis AC, Thomas SR. Human indoleamine 2,3-dioxygenase is a catalyst of physiological heme peroxidase reactions: implications for the inhibition of dioxygenase activity by hydrogen peroxide. J Biol Chem 2012; 288:1548-67. [PMID: 23209301 DOI: 10.1074/jbc.m112.410993] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The heme enzyme indoleamine 2,3-dioxygenase (IDO) is a key regulator of immune responses through catalyzing l-tryptophan (l-Trp) oxidation. Here, we show that hydrogen peroxide (H(2)O(2)) activates the peroxidase function of IDO to induce protein oxidation and inhibit dioxygenase activity. Exposure of IDO-expressing cells or recombinant human IDO (rIDO) to H(2)O(2) inhibited dioxygenase activity in a manner abrogated by l-Trp. Dioxygenase inhibition correlated with IDO-catalyzed H(2)O(2) consumption, compound I-mediated formation of protein-centered radicals, altered protein secondary structure, and opening of the distal heme pocket to promote nonproductive substrate binding; these changes were inhibited by l-Trp, the heme ligand cyanide, or free radical scavengers. Protection by l-Trp coincided with its oxidation into oxindolylalanine and kynurenine and the formation of a compound II-type ferryl-oxo heme. Physiological peroxidase substrates, ascorbate or tyrosine, enhanced rIDO-mediated H(2)O(2) consumption and attenuated H(2)O(2)-induced protein oxidation and dioxygenase inhibition. In the presence of H(2)O(2), rIDO catalytically consumed nitric oxide (NO) and utilized nitrite to promote 3-nitrotyrosine formation on IDO. The promotion of H(2)O(2) consumption by peroxidase substrates, NO consumption, and IDO nitration was inhibited by l-Trp. This study identifies IDO as a heme peroxidase that, in the absence of substrates, self-inactivates dioxygenase activity via compound I-initiated protein oxidation. l-Trp protects against dioxygenase inactivation by reacting with compound I and retarding compound II reduction to suppress peroxidase turnover. Peroxidase-mediated dioxygenase inactivation, NO consumption, or protein nitration may modulate the biological actions of IDO expressed in inflammatory tissues where the levels of H(2)O(2) and NO are elevated and l-Trp is low.
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Affiliation(s)
- Mohammed Freewan
- Centre for Vascular Research and School of Medical Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
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34
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Chauhan N, Basran J, Rafice SA, Efimov I, Millett ES, Mowat CG, Moody PCE, Handa S, Raven EL. How is the distal pocket of a heme protein optimized for binding of tryptophan? FEBS J 2012; 279:4501-9. [DOI: 10.1111/febs.12036] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 10/15/2012] [Accepted: 10/16/2012] [Indexed: 12/30/2022]
Affiliation(s)
- Nishma Chauhan
- Department of Chemistry; Henry Wellcome Building; University of Leicester; UK
| | - Jaswir Basran
- Department of Biochemistry; Henry Wellcome Building; University of Leicester; UK
| | - Sara A. Rafice
- Department of Chemistry; Henry Wellcome Building; University of Leicester; UK
| | - Igor Efimov
- Department of Chemistry; Henry Wellcome Building; University of Leicester; UK
| | | | | | | | - Sandeep Handa
- Department of Chemistry; Henry Wellcome Building; University of Leicester; UK
| | - Emma L. Raven
- Department of Chemistry; Henry Wellcome Building; University of Leicester; UK
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35
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Chauviac FX, Bommer M, Yan J, Parkin G, Daviter T, Lowden P, Raven EL, Thalassinos K, Keep NH. Crystal structure of reduced MsAcg, a putative nitroreductase from Mycobacterium smegmatis and a close homologue of Mycobacterium tuberculosis Acg. J Biol Chem 2012; 287:44372-83. [PMID: 23148223 DOI: 10.1074/jbc.m112.406264] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
This paper presents the structure of MsAcg (MSMEG_5246), a Mycobacterium smegmatis homologue of Mycobacterium tuberculosis Acg (Rv2032) in its reduced form at 1.6 Å resolution using x-ray crystallography. Rv2032 is one of the most induced genes under the hypoxic model of tuberculosis dormancy. The Acg family turns out to be unusual flavin mononucleotide (FMN)-binding proteins that have probably arisen by gene duplication and fusion from a classical homodimeric nitroreductase such that the monomeric protein resembles a classical nitroreductase dimer but with one active site deleted and the other active site covered by a unique lid. The FMN cofactor is not reduced by either NADH or NADPH, but the chemically reduced enzyme is capable of reduction of nitro substrates, albeit at no kinetic advantage over free FMN. The reduced enzyme is rapidly oxidized by oxygen but without any evidence for a radical state commonly seen in oxygen-sensitive nitroreductases. The presence of the unique lid domain, the lack of reduction by NAD(P)H, and the slow rate of reaction of the chemically reduced protein raises a possible alternative function of Acg proteins in FMN storage or sequestration from other biochemical pathways as part of the bacteria's adaptation to a dormancy state.
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Affiliation(s)
- François-Xavier Chauviac
- Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London, WC1E 7HX, United Kingdom
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36
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Geng J, Dornevil K, Liu A. Chemical Rescue of the Distal Histidine Mutants of Tryptophan 2,3-Dioxygenase. J Am Chem Soc 2012; 134:12209-18. [DOI: 10.1021/ja304164b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Jiafeng Geng
- Department of Chemistry & Center for Diagnostics and Therapeutics, Georgia State University, 161 Jesse Hill Jr. Drive, Atlanta, Georgia 30303, United States
| | - Kednerlin Dornevil
- Department of Chemistry & Center for Diagnostics and Therapeutics, Georgia State University, 161 Jesse Hill Jr. Drive, Atlanta, Georgia 30303, United States
| | - Aimin Liu
- Department of Chemistry & Center for Diagnostics and Therapeutics, Georgia State University, 161 Jesse Hill Jr. Drive, Atlanta, Georgia 30303, United States
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37
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Yuasa HJ, Ball HJ. The evolution of three types of indoleamine 2,3 dioxygenases in fungi with distinct molecular and biochemical characteristics. Gene 2012; 504:64-74. [PMID: 22564706 DOI: 10.1016/j.gene.2012.04.082] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 03/07/2012] [Accepted: 04/27/2012] [Indexed: 12/01/2022]
Abstract
Indoleamine 2,3-dioxygenase (IDO) is a tryptophan-degrading enzyme and known as a mammalian immunosuppressive molecule. In fungi, the primary role of IDO is to supply nicotinamide adenine dinucleotide (NAD(+)) via the kynurenine pathway. We previously reported that the koji-mold, Aspergillus oryzae has two IDO genes, IDOα and IDOβ. In the present study, we found that A. oryzae also has the third IDO, IDOγ. These three-types of IDOs are widely distributed among the Pezizomycotina fungi, although the black truffle, Tuber melanosporum has only one corresponding gene to IDOα/IDOβ. The yeast, Saccharomyces cerevisiae has a single IDO gene. Generally, Pezizomycotina IDOα showed similar enzymatic properties to the yeast IDO, suggesting that the IDOα is a functional homologue of the S. cerevisiae IDO. In contrast to IDOα, the K(m) value of IDOβ is higher. However, the reaction velocity of IDOβ is very fast, resulting in comparable or higher catalytic efficiency than IDOα. Thus IDOβ may functionally substitute for IDOα in fungal L-Trp metabolism. The enzymatic activity of IDOγ was comparatively very low with the values of enzymatic parameters comparable to vertebrate IDO2 enzymes. IDOα and IDOβ have similar gene structures, suggesting that they were generated by gene duplication which occurred rather early in Pezizomycotina evolution, although the timing of the duplication remains debatable. In contrast, the phylogenetic trees suggest that IDOγs form an evolutionarily distinct group of IDO enzymes, with a closer relationship to group I bacterial IDOs than other fungal IDOs. The ancestor of the IDOγ family is likely to have diverged from other eukaryotic IDOs at a very early stage of eukaryotic evolution.
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Affiliation(s)
- Hajime J Yuasa
- Laboratory of Biochemistry, Department of Applied Science, Faculty of Science, National University Corporation Kochi University, Kochi 780-8520, Japan.
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38
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Millett ES, Efimov I, Basran J, Handa S, Mowat CG, Raven EL. Heme-containing dioxygenases involved in tryptophan oxidation. Curr Opin Chem Biol 2012; 16:60-6. [DOI: 10.1016/j.cbpa.2012.01.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 01/18/2012] [Accepted: 01/25/2012] [Indexed: 10/28/2022]
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Efimov I, Basran J, Sun X, Chauhan N, Chapman S, Mowat CG, Raven EL. The mechanism of substrate inhibition in human indoleamine 2,3-dioxygenase. J Am Chem Soc 2012; 134:3034-41. [PMID: 22299628 PMCID: PMC3280726 DOI: 10.1021/ja208694g] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Indexed: 01/22/2023]
Abstract
Indoleamine 2,3-dioxygenase catalyzes the O(2)-dependent oxidation of L-tryptophan (L-Trp) to N-formylkynurenine (NFK) as part of the kynurenine pathway. Inhibition of enzyme activity at high L-Trp concentrations was first noted more than 30 years ago, but the mechanism of inhibition has not been established. Using a combination of kinetic and reduction potential measurements, we present evidence showing that inhibition of enzyme activity in human indoleamine 2,3-dioxygenase (hIDO) and a number of site-directed variants during turnover with L-tryptophan (L-Trp) can be accounted for by the sequential, ordered binding of O(2) and L-Trp. Analysis of the data shows that at low concentrations of L-Trp, O(2) binds first followed by the binding of L-Trp; at higher concentrations of L-Trp, the order of binding is reversed. In addition, we show that the heme reduction potential (E(m)(0)) has a regulatory role in controlling the overall rate of catalysis (and hence the extent of inhibition) because there is a quantifiable correlation between E(m)(0) (that increases in the presence of L-Trp) and the rate constant for O(2) binding. This means that the initial formation of ferric superoxide (Fe(3+)-O(2)(•-)) from Fe(2+)-O(2) becomes thermodynamically less favorable as substrate binds, and we propose that it is the slowing down of this oxidation step at higher concentrations of substrate that is the origin of the inhibition. In contrast, we show that regeneration of the ferrous enzyme (and formation of NFK) in the final step of the mechanism, which formally requires reduction of the heme, is facilitated by the higher reduction potential in the substrate-bound enzyme and the two constants (k(cat) and E(m)(0)) are shown also to be correlated. Thus, the overall catalytic activity is balanced between the equal and opposite dependencies of the initial and final steps of the mechanism on the heme reduction potential. This tuning of the reduction potential provides a simple mechanism for regulation of the reactivity, which may be used more widely across this family of enzymes.
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Affiliation(s)
- Igor Efimov
- Department of Chemistry, University of Leicester, University Road, Leicester
LE1 7RH, United Kingdom
| | - Jaswir Basran
- Department of Biochemistry, University of Leicester, Lancaster Road, Leicester
LE1 9HN, United Kingdom
| | - Xiao Sun
- Department of Chemistry, University of Leicester, University Road, Leicester
LE1 7RH, United Kingdom
| | - Nishma Chauhan
- Department of Chemistry, University of Leicester, University Road, Leicester
LE1 7RH, United Kingdom
| | - Stephen
K. Chapman
- Heriot-Watt University, George Heriot Wing, Edinburgh
EH14 4AS, United Kingdom
| | - Christopher G. Mowat
- EaStCHEM, School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom
| | - Emma Lloyd Raven
- Department of Chemistry, University of Leicester, University Road, Leicester
LE1 7RH, United Kingdom
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40
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Basran J, Efimov I, Chauhan N, Thackray SJ, Krupa JL, Eaton G, Griffith GA, Mowat CG, Handa S, Raven EL. The mechanism of formation of N-formylkynurenine by heme dioxygenases. J Am Chem Soc 2011; 133:16251-7. [PMID: 21892828 PMCID: PMC3210546 DOI: 10.1021/ja207066z] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Indexed: 01/22/2023]
Abstract
Heme dioxygenases catalyze the oxidation of L-tryptophan to N-formylkynurenine (NFK), the first and rate-limiting step in tryptophan catabolism. Although recent progress has been made on early stages in the mechanism, there is currently no experimental data on the mechanism of product (NFK) formation. In this work, we have used mass spectrometry to examine product formation in a number of dioxygenases. In addition to NFK formation (m/z = 237), the data identify a species (m/z = 221) that is consistent with insertion of a single atom of oxygen into the substrate during O(2)-driven turnover. The fragmentation pattern for this m/z = 221 species is consistent with a cyclic amino acetal structure; independent chemical synthesis of the 3a-hydroxypyrroloindole-2-carboxylic acid compound is in agreement with this assignment. Labeling experiments with (18)O(2) confirm the origin of the oxygen atom as arising from O(2)-dependent turnover. These data suggest that the dioxygenases use a ring-opening mechanism during NFK formation, rather than Criegee or dioxetane mechanisms as previously proposed.
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Affiliation(s)
- Jaswir Basran
- Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, United Kingdom
| | - Igor Efimov
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Nishma Chauhan
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Sarah J. Thackray
- EaStCHEM, School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom
| | - James L. Krupa
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Graham Eaton
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Gerry A. Griffith
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Christopher G. Mowat
- EaStCHEM, School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom
| | - Sandeep Handa
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Emma Lloyd Raven
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
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41
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Rosell FI, Kuo HH, Mauk AG. NADH oxidase activity of indoleamine 2,3-dioxygenase. J Biol Chem 2011; 286:29273-29283. [PMID: 21690092 PMCID: PMC3190733 DOI: 10.1074/jbc.m111.262139] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 06/10/2011] [Indexed: 12/12/2022] Open
Abstract
The heme enzyme indoleamine 2,3-dioxygenase (IDO) was found to oxidize NADH under aerobic conditions in the absence of other enzymes or reactants. This reaction led to the formation of the dioxygen adduct of IDO and supported the oxidation of Trp to N-formylkynurenine. Formation of the dioxygen adduct and oxidation of Trp were accelerated by the addition of small amounts of hydrogen peroxide, and both processes were inhibited in the presence of either superoxide dismutase or catalase. Anaerobic reaction of IDO with NADH proceeded only in the presence of a mediator (e.g. methylene blue) and resulted in formation of the ferrous form of the enzyme. We propose that trace amounts of peroxide previously proposed to occur in NADH solutions as well as solid NADH activate IDO and lead to aerobic formation of superoxide and the reactive dioxygen adduct of the enzyme.
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Affiliation(s)
- Federico I Rosell
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, Life Sciences Centre, 2350 Health Sciences Mall, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Hsin H Kuo
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, Life Sciences Centre, 2350 Health Sciences Mall, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - A Grant Mauk
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, Life Sciences Centre, 2350 Health Sciences Mall, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
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42
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Fu R, Gupta R, Geng J, Dornevil K, Wang S, Zhang Y, Hendrich MP, Liu A. Enzyme reactivation by hydrogen peroxide in heme-based tryptophan dioxygenase. J Biol Chem 2011; 286:26541-54. [PMID: 21632548 PMCID: PMC3143619 DOI: 10.1074/jbc.m111.253237] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 05/29/2011] [Indexed: 11/06/2022] Open
Abstract
An intriguing mystery about tryptophan 2,3-dioxygenase is its hydrogen peroxide-triggered enzyme reactivation from the resting ferric oxidation state to the catalytically active ferrous form. In this study, we found that such an odd Fe(III) reduction by an oxidant depends on the presence of L-Trp, which ultimately serves as the reductant for the enzyme. In the peroxide reaction with tryptophan 2,3-dioxygenase, a previously unknown catalase-like activity was detected. A ferryl species (δ = 0.055 mm/s and ΔE(Q) = 1.755 mm/s) and a protein-based free radical (g = 2.0028 and 1.72 millitesla linewidth) were characterized by Mössbauer and EPR spectroscopy, respectively. This is the first compound ES-type of ferryl intermediate from a heme-based dioxygenase characterized by EPR and Mössbauer spectroscopy. Density functional theory calculations revealed the contribution of secondary ligand sphere to the spectroscopic properties of the ferryl species. In the presence of L-Trp, the reactivation was demonstrated by enzyme assays and by various spectroscopic techniques. A Trp-Trp dimer and a monooxygenated L-Trp were both observed as the enzyme reactivation by-products by mass spectrometry. Together, these results lead to the unraveling of an over 60-year old mystery of peroxide reactivation mechanism. These results may shed light on how a metalloenzyme maintains its catalytic activity in an oxidizing environment.
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Affiliation(s)
- Rong Fu
- From the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Rupal Gupta
- the Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, and
| | - Jiafeng Geng
- From the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Kednerlin Dornevil
- From the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Siming Wang
- From the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Yong Zhang
- the Department of Chemistry, Chemical Biology, and Biomedical Engineering, Stevens Institute of Technology, Castle Point on Hudson, Hoboken, New Jersey 07030
| | - Michael P. Hendrich
- the Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, and
| | - Aimin Liu
- From the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
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Nienhaus K, Nickel E, Lu C, Yeh SR, Nienhaus GU. Ligand migration in human indoleamine-2,3 dioxygenase. IUBMB Life 2011; 63:153-9. [PMID: 21445845 DOI: 10.1002/iub.431] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Human indoleamine 2,3-dioxygenase (hIDO), a monomeric heme enzyme, catalyzes the oxidative degradation of L-tryptophan (L-Trp) and other indoleamine derivatives. Its activity follows typical Michaelis-Menten behavior only for L-Trp concentrations up to 50 μM; a further increase in the concentration of L-Trp causes a decrease in the activity. This substrate inhibition of hIDO is a result of the binding of a second L-Trp molecule in an inhibitory substrate binding site of the enzyme. The molecular details of the reaction and the inhibition are not yet known. In the following, we summarize the present knowledge about this heme enzyme.
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Affiliation(s)
- Karin Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe, Germany.
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44
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Yuasa HJ, Ushigoe A, Ball HJ. Molecular evolution of bacterial indoleamine 2,3-dioxygenase. Gene 2011; 485:22-31. [PMID: 21689736 DOI: 10.1016/j.gene.2011.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 05/30/2011] [Accepted: 06/03/2011] [Indexed: 12/31/2022]
Abstract
Indoleamine 2,3-dioxygenase (IDO) and tryptophan 2,3-dioxygenase (TDO) are tryptophan-degrading enzymes that catalyze the first step in L-Trp catabolism via the kynurenine pathway. In mammals, TDO is mainly expressed in the liver and primarily supplies nicotinamide adenine dinucleotide (NAD(+)). TDO is widely distributed from mammals to bacteria. Active IDO enzymes have been reported only in vertebrates and fungi. In mammals, IDO activity plays a significant role in the immune system while in fungal species, IDO is constitutively expressed and supplies NAD(+), like mammalian TDO. A search of genomic databases reveals that some bacterial species also have a putative IDO gene. A phylogenetic analysis clustered bacterial IDOs into two groups, group I or group II bacterial IDOs. The catalytic efficiencies of group I bacterial IDOs were very low and they are suspected not to contribute significantly to L-Trp metabolism. The bacterial species bearing the group I bacterial IDO are scattered across a few phyla and no phylogenetically close relationship is observed between them. This suggests that the group I bacterial IDOs might be acquired by horizontal gene transmission that occurred in each lineage independently. In contrast, group II bacterial IDOs showed rather high catalytic efficiency. Particularly, the enzymatic characteristics (K(m), V(max) and inhibitor selectivity) of the Gemmatimonas aurantiaca IDO are comparable to those of mammalian IDO1, although comparison of the IDO sequences does not suggest a close evolutionary relationship. In several bacteria, TDO and the kynureninase gene (kynU) are clustered on their chromosome suggesting that these genes could be transcribed in an operon. Interestingly, G. aurantiaca has no TDO, and the IDO is clustered with kynU on its chromosome. Although the G. aurantiaca also has NadA and NadB to synthesize a quinolinic acid (a precursor of NAD(+)) via the aspartate pathway, the high activity of the G. aurantiaca IDO flanking the kynU gene suggests its IDO has a function similar to eukaryotic enzymes.
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Affiliation(s)
- Hajime J Yuasa
- Laboratory of Biochemistry, Department of Applied Science, National University Corporation Kochi University, Japan.
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45
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Abstract
The critical role of the ferryl intermediate in catalyzing the oxygen chemistry of monooxygenases, oxidases, or peroxidases has been known for decades. In contrast, its involvement in heme-based dioxygenases, such as human indoleamine 2,3-dioxygenase (hIDO), was not recognized until recently. In this study, H(2)O(2) was used as a surrogate to generate the ferryl intermediate of hIDO. Spectroscopic data demonstrate that the ferryl species is capable of oxidizing azinobis(3-ethylbenzothiazoline-6-sulfonic acid) but not L-Trp. Kinetic studies reveal that the conversion of the ferric enzyme to the ferryl intermediate facilitates the L-Trp binding rate by >400-fold; conversely, L-Trp binding to the enzyme retards the peroxide reaction rate by ∼9-fold, because of the significant elevation of the entropic barrier. The unfavorable entropic factor for the peroxide reaction highlights the scenario that the structure of hIDO is not optimized for utilizing H(2)O(2) as a co-substrate for oxidizing L-Trp. Titration studies show that the ferryl intermediate possesses two substrate-binding sites with a K(d) of 0.3 and 440 μM and that the electronic properties of the ferryl moiety are sensitive to the occupancy of the two substrate-binding sites. The implications of the data are discussed in the context of the structural and functional relationships of the enzyme.
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Affiliation(s)
- Changyuan Lu
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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46
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Efimov I, Basran J, Thackray SJ, Handa S, Mowat CG, Raven EL. Structure and reaction mechanism in the heme dioxygenases. Biochemistry 2011; 50:2717-24. [PMID: 21361337 PMCID: PMC3092302 DOI: 10.1021/bi101732n] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
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As members of the family of heme-dependent enzymes, the heme dioxygenases are differentiated by virtue of their ability to catalyze the oxidation of l-tryptophan to N-formylkynurenine, the first and rate-limiting step in tryptophan catabolism. In the past several years, there have been a number of important developments that have meant that established proposals for the reaction mechanism in the heme dioxygenases have required reassessment. This focused review presents a summary of these recent advances, written from a structural and mechanistic perspective. It attempts to present answers to some of the long-standing questions, to highlight as yet unresolved issues, and to explore the similarities and differences of other well-known catalytic heme enzymes such as the cytochromes P450, NO synthase, and peroxidases.
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Affiliation(s)
- Igor Efimov
- Department of Chemistry, George Porter Building, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
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47
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Yuasa HJ, Ball HJ. Molecular evolution and characterization of fungal indoleamine 2,3-dioxygenases. J Mol Evol 2010; 72:160-8. [PMID: 21170645 DOI: 10.1007/s00239-010-9412-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 11/12/2010] [Indexed: 11/26/2022]
Abstract
Indoleamine 2,3-dioxygenase (IDO) and tryptophan 2,3-dioxygenase (TDO) are tryptophan-degrading enzymes. Mammalian IDO expression is induced by cytokines and has antimicrobial and immunomodulatory effects. A major role of mammalian TDO is to supply nicotinamide adenine dinucleotide (NAD(+)). In fungi, the IDO homologue is thought to be expressed constitutively and supply NAD(+), as TDO is absent from their genomes. Here, we reveal the distribution of IDO genes among fungal species and characterize their enzymatic activity. The yeast, Saccharomyces cerevisiae has only one IDO gene, whereas the koji-mold, Aspergillus oryzae has two genes, IDOα and IDOβ. The A. oryzae IDOα showed more similar enzymatic properties to those of S. cerevisiae IDO than IDOβ, suggesting that the A. oryzae IDOα is a functional homologue of the S. cerevisiae IDO. From the IDOβ gene, two isoforms, IDOβ and IDOβ(+) could be generated by alternative splicing. The latter contained a 17 amino acids insertion which were encoded by the first intron of IDOβ gene. In comparison to IDOβ(+), bacterially expressed IDOβ showed much lower K(m) value and more than five-times faster V(max) value, resulting in 85 times higher catalytic efficiency; i.e., the removal of the domain encoded by the first intron from IDOβ(+) increases its enzymatic activity drastically. This might be a unique regulation mechanism of the L-Trp metabolism in the A. oryzae. The levo-1-methyl tryptophan (L-1MT) is a good inhibitor of both IDO1 and IDO2. However, the activity of fungal IDOs tested was not inhibited at all by L-1MT.
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Affiliation(s)
- Hajime J Yuasa
- Laboratory of Biochemistry, Department of Applied Science, Faculty of Science, National University Corporation Kochi University, Kochi 780-8520, Japan.
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48
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Yuasa HJ, Ball HJ, Austin CJ, Hunt NH. 1-l-methyltryptophan is a more effective inhibitor of vertebrate IDO2 enzymes than 1-d-methyltryptophan. Comp Biochem Physiol B Biochem Mol Biol 2010; 157:10-5. [DOI: 10.1016/j.cbpb.2010.04.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 04/12/2010] [Accepted: 04/13/2010] [Indexed: 01/23/2023]
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49
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Lu C, Lin Y, Yeh SR. Spectroscopic studies of ligand and substrate binding to human indoleamine 2,3-dioxygenase. Biochemistry 2010; 49:5028-34. [PMID: 20476772 DOI: 10.1021/bi1005078] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human indoleamine 2,3-dioxygenase (hIDO) is an intracellular heme-containing enzyme, which catalyzes the initial and rate-determining step of l-tryptophan (l-Trp) metabolism via the kynurenine pathway in nonhepatic tissues. Steady-state kinetic data showed that hIDO exhibits substrate inhibition behavior, implying the existence of a second substrate binding site in the enzyme, although so far there is no direct evidence supporting it. The kinetic data also revealed that the K(m) of l-Trp (15 microM) is approximately 27-fold lower than the K(d) of l-Trp (0.4 mM) for the ligand-free ferrous enzyme, suggesting that O(2) binding proceeds l-Trp binding during the catalytic cycle. With cyanide as a structural probe, we have investigated the thermodynamic and kinetic parameters associated with ligand and substrate binding to hIDO. Equilibrium titration studies show that the cyanide adduct is capable of binding two l-Trp molecules, with K(d) values of 18 microM and 26 mM. The data offer the first direct evidence of the second substrate binding site in hIDO. Kinetic studies demonstrate that prebinding of l-Trp to the enzyme retards cyanide binding by approximately 13-fold, while prebinding of cyanide to the enzyme facilitates l-Trp binding by approximately 22-fold. The data support the view that during the active turnover of the enzyme it is kinetically more favored to bind O(2) prior to l-Trp.
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Affiliation(s)
- Changyuan Lu
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
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50
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Davydov RM, Chauhan N, Thackray SJ, Anderson JLR, Papadopoulou ND, Mowat CG, Chapman SK, Raven EL, Hoffman BM. Probing the ternary complexes of indoleamine and tryptophan 2,3-dioxygenases by cryoreduction EPR and ENDOR spectroscopy. J Am Chem Soc 2010; 132:5494-500. [PMID: 20353179 PMCID: PMC2903012 DOI: 10.1021/ja100518z] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Indexed: 11/30/2022]
Abstract
We have applied cryoreduction/EPR/ENDOR techniques to characterize the active-site structure of the ferrous-oxy complexes of human (hIDO) and Shewanella oneidensis (sIDO) indoleamine 2,3-dioxygenases, Xanthomonas campestris (XcTDO) tryptophan 2,3-dioxygenase, and the H55S variant of XcTDO in the absence and in the presence of the substrate L-Trp and a substrate analogue, L-Me-Trp. The results reveal the presence of multiple conformations of the binary ferrous-oxy species of the IDOs. In more populated conformers, most likely a water molecule is within hydrogen-bonding distance of the bound ligand, which favors protonation of a cryogenerated ferric peroxy species at 77 K. In contrast to the binary complexes, cryoreduction of all of the studied ternary [enzyme-O(2)-Trp] dioxygenase complexes generates a ferric peroxy heme species with very similar EPR and (1)H ENDOR spectra in which protonation of the basic peroxy ligand does not occur at 77 K. Parallel studies with L-Me-Trp, in which the proton of the indole nitrogen is replaced with a methyl group, eliminate the possibility that the indole NH group of the substrate acts as a hydrogen bond donor to the bound O(2), and we suggest instead that the ammonium group of the substrate hydrogen-bonds to the dioxygen ligand. The present data show that substrate binding, primarily through this H-bond, causes the bound dioxygen to adopt a new conformation, which presumably is oriented for insertion of O(2) into the C(2)-C(3) double bond of the substrate. This substrate interaction further helps control the reactivity of the heme-bound dioxygen by "shielding" it from water.
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