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Schwartz M, Petiot N, Chaloyard J, Senty-Segault V, Lirussi F, Senet P, Nicolai A, Heydel JM, Canon F, Sonkaria S, Khare V, Didierjean C, Neiers F. Structural and Thermodynamic Insights into Dimerization Interfaces of Drosophila Glutathione Transferases. Biomolecules 2024; 14:758. [PMID: 39062472 PMCID: PMC11274453 DOI: 10.3390/biom14070758] [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] [Received: 05/24/2024] [Revised: 06/17/2024] [Accepted: 06/23/2024] [Indexed: 07/28/2024] Open
Abstract
This study presents a comprehensive analysis of the dimerization interfaces of fly GSTs through sequence alignment. Our investigation revealed GSTE1 as a particularly intriguing target, providing valuable insights into the variations within Delta and Epsilon GST interfaces. The X-ray structure of GSTE1 was determined, unveiling remarkable thermal stability and a distinctive dimerization interface. Utilizing circular dichroism, we assessed the thermal stability of GSTE1 and other Drosophila GSTs with resolved X-ray structures. The subsequent examination of GST dimer stability correlated with the dimerization interface supported by findings from X-ray structural analysis and thermal stability measurements. Our discussion extends to the broader context of GST dimer interfaces, offering a generalized perspective on their stability. This research enhances our understanding of the structural and thermodynamic aspects of GST dimerization, contributing valuable insights to the field.
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Affiliation(s)
- Mathieu Schwartz
- Flavour Perception: Molecular Mechanisms (Flavours), INRAE, CNRS, Université de Bourgogne, 21000 Dijon, France; (M.S.); (J.C.); (V.S.-S.); (J.-M.H.)
| | - Nicolas Petiot
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS, Université de Bourgogne Franche-Comté, 21078 Dijon, France; (N.P.); (P.S.); (A.N.)
| | - Jeanne Chaloyard
- Flavour Perception: Molecular Mechanisms (Flavours), INRAE, CNRS, Université de Bourgogne, 21000 Dijon, France; (M.S.); (J.C.); (V.S.-S.); (J.-M.H.)
| | - Véronique Senty-Segault
- Flavour Perception: Molecular Mechanisms (Flavours), INRAE, CNRS, Université de Bourgogne, 21000 Dijon, France; (M.S.); (J.C.); (V.S.-S.); (J.-M.H.)
| | - Frédéric Lirussi
- UMR 1231, Lipides Nutrition Cancer, INSERM, 21000 Dijon, France;
- UFR des Sciences de Santé, Université de Bourgogne Franche-Comté, 25000 Besançon, France
- Plateforme PACE, Laboratoire de Pharmacologie-Toxicologie, Centre Hospitalo-Universitaire Besançon, 25000 Besançon, France
| | - Patrick Senet
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS, Université de Bourgogne Franche-Comté, 21078 Dijon, France; (N.P.); (P.S.); (A.N.)
| | - Adrien Nicolai
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS, Université de Bourgogne Franche-Comté, 21078 Dijon, France; (N.P.); (P.S.); (A.N.)
| | - Jean-Marie Heydel
- Flavour Perception: Molecular Mechanisms (Flavours), INRAE, CNRS, Université de Bourgogne, 21000 Dijon, France; (M.S.); (J.C.); (V.S.-S.); (J.-M.H.)
| | | | - Sanjiv Sonkaria
- Soft Foundry Institute, Seoul National University, Kwanak-gu, Seoul 39-131, Republic of Korea; (S.S.); (V.K.)
| | - Varsha Khare
- Soft Foundry Institute, Seoul National University, Kwanak-gu, Seoul 39-131, Republic of Korea; (S.S.); (V.K.)
| | | | - Fabrice Neiers
- Flavour Perception: Molecular Mechanisms (Flavours), INRAE, CNRS, Université de Bourgogne, 21000 Dijon, France; (M.S.); (J.C.); (V.S.-S.); (J.-M.H.)
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Moural TW, Koirala B K S, Bhattarai G, He Z, Guo H, Phan NT, Rajotte EG, Biddinger DJ, Hoover K, Zhu F. Architecture and potential roles of a delta-class glutathione S-transferase in protecting honey bee from agrochemicals. CHEMOSPHERE 2024; 350:141089. [PMID: 38163465 DOI: 10.1016/j.chemosphere.2023.141089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 12/19/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
The European honey bee, Apis mellifera, serves as the principle managed pollinator species globally. In recent decades, honey bee populations have been facing serious health threats from combined biotic and abiotic stressors, including diseases, limited nutrition, and agrochemical exposure. Understanding the molecular mechanisms underlying xenobiotic adaptation of A. mellifera is critical, considering its extensive exposure to phytochemicals and agrochemicals present in the environment. In this study, we conducted a comprehensive structural and functional characterization of AmGSTD1, a delta class glutathione S-transferase (GST), to unravel its roles in agrochemical detoxification and antioxidative stress responses. We determined the 3-dimensional (3D) structure of a honey bee GST using protein crystallography for the first time, providing new insights into its molecular structure. Our investigations revealed that AmGSTD1 metabolizes model substrates, including 1-chloro-2,4-dinitrobenzene (CDNB), p-nitrophenyl acetate (PNA), phenylethyl isothiocyanate (PEITC), propyl isothiocyanate (PITC), and the oxidation byproduct 4-hydroxynonenal (HNE). Moreover, we discovered that AmGSTD1 exhibits binding affinity with the fluorophore 8-Anilinonaphthalene-1-sulfonic acid (ANS), which can be inhibited with various herbicides, fungicides, insecticides, and their metabolites. These findings highlight the potential contribution of AmGSTD1 in safeguarding honey bee health against various agrochemicals, while also mitigating oxidative stress resulting from exposure to these substances.
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Affiliation(s)
- Timothy W Moural
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Sonu Koirala B K
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Gaurab Bhattarai
- Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Athens, GA 30602, USA.
| | - Ziming He
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Haoyang Guo
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Ngoc T Phan
- Department of Entomology and Plant Pathology, University of Arkansas, AR 72701, USA; Research Center for Tropical Bees and Beekeeping, Vietnam National University of Agriculture, Gia Lam, Hanoi 100000, Viet Nam.
| | - Edwin G Rajotte
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA.
| | - David J Biddinger
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA; Penn State Fruit Research and Extension Center, Biglerville, PA 17307, USA.
| | - Kelli Hoover
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Fang Zhu
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA; Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.
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Koirala B K S, Moural T, Zhu F. Functional and Structural Diversity of Insect Glutathione S-transferases in Xenobiotic Adaptation. Int J Biol Sci 2022; 18:5713-5723. [PMID: 36263171 PMCID: PMC9576527 DOI: 10.7150/ijbs.77141] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/29/2022] [Indexed: 01/12/2023] Open
Abstract
As a superfamily of multifunctional enzymes that is mainly associated with xenobiotic adaptation, glutathione S-transferases (GSTs) facilitate insects' survival under chemical stresses in their environment. GSTs confer xenobiotic adaptation through direct metabolism or sequestration of xenobiotics, and/or indirectly by providing protection against oxidative stress induced by xenobiotic exposure. In this article, a comprehensive overview of current understanding on the versatile functions of insect GSTs in detoxifying chemical compounds is presented. The diverse structures of different classes of insect GSTs, specifically the spatial localization and composition of their amino acid residues constituted in their active sites are also summarized. Recent availability of whole genome sequences of numerous insect species, accompanied by RNA interference, X-ray crystallography, enzyme kinetics and site-directed mutagenesis techniques have significantly enhanced our understanding of functional and structural diversity of insect GSTs.
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Affiliation(s)
- Sonu Koirala B K
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA
| | - Timothy Moural
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA
| | - Fang Zhu
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA.,Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.,✉ Corresponding author: Dr. Fang Zhu, Department of Entomology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA. Phone: +1-814-863-4432; Fax: +1- 814-865-3048; E-mail:
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Mosquitocidal Activity of the Methanolic Extract of Annickiachlorantha and Its Isolated Compounds against Culex pipiens, and Their Impact on the Non-Target Organism Zebrafish, Danio rerio. INSECTS 2022; 13:insects13080676. [PMID: 36005300 PMCID: PMC9409109 DOI: 10.3390/insects13080676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 07/18/2022] [Accepted: 07/22/2022] [Indexed: 02/04/2023]
Abstract
In this study, the crude extract and its isolated compounds from the stem bark of Annickia chlorantha were tested for their larvicidal, developmental, and repellent activity against the mosquito vector, Culex pipiens, besides their toxicity to the non-target aquatic organism, the zebrafish (Danio rerio). The acute larvicidal activity of isolated compounds; namely, palmatine, jatrorrhizine, columbamine, β-sitosterol, and Annickia chlorantha methanolic extract (AC), was observed. Developmentally, the larval duration was significantly prolonged when palmatine and β-sitosterol were applied, whereas the pupal duration was significantly prolonged for almost all treatments except palmatine and jatrorrhizine, where it shortened from those in the control. Acetylcholinesterase (AChE) enzyme showed different activity patterns, where it significantly increased in columbamine and β-sitosterol, and decreased in (AC), palmatine, and jatrorrhizine treatments, whereas glutathione S-transferase (GST) enzyme was significantly increased when AC methanolic extract/isolated compounds were applied, compared to the control. The adult emergence percentages were significantly decreased in all treatments, whereas tested compounds revealed non-significant (p > 0.05) changes in the sex ratio percentages, with a slight female-to-male preference presented in the AC-treated group. Additionally, the tested materials revealed repellence action; interestingly, palmatine and jatrorrhizine recorded higher levels of protection, followed by AC, columbamine, and β-sitosterol for 7 consecutive hours compared to the negative and positive control groups. The non-target assay confirms that the tested materials have very low toxic activity compared to the reported toxicity against mosquito larvae. A docking simulation was employed to better understand the interaction of the isolated compounds with the enzymes, AChE and GST. Additionally, DFT calculations revealed that the reported larvicidal activity may be due to the differing electron distributions among tested compounds. Overall, this study highlights the potential of A. chlorantha extract and its isolated compounds as effective mosquitocidal agents with a very low toxic effect on non-target organisms.
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Expression Patterns of Drosophila Melanogaster Glutathione Transferases. INSECTS 2022; 13:insects13070612. [PMID: 35886788 PMCID: PMC9318439 DOI: 10.3390/insects13070612] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 11/17/2022]
Abstract
Glutathione transferases (GSTs) are ubiquitous enzymes that catalyze the conjugation of glutathione to various molecules. Among the 42 GSTs identified in Drosophila melanogaster, Delta and Epsilon are the largest classes, with 25 members. The Delta and Epsilon classes are involved in different functions, such as insecticide resistance and ecdysone biosynthesis. The insect GST number variability is due mainly to these classes. Thus, they are generally considered supports during the evolution for the adaptability of the insect species. To explore the link between Delta and Epsilon GST and their evolution, we analyzed the sequences using bioinformatic tools. Subgroups appear within the Delta and Epsilon GSTs with different levels of diversification. The diversification also appears in the sequences showing differences in the active site. Additionally, amino acids essential for structural stability or dimerization appear conserved in all GSTs. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis revealed that the transcripts corresponding to these two classes are heterogeneously expressed within D. melanogaster. Some GSTs, such as GSTD1, are highly expressed in all tissues, suggesting their general function in detoxification. Conversely, some others, such as GSTD11 or GSTE4, are specifically expressed at a high level specifically in antennae, suggesting a potential role in olfaction.
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Structural and Functional Characterization of One Unclassified Glutathione S-Transferase in Xenobiotic Adaptation of Leptinotarsa decemlineata. Int J Mol Sci 2021; 22:ijms222111921. [PMID: 34769352 PMCID: PMC8584303 DOI: 10.3390/ijms222111921] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 11/18/2022] Open
Abstract
Arthropod Glutathione S-transferases (GSTs) constitute a large family of multifunctional enzymes that are mainly associated with xenobiotic or stress adaptation. GST-mediated xenobiotic adaptation takes place through direct metabolism or sequestration of xenobiotics, and/or indirectly by providing protection against oxidative stress induced by xenobiotic exposure. To date, the roles of GSTs in xenobiotic adaptation in the Colorado potato beetle (CPB), a notorious agricultural pest of plants within Solanaceae, have not been well studied. Here, we functionally expressed and characterized an unclassified-class GST, LdGSTu1. The three-dimensional structure of the LdGSTu1 was solved with a resolution up to 1.8 Å by X-ray crystallography. The signature motif VSDGPPSL was identified in the “G-site”, and it contains the catalytically active residue Ser14. Recombinant LdGSTu1 was used to determine enzyme activity and kinetic parameters using 1-chloro-2, 4-dinitrobenzene (CDNB), GSH, p-nitrophenyl acetate (PNA) as substrates. The enzyme kinetic parameters and enzyme-substrate interaction studies demonstrated that LdGSTu1 could catalyze the conjugation of GSH to both CDNB and PNA, with a higher turnover number for CDNB than PNA. The LdGSTu1 enzyme inhibition assays demonstrated that the enzymatic conjugation of GSH to CDNB was inhibited by multiple pesticides, suggesting a potential function of LdGSTu1 in xenobiotic adaptation.
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Daneshian L, Schlachter C, Timmers LFSM, Radford T, Kapingidza B, Dias T, Liese J, Sperotto RA, Grbic V, Grbic M, Chruszcz M. Delta class glutathione S-transferase (TuGSTd01) from the two-spotted spider mite Tetranychus urticae is inhibited by abamectin. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2021; 176:104873. [PMID: 34119218 DOI: 10.1016/j.pestbp.2021.104873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 04/28/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
GSTs (Glutathione S-transferases) are known to catalyze the nucleophilic attack of the sulfhydryl group of reduced glutathione (GSH) on electrophilic centers of xenobiotic compounds, including insecticides and acaricides. Genome analyses of the polyphagous spider mite herbivore Tetranychus urticae (two-spotted spider mite) revealed the presence of a set of 32 genes that code for secreted proteins belonging to the GST family of enzymes. To better understand the role of these proteins in T. urticae, we have functionally characterized TuGSTd01. Moreover, we have modeled the structure of the enzyme in apo form, as well as in the form with bound inhibitor. We demonstrated that this protein is a glutathione S-transferase that can conjugate glutathione to 1-chloro-2,4-dinitrobenzene (CDNB). We have tested TuGSTd01 activity with a range of potential substrates such as cinnamic acid, cumene hydroperoxide, and allyl isothiocyanate; however, the enzyme was unable to process these compounds. Using mutagenesis, we showed that putative active site variants S11A, E66A, S67A, and R68A mutants, which were residues predicted to interact directly with GSH, have no measurable activity, and these residues are required for the enzymatic activity of TuGSTd01. There are several reports that associate some T. urticae acaricide resistance with increased activity of GSTs . However, we found that TuGSTd01 is not able to detoxify abamectin; in fact, the acaricide inhibits the enzyme with Ki = 101 μM. Therefore, we suggest that the increased GST activity observed in abamectin resistant T. urticae field populations is a part of the compensatory feedback loop. In this case, the increased production of GSTs and relatively high concentration of GSH in cells allow GSTs to maintain physiological functions despite the presence of the acaricide.
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Affiliation(s)
- Leily Daneshian
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Caleb Schlachter
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | | | - Taylor Radford
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Brenda Kapingidza
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Travis Dias
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Jana Liese
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Raul Antonio Sperotto
- Graduate Program in Biotechnology, University of Taquari Valley - Univates, Lajeado, Rio Grande do Sul, Brazil
| | - Vojislava Grbic
- Department of Biology, Western University, London, Ontario N6A 5B7, Canada; The University of La Rioja, Logrono, Spain
| | - Miodrag Grbic
- Department of Biology, Western University, London, Ontario N6A 5B7, Canada; The University of La Rioja, Logrono, Spain
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA.
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Sharma S, Arora B, Gaur SN, Arora N. Bioinformatic and immunological investigation of Per a 5 (delta class GST) allergen from Periplaneta americana. Mol Immunol 2021; 132:93-101. [PMID: 33556711 DOI: 10.1016/j.molimm.2021.01.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/13/2021] [Accepted: 01/20/2021] [Indexed: 11/18/2022]
Abstract
INTRODUCTION GSTs are multifunctional enzymes involved in cellular detoxification and present as potent allergens in several sources. Present study investigates allergenic relevance of GST from P. americana and determine its cross reactive potential with other indoor allergen sources. METHODS Computational analysis with FASTA and ConSurf webserver was performed to determine potentially cross reactive allergens. Further, Per a 5 gene was cloned in pET 22b+ vector and expressed in E.coli BL21 cells and the rPer a 5 protein was purified using Ni-NTA affinity chromatography. Enzymatic activity of rPer a 5 was assessed using CDNB and cumene hydroperoxide. ELISA and immunoblot were performed using cockroach hypersensitive patient's sera. Functional activity of rPer a 5 was evaluated by basophil activation test. Inhibition studies were carried out with D. pteronyssinus, A. alternata and C. lunata extracts. RESULTS Per a 5 demonstrates highest sequence similarity with delta class GST of Blattella germanica (94.9%). It also exhibits significant sequence similarity (50-58%) with mite, fungal and helminth allergenic GSTs. ConSurf analysis reveals high degree of evolutionary similarity in N terminal region of Per a 5, especially at GST dimerization interface. The purified rPer a 5 protein resolved at 27 kDa on SDS-PAGE. The rPer a 5 protein exhibits GST activity and possess upto 65% immunoreactivity with cockroach hypersensitive patient's sera in ELISA and immunoblot. It upregulates expression of CD203c on basophils signifying its biological ability to activate effector cells. rPer a 5 significantly inhibits corresponding GSTs in P. americana, D. pteronyssinus, A. alternata and C. lunata with EC50 values of 15.5 ng. 38.38 ng, 41.4 ng and 61.66 ng, respectively. CONCLUSION Recombinant delta class GST of P. americana is a clinically relevant allergen showing upto 65% immunoreactivity with hypersensitive patient's sera. Per a 5 GST allergen showed phylogenetic similarity with dust mite, fungal and birch allergens thereby demonstrating allergen cross reactivity.
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Affiliation(s)
- Swati Sharma
- Allergy and Immunology Section, CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110007, India; Academy of Scientific and Innovative Research, Ghaziabad, U.P., 201002, India
| | - Bharti Arora
- Allergy and Immunology Section, CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110007, India; Academy of Scientific and Innovative Research, Ghaziabad, U.P., 201002, India
| | - S N Gaur
- Department of Pulmonary Medicine, V.P. Chest Institute, University of Delhi, New Delhi, 110007, India
| | - Naveen Arora
- Allergy and Immunology Section, CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110007, India; Academy of Scientific and Innovative Research, Ghaziabad, U.P., 201002, India.
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Yamamoto K, Yamaguchi M, Yamada N. Investigation of the active site of an unclassified glutathione transferase in Bombyx mori by alanine scanning. JOURNAL OF PESTICIDE SCIENCE 2020; 45:238-240. [PMID: 33304193 PMCID: PMC7691559 DOI: 10.1584/jpestics.d20-036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 07/20/2020] [Indexed: 06/12/2023]
Abstract
Glutathione transferase (GST) is an important class of detoxification enzymes that are vital for defense against various xenobiotics and cellular oxidative stress. Previously, we had reported an unclassified glutathione transferase 2 in Bombyx mori (bmGSTu2) to be responsible for detoxifying diazinon. In this study, we aimed to identify the amino acid residues that constitute a hydrogen-bonding network important for GST activity. Site-directed mutagenesis of bmGSTu2 suggested that residues Asn102, Pro162, and Ser166 contribute to its catalytic activity.
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Affiliation(s)
- Kohji Yamamoto
- Department of Bioscience and Biotechnology, Kyushu University Graduate School
| | - Misuzu Yamaguchi
- Department of Bioscience and Biotechnology, Kyushu University Graduate School
| | - Naotaka Yamada
- Department of Bioscience and Biotechnology, Kyushu University Graduate School
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Park JC, Lee MC, Yoon DS, Han J, Park HG, Hwang UK, Lee JS. Genome-wide identification and expression of the entire 52 glutathione S-transferase (GST) subfamily genes in the Cu 2+-exposed marine copepods Tigriopus japonicus and Paracyclopina nana. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 209:56-69. [PMID: 30735907 DOI: 10.1016/j.aquatox.2019.01.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 01/23/2019] [Accepted: 01/23/2019] [Indexed: 06/09/2023]
Abstract
In this study, the entire glutathione S-transferases (GSTs), the major phase II detoxification enzyme, were identified in two marine copepod species Tigriopus japonicus and Paracyclopina nana. The genome-wide identification of GSTs in T. japonicus and P. nana resulted in 32 and 20 GSTs in total, respectively. Among the identified GSTs, two specific classes of GSTs, specifically sigma and delta/epsilon GSTs were the dominant form of cytosolic GSTs in T. japonicus, while delta/epsilon and mu classes were dominant cytosolic GSTs in P. nana. In addition, Membrane-Associated Proteins in Eicosanoid and Glutathione metabolism (MAPEG) family were found in relatively higher proportion compared to other classes. Moreover, sigma, delta/epsilon, and microsomal GSTs have shown to expand through tandem duplication. To validate the detoxification function of the identified GSTs, both copepods were exposed to copper (Cu2+) and the reactive oxygen species (ROS) level and GST activity were measured. With integration of phylogenetic analysis and xenobiotic-mediated GST mRNA expression patterns along with previous enzymatic activities, the functional divergence among species-specific GST genes was clearly observed. This study covers full identification of GST classes in two marine copepod species and their important role in marine environmental ecotoxicology.
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Affiliation(s)
- Jun Chul Park
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Chul Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Deok-Seo Yoon
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jeonghoon Han
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Heum Gi Park
- Department of Marine Resource Development, College of Life Sciences, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Un-Ki Hwang
- Marine Ecological Risk Assessment Center, West Sea Fisheries Research Institute, National Institute of Fisheries Science, Incheon 46083, South Korea
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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Malik A, Khan JM, Alamery SF, Fouad D, Labrou NE, Daoud MS, Abdelkader MO, Ataya FS. Monomeric Camelus dromedarius GSTM1 at low pH is structurally more thermostable than its native dimeric form. PLoS One 2018; 13:e0205274. [PMID: 30303997 PMCID: PMC6179282 DOI: 10.1371/journal.pone.0205274] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 09/21/2018] [Indexed: 01/01/2023] Open
Abstract
Glutathione S‒transferases (GSTs) are multifunctional enzymes that play an important role in detoxification, cellular signalling, and the stress response. Camelus dromedarius is well-adapted to survive in extreme desert climate and it has GSTs, for which limited information is available. This study investigated the structure-function and thermodynamic properties of a mu-class camel GST (CdGSTM1) at different pH. Recombinant CdGSTM1 (25.7 kDa) was expressed in E. coli and purified to homogeneity. Dimeric CdGSTM1 dissociated into stable but inactive monomeric subunits at low pH. Conformational and thermodynamic changes during the thermal unfolding pathway of dimeric and monomeric CdGSTM1 were characterised via a thermal shift assay and dynamic multimode spectroscopy (DMS). The thermal shift assay based on intrinsic tryptophan fluorescence revealed that CdGSTM1 underwent a two-state unfolding pathway at pH 1.0-10.0. Its Tm value varied with varying pH. Another orthogonal technique based on far-UV CD also exhibited two-state unfolding in the dimeric and monomeric states. Generally, proteins tend to lose structural integrity and stability at low pH; however, monomeric CdGSTM1 at pH 2.0 was thermally more stable and unfolded with lower van't Hoff enthalpy. The present findings provide essential information regarding the structural, functional, and thermodynamic properties of CdGSTM1 at pH 1.0-10.0.
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Affiliation(s)
- Ajamaluddin Malik
- Department of Biochemistry, Protein Research Chair, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Javed M. Khan
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Salman F. Alamery
- Department of Biochemistry, Protein Research Chair, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Dalia Fouad
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Zoology and Entomology, Faculty of Science, Helwan University, Ein Helwan, Cairo, Egypt
| | - Nikolaos E. Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece
| | - Mohamed S. Daoud
- Department of Biochemistry, Protein Research Chair, College of Science, King Saud University, Riyadh, Saudi Arabia
- King Fahd Unit Laboratory, Department of Clinical and Chemical Pathology, Kasr Al-Ainy University Hospital, Cairo University, El-Manial, Cairo, Egypt
| | - Mohamed O. Abdelkader
- Department of Biochemistry, Protein Research Chair, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Farid S. Ataya
- Department of Biochemistry, Protein Research Chair, College of Science, King Saud University, Riyadh, Saudi Arabia
- Molecular Biology Department, Genetic Engineering Division, National Research Centre, Dokki, Giza, Egypt
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12
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Crystal structure of the delta-class glutathione transferase in Musca domestica. Biochem Biophys Res Commun 2018; 502:345-350. [DOI: 10.1016/j.bbrc.2018.05.161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 05/24/2018] [Indexed: 11/20/2022]
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13
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Gonzalez D, Fraichard S, Grassein P, Delarue P, Senet P, Nicolaï A, Chavanne E, Mucher E, Artur Y, Ferveur JF, Heydel JM, Briand L, Neiers F. Characterization of a Drosophila glutathione transferase involved in isothiocyanate detoxification. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 95:33-43. [PMID: 29578047 DOI: 10.1016/j.ibmb.2018.03.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/16/2018] [Accepted: 03/16/2018] [Indexed: 05/20/2023]
Abstract
Glutathione transferases (GSTs) are ubiquitous key enzymes that catalyse the conjugation of glutathione to xenobiotic compounds in the detoxification process. GSTs have been proposed to play a dual role in the signal termination of insect chemodetection by modifying odorant and tasting molecules and by protecting the chemosensory system. Among the 40 GSTs identified in Drosophila melanogaster, the Delta and Epsilon groups are insect-specific. GSTs Delta and Epsilon may have evolved to serve in detoxification, and have been associated with insecticide resistance. Here, we report the heterologous expression and purification of the D. melanogaster GST Delta 2 (GSTD2). We investigated the capacity of GSTD2 to bind tasting molecules. Among them, we found that isothiocyanates (ITC), insecticidal compounds naturally present in cruciferous plant and perceived as bitter, are good substrates for GSTD2. The X-ray structure of GSTD2 was solved, showing the absence of the classical Ser catalytic residue, conserved in the Delta and Epsilon GSTs. Using molecular dynamics, the interaction of ITC with the GSTD2 three-dimensional structure is analysed and discussed. These findings allow us to consider a biological role for GSTD2 in chemoperception, considering GSTD2 expression in the chemosensory organs and the potential consequences of insect exposure to ITC.
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Affiliation(s)
- Daniel Gonzalez
- Centre des Sciences du Goût et de l'Alimentation (CSGA), Université de Bourgogne Franche-Comté, INRA, CNRS, France
| | - Stéphane Fraichard
- Centre des Sciences du Goût et de l'Alimentation (CSGA), Université de Bourgogne Franche-Comté, INRA, CNRS, France
| | - Paul Grassein
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Univ. Bourgogne Franche-Comté, 9 Av. A. Savary, BP 47 870, F-21078, Dijon Cedex, France
| | - Patrice Delarue
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Univ. Bourgogne Franche-Comté, 9 Av. A. Savary, BP 47 870, F-21078, Dijon Cedex, France
| | - Patrick Senet
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Univ. Bourgogne Franche-Comté, 9 Av. A. Savary, BP 47 870, F-21078, Dijon Cedex, France
| | - Adrien Nicolaï
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Univ. Bourgogne Franche-Comté, 9 Av. A. Savary, BP 47 870, F-21078, Dijon Cedex, France
| | - Evelyne Chavanne
- Centre des Sciences du Goût et de l'Alimentation (CSGA), Université de Bourgogne Franche-Comté, INRA, CNRS, France
| | - Elodie Mucher
- Centre des Sciences du Goût et de l'Alimentation (CSGA), Université de Bourgogne Franche-Comté, INRA, CNRS, France
| | - Yves Artur
- Centre des Sciences du Goût et de l'Alimentation (CSGA), Université de Bourgogne Franche-Comté, INRA, CNRS, France
| | - Jean-François Ferveur
- Centre des Sciences du Goût et de l'Alimentation (CSGA), Université de Bourgogne Franche-Comté, INRA, CNRS, France
| | - Jean-Marie Heydel
- Centre des Sciences du Goût et de l'Alimentation (CSGA), Université de Bourgogne Franche-Comté, INRA, CNRS, France
| | - Loïc Briand
- Centre des Sciences du Goût et de l'Alimentation (CSGA), Université de Bourgogne Franche-Comté, INRA, CNRS, France
| | - Fabrice Neiers
- Centre des Sciences du Goût et de l'Alimentation (CSGA), Université de Bourgogne Franche-Comté, INRA, CNRS, France.
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14
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Bakari S, Lembrouk M, Sourd L, Ousalem F, André F, Orlowski S, Delaforge M, Frelet-Barrand A. Lactococcus lactis is an Efficient Expression System for Mammalian Membrane Proteins Involved in Liver Detoxification, CYP3A4, and MGST1. Mol Biotechnol 2016; 58:299-310. [PMID: 26961909 DOI: 10.1007/s12033-016-9928-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Despite the great importance of human membrane proteins involved in detoxification mechanisms, their wide use for biochemical approaches is still hampered by several technical difficulties considering eukaryotic protein expression in order to obtain the large amounts of protein required for functional and/or structural studies. Lactococcus lactis has emerged recently as an alternative heterologous expression system to Escherichia coli for proteins that are difficult to express. The aim of this work was to check its ability to express mammalian membrane proteins involved in liver detoxification, i.e., CYP3A4 and two isoforms of MGST1 (rat and human). Genes were cloned using two different strategies, i.e., classical or Gateway-compatible cloning, and we checked the possible influence of two affinity tags (6×-His-tag and Strep-tag II). Interestingly, all proteins could be successfully expressed in L. lactis at higher yields than those previously obtained for these proteins with classical expression systems (E. coli, Saccharomyces cerevisiae) or those of other eukaryotic membrane proteins expressed in L. lactis. In addition, rMGST1 was fairly active after expression in L. lactis. This study highlights L. lactis as an attractive system for efficient expression of mammalian detoxification membrane proteins at levels compatible with further functional and structural studies.
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Affiliation(s)
- Sana Bakari
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Mehdi Lembrouk
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Laura Sourd
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Fares Ousalem
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - François André
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Stéphane Orlowski
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Marcel Delaforge
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Annie Frelet-Barrand
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France. .,Institute FEMTO-ST, UMR6174 CNRS-Université de Franche-Comté, 25044, Besançon Cedex, France.
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15
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Chaurasia MK, Ravichandran G, Nizam F, Arasu MV, Al-Dhabi NA, Arshad A, Harikrishnan R, Arockiaraj J. In-silico analysis and mRNA modulation of detoxification enzymes GST delta and kappa against various biotic and abiotic oxidative stressors. FISH & SHELLFISH IMMUNOLOGY 2016; 54:353-363. [PMID: 27109581 DOI: 10.1016/j.fsi.2016.04.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/15/2016] [Accepted: 04/20/2016] [Indexed: 06/05/2023]
Abstract
This study reports the comprehensive comparative information of two different detoxification enzymes such as glutathione S-transferases (GSTs) delta and kappa from freshwater giant prawn Macrobrachium rosenbergii (designated as MrGSTD and MrGSTK) by investigating their in-silico characters and mRNA modulation against various biotic and abiotic oxidative stressors. The physico-chemical properties of these cDNA and their polypeptide structure were analyzed using various bioinformatics program. The analysis indicated the variation in size of the polypeptides, presence or absence of domains and motifs and structure. Homology and phylogenetic analysis revealed that MrGSTD shared maximum identity (83%) with crustaceans GST delta, whereas MrGSTK fell in arthropods GST kappa. It is interesting to note that MrGSTD and MrGSTK shared only 21% identity; it indicated their structural difference. Structural analysis indicated that MrGSTD to be canonical dimer like shape and MrGSTK appeared to be butterfly dimer like shape, in spite of four β-sheets being conserved in both GSTs. Tissue specific gene expression analysis showed that both MrGSTD and MrGSTK are highly expressed in immune organs such as haemocyte and hepatopancreas, respectively. To understand the role of mRNA modulation of MrGSTD and MrGSTK, the prawns were inducted with oxidative stressors such as bacteria (Vibrio harveyi), virus [white spot syndrome virus (WSSV)] and heavy metal, cadmium (Cd). The analysis revealed an interesting fact that both MrGSTD and MrGSTK showed higher (P < 0.05) up-regulation at 48 h post-challenge, except MrGSTD stressed with bacteria, where it showed up-regulation at 24 h post-challenge. Overall, the results suggested that GSTs are diverse in their structure and possibly conferring their potential involvement in immune protection in crustaceans. However, further study is necessary to focus their functional differences at proteomic level.
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Affiliation(s)
- Mukesh Kumar Chaurasia
- Division of Fisheries Biotechnology & Molecular Biology, Department of Biotechnology, Faculty of Science and Humanities, SRM University, Kattankulathur, 603 203 Chennai, Tamil Nadu, India
| | - Gayathri Ravichandran
- Division of Fisheries Biotechnology & Molecular Biology, Department of Biotechnology, Faculty of Science and Humanities, SRM University, Kattankulathur, 603 203 Chennai, Tamil Nadu, India; SRM Research Institute, SRM University, Kattankulathur, 603 203 Chennai, Tamil Nadu, India
| | - Faizal Nizam
- Division of Fisheries Biotechnology & Molecular Biology, Department of Biotechnology, Faculty of Science and Humanities, SRM University, Kattankulathur, 603 203 Chennai, Tamil Nadu, India
| | - Mariadhas Valan Arasu
- Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Naif Abdullah Al-Dhabi
- Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Aziz Arshad
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Ramasamy Harikrishnan
- Department of Zoology, Pachaiyappa's College for Men, Kanchipuram 631 501, Tamil Nadu, India
| | - Jesu Arockiaraj
- Division of Fisheries Biotechnology & Molecular Biology, Department of Biotechnology, Faculty of Science and Humanities, SRM University, Kattankulathur, 603 203 Chennai, Tamil Nadu, India.
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16
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Scian M, Le Trong I, Mazari AMA, Mannervik B, Atkins WM, Stenkamp RE. Comparison of epsilon- and delta-class glutathione S-transferases: the crystal structures of the glutathione S-transferases DmGSTE6 and DmGSTE7 from Drosophila melanogaster. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:2089-98. [PMID: 26457432 PMCID: PMC4601370 DOI: 10.1107/s1399004715013929] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 07/22/2015] [Indexed: 12/30/2022]
Abstract
Cytosolic glutathione transferases (GSTs) comprise a large family of enzymes with canonical structures that diverge functionally and structurally among mammals, invertebrates and plants. Whereas mammalian GSTs have been characterized extensively with regard to their structure and function, invertebrate GSTs remain relatively unstudied. The invertebrate GSTs do, however, represent potentially important drug targets for infectious diseases and agricultural applications. In addition, it is essential to fully understand the structure and function of invertebrate GSTs, which play important roles in basic biological processes. Invertebrates harbor delta- and epsilon-class GSTs, which are not found in other organisms. Drosophila melanogaster GSTs (DmGSTs) are likely to contribute to detoxication or antioxidative stress during development, but they have not been fully characterized. Here, the structures of two epsilon-class GSTs from Drosophila, DmGSTE6 and DmGSTE7, are reported at 2.1 and 1.5 Å resolution, respectively, and are compared with other GSTs to identify structural features that might correlate with their biological functions. The structures of DmGSTE6 and DmGSTE7 are remarkably similar; the structures do not reveal obvious sources of the minor functional differences that have been observed. The main structural difference between the epsilon- and delta-class GSTs is the longer helix (A8) at the C-termini of the epsilon-class enzymes.
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Affiliation(s)
- Michele Scian
- Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, WA 98195-7610, USA
| | - Isolde Le Trong
- Department of Biological Structure, University of Washington, Box 357420, Seattle, WA 98195-7420, USA
- Biomolecular Structure Center, University of Washington, Box 357742, Seattle, WA 98195-7742, USA
| | - Aslam M. A. Mazari
- Department of Neurochemistry, Arrhenius Laboratories, Stockholm University, SE-10 691 Stockholm, Sweden
| | - Bengt Mannervik
- Department of Neurochemistry, Arrhenius Laboratories, Stockholm University, SE-10 691 Stockholm, Sweden
| | - William M. Atkins
- Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, WA 98195-7610, USA
| | - Ronald E. Stenkamp
- Department of Biological Structure, University of Washington, Box 357420, Seattle, WA 98195-7420, USA
- Biomolecular Structure Center, University of Washington, Box 357742, Seattle, WA 98195-7742, USA
- Department of Biochemistry, University of Washington, Box 357430, Seattle, WA 98195-7430, USA
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17
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Leuthaeuser JB, Knutson ST, Kumar K, Babbitt PC, Fetrow JS. Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity. Protein Sci 2015; 24:1423-39. [PMID: 26073648 PMCID: PMC4570537 DOI: 10.1002/pro.2724] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 06/10/2015] [Indexed: 01/27/2023]
Abstract
The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information. In this contribution, this assumption is evaluated by observing topologies in similarity networks using three different edge metrics: sequence (BLAST), structure (TM-Align), and active site similarity (active site profiling, implemented in DASP). Network topologies for four well-studied protein superfamilies (enolase, peroxiredoxin (Prx), glutathione transferase (GST), and crotonase) were compared with curated functional hierarchies and structure. As expected, network topology differs, depending on edge metric; comparison of topologies provides valuable information on structure/function relationships. Subnetworks based on active site similarity correlate with known functional hierarchies at a single edge threshold more often than sequence- or structure-based networks. Sequence- and structure-based networks are useful for identifying sequence and domain similarities and differences; therefore, it is important to consider the clustering goal before deciding appropriate edge metric. Further, conserved active site residues identified in enolase and GST active site subnetworks correspond with published functionally important residues. Extension of this analysis yields predictions of functionally determinant residues for GST subgroups. These results support the hypothesis that active site similarity-based networks reveal clusters that share functional details and lay the foundation for capturing functionally relevant hierarchies using an approach that is both automatable and can deliver greater precision in function annotation than current similarity-based methods.
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Affiliation(s)
- Janelle B Leuthaeuser
- Department of Molecular Genetics and Genomics, Wake Forest University, Winston-Salem, North Carolina, 27106
| | - Stacy T Knutson
- Departments of Computer Science and Physics, Wake Forest University, Winston-Salem, North Carolina, 27106
| | - Kiran Kumar
- Departments of Computer Science and Physics, Wake Forest University, Winston-Salem, North Carolina, 27106
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences, Institute for Quantitative Biosciences University of California San Francisco, San Francisco, California, 94158.,Department of Pharmaceutical Chemistry, Institute for Quantitative Biosciences University of California San Francisco, San Francisco, California, 94158
| | - Jacquelyn S Fetrow
- Department of Molecular Genetics and Genomics, Wake Forest University, Winston-Salem, North Carolina, 27106.,Departments of Computer Science and Physics, Wake Forest University, Winston-Salem, North Carolina, 27106.,Office of the Provost, Maryland Hall 202, University of Richmond, VA, 23173
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18
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Aksoy M, Ozaslan MS, Kufrevioglu OI. Purification of glutathione S-transferase from Van Lake fish (Chalcalburnus tarichii Pallas) muscle and investigation of some metal ions effect on enzyme activity. J Enzyme Inhib Med Chem 2015; 31:546-50. [DOI: 10.3109/14756366.2015.1046063] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Mine Aksoy
- Department of Chemistry, Science Faculty, Atatürk University, Erzurum, Turkey
| | - M. Serhat Ozaslan
- Department of Chemistry, Science Faculty, Atatürk University, Erzurum, Turkey
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19
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Hossain MT, Yamamoto K. Structural insight into the active site of a Bombyx mori unclassified glutathione transferase. Biosci Biotechnol Biochem 2015; 79:989-91. [PMID: 25608724 DOI: 10.1080/09168451.2014.1002450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Glutathione transferases (GSTs) are major detoxification enzymes that play central roles in the defense against various environmental toxicants as well as oxidative stress. Here, we identify amino acid residues of an unclassified GST from Bombyx mori, bmGSTu-interacting glutathione (GSH). Site-directed mutagenesis of bmGSTu mutants indicated that amino acid residues Asp103, Ser162, and Ser166 contribute to catalytic activity.
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Affiliation(s)
- Md Tofazzal Hossain
- a Faculty of Agriculture , Kyushu University Graduate School , Fukuoka , Japan
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20
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Lallement PA, Brouwer B, Keech O, Hecker A, Rouhier N. The still mysterious roles of cysteine-containing glutathione transferases in plants. Front Pharmacol 2014; 5:192. [PMID: 25191271 PMCID: PMC4138524 DOI: 10.3389/fphar.2014.00192] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 07/26/2014] [Indexed: 12/31/2022] Open
Abstract
Glutathione transferases (GSTs) represent a widespread multigenic enzyme family able to modify a broad range of molecules. These notably include secondary metabolites and exogenous substrates often referred to as xenobiotics, usually for their detoxification, subsequent transport or export. To achieve this, these enzymes can bind non-substrate ligands (ligandin function) and/or catalyze the conjugation of glutathione onto the targeted molecules, the latter activity being exhibited by GSTs having a serine or a tyrosine as catalytic residues. Besides, other GST members possess a catalytic cysteine residue, a substitution that radically changes enzyme properties. Instead of promoting GSH-conjugation reactions, cysteine-containing GSTs (Cys-GSTs) are able to perform deglutathionylation reactions similarly to glutaredoxins but the targets are usually different since glutaredoxin substrates are mostly oxidized proteins and Cys-GST substrates are metabolites. The Cys-GSTs are found in most organisms and form several classes. While Beta and Omega GSTs and chloride intracellular channel proteins (CLICs) are not found in plants, these organisms possess microsomal ProstaGlandin E-Synthase type 2, glutathionyl hydroquinone reductases, Lambda, Iota and Hemerythrin GSTs and dehydroascorbate reductases (DHARs); the four last classes being restricted to the green lineage. In plants, whereas the role of DHARs is clearly associated to the reduction of dehydroascorbate to ascorbate, the physiological roles of other Cys-GSTs remain largely unknown. In this context, a genomic and phylogenetic analysis of Cys-GSTs in photosynthetic organisms provides an updated classification that is discussed in the light of the recent literature about the functional and structural properties of Cys-GSTs. Considering the antioxidant potencies of phenolic compounds and more generally of secondary metabolites, the connection of GSTs with secondary metabolism may be interesting from a pharmacological perspective.
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Affiliation(s)
- Pierre-Alexandre Lallement
- UMR1136, Interactions Arbres - Microorganismes, Université de Lorraine Vandoeuvre-lès-Nancy, France ; UMR1136, Interactions Arbres - Microorganismes, INRA Champenoux, France
| | - Bastiaan Brouwer
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University Umeå, Sweden
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University Umeå, Sweden
| | - Arnaud Hecker
- UMR1136, Interactions Arbres - Microorganismes, Université de Lorraine Vandoeuvre-lès-Nancy, France ; UMR1136, Interactions Arbres - Microorganismes, INRA Champenoux, France
| | - Nicolas Rouhier
- UMR1136, Interactions Arbres - Microorganismes, Université de Lorraine Vandoeuvre-lès-Nancy, France ; UMR1136, Interactions Arbres - Microorganismes, INRA Champenoux, France
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21
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Bocedi A, Fabrini R, Farrotti A, Stella L, Ketterman AJ, Pedersen JZ, Allocati N, Lau PCK, Grosse S, Eltis LD, Ruzzini A, Edwards TE, Morici L, Del Grosso E, Guidoni L, Bovi D, Lo Bello M, Federici G, Parker MW, Board PG, Ricci G. The impact of nitric oxide toxicity on the evolution of the glutathione transferase superfamily: a proposal for an evolutionary driving force. J Biol Chem 2013; 288:24936-47. [PMID: 23828197 DOI: 10.1074/jbc.m113.476135] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glutathione transferases (GSTs) are protection enzymes capable of conjugating glutathione (GSH) to toxic compounds. During evolution an important catalytic cysteine residue involved in GSH activation was replaced by serine or, more recently, by tyrosine. The utility of these replacements represents an enigma because they yield no improvements in the affinity toward GSH or in its reactivity. Here we show that these changes better protect the cell from nitric oxide (NO) insults. In fact the dinitrosyl·diglutathionyl·iron complex (DNDGIC), which is formed spontaneously when NO enters the cell, is highly toxic when free in solution but completely harmless when bound to GSTs. By examining 42 different GSTs we discovered that only the more recently evolved Tyr-based GSTs display enough affinity for DNDGIC (KD < 10(-9) M) to sequester the complex efficiently. Ser-based GSTs and Cys-based GSTs show affinities 10(2)-10(4) times lower, not sufficient for this purpose. The NO sensitivity of bacteria that express only Cys-based GSTs could be related to the low or null affinity of their GSTs for DNDGIC. GSTs with the highest affinity (Tyr-based GSTs) are also over-represented in the perinuclear region of mammalian cells, possibly for nucleus protection. On the basis of these results we propose that GST evolution in higher organisms could be linked to the defense against NO.
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Affiliation(s)
- Alessio Bocedi
- Department of Chemical Sciences and Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
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22
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Darracq A, Adams KL. Features of evolutionarily conserved alternative splicing events between Brassica and Arabidopsis. THE NEW PHYTOLOGIST 2013; 199:252-263. [PMID: 23551259 DOI: 10.1111/nph.12238] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 02/18/2013] [Indexed: 06/02/2023]
Abstract
Alternative splicing (AS) generates multiple types of mRNA from a single type of pre-mRNA by differential intron splicing. It can result in new protein isoforms or down-regulation of gene expression by transcript decay. The evolutionary conservation of AS events in plants is largely unexplored and only a small number of AS events have been identified as conserved between divergent species. We performed a large-scale analysis of cDNA data from Brassica and Arabidopsis to identify and further characterize conserved AS events. We identified 537 conserved AS events in 485 genes. Alternative donor and acceptor events are significantly overrepresented among conserved events, whereas intron retention and exon skipping events are underrepresented. Conserved AS events are significantly shorter, less likely to be in the 3'UTR, and they are enriched for genes whose products function in the chloroplast. AS modified a functional domain for about half of the genes with conserved events. We further characterized three genes with conserved AS events. This study identifies many AS events that are conserved between Brassica and Arabidopsis, revealing features of conserved AS events. Many of the conserved AS events may have important, but uncharacterized, functions.
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Affiliation(s)
- Aude Darracq
- Department of Botany, and UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Keith L Adams
- Department of Botany, and UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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Vila-Viçosa D, Teixeira VH, Santos HAF, Machuqueiro M. Conformational Study of GSH and GSSG Using Constant-pH Molecular Dynamics Simulations. J Phys Chem B 2013; 117:7507-17. [DOI: 10.1021/jp401066v] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Diogo Vila-Viçosa
- Centro de Química
e Bioquímica and Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Vitor H. Teixeira
- Centro de Química
e Bioquímica and Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Hugo A. F. Santos
- Centro de Química
e Bioquímica and Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Miguel Machuqueiro
- Centro de Química
e Bioquímica and Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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Zhang X, Li T, Zhang J, Li D, Guo Y, Qin G, Zhu KY, Ma E, Zhang J. Structural and catalytic role of two conserved tyrosines in Delta-class glutathione S-transferase from Locusta migratoria. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2012; 80:77-91. [PMID: 22581614 DOI: 10.1002/arch.21025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Glutathione S-transferases (GSTs) are an important family of detoxifying enzymes and play a key role in pesticide resistance in the insect. Tyrosine is essential for its detoxification function. In the present study, two conserved tyrosine residues are located at positions 108 and 116 in H-site of LmGSTD1. To elucidate how the two residues participate in the catalytic process and keeping structural stability, four mutants, Y108A, Y108E, Y116A, and Y116E, were generated. It was found that the four mutants affected the specific activity of LmGSTD1 in various degrees, depending on the types of substrate and reaction mechanism. Steady-state kinetics assay revealed that Y108E and Y116E had a significant influence on GSH-binding ability, which indicates the two tyrosine residues of H-site contribute to topology rearrangement of G-site. Both Y116A and Y116E exhibited lower CDNB-binding affinity, suggesting that Y116 takes part in hydrophobic substrate binding. The thermostability assay, intrinsic, and 8-anilino-1-naphthalenesulfonic acid (ANS) florescence results showed that the two tyrosine residues were involved in regulation of active-site conformation. Finally, homology modeling provided evidence that the two tyrosines in H-site participate in hydrophobic substrate binding. Furthermore, Y108 is closer to the S atom of S-hexylglutathione. In conclusion, the two tyrosines in LmGSTD1 are important residues in both the catalytic process and protein stability.
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Affiliation(s)
- Xueyao Zhang
- Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China
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25
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Barbany M, Morata J, Meyer T, Lois S, Orozco M, de la Cruz X. Characterization of the impact of alternative splicing on protein dynamics: the cases of glutathione S-transferase and ectodysplasin-A isoforms. Proteins 2012; 80:2235-49. [PMID: 22576332 DOI: 10.1002/prot.24112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 04/24/2012] [Accepted: 05/02/2012] [Indexed: 12/31/2022]
Abstract
Recent studies have shown how alternative splicing (AS), the process by which eukaryotic genes express more than one product, affects protein sequence and structure. However, little information is available on the impact of AS on protein dynamics, a property fundamental for protein function. In this work, we have addressed this issue using molecular dynamics simulations of the isoforms of two model proteins: glutathione S-transferase and ectodysplasin-A. We have found that AS does not have a noticeable impact on global or local structure fluctuations. We have also found that, quite interestingly, AS has a significant effect on the coupling between key structural elements such as surface cavities. Our results provide the first atom-level view of the impact of AS on protein dynamics, as far as we know. They can contribute to refine our present view of the relationship between AS and protein disorder and, more importantly, they reveal how AS may modify structural dynamic couplings in proteins.
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Edwards TE, Bryan CM, Leibly DJ, Dieterich SH, Abendroth J, Sankaran B, Sivam D, Staker BL, Van Voorhis WC, Myler PJ, Stewart LJ. Structures of a putative ζ-class glutathione S-transferase from the pathogenic fungus Coccidioides immitis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1038-43. [PMID: 21904047 PMCID: PMC3169399 DOI: 10.1107/s1744309111009493] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 03/12/2011] [Indexed: 11/25/2022]
Abstract
Coccidioides immitis is a pathogenic fungus populating the southwestern United States and is a causative agent of coccidioidomycosis, sometimes referred to as Valley Fever. Although the genome of this fungus has been sequenced, many operons are not properly annotated. Crystal structures are presented for a putative uncharacterized protein that shares sequence similarity with ζ-class glutathione S-transferases (GSTs) in both apo and glutathione-bound forms. The apo structure reveals a nonsymmetric homodimer with each protomer comprising two subdomains: a C-terminal helical domain and an N-terminal thioredoxin-like domain that is common to all GSTs. Half-site binding is observed in the glutathione-bound form. Considerable movement of some components of the active site relative to the glutathione-free form was observed, indicating an induced-fit mechanism for cofactor binding. The sequence homology, structure and half-site occupancy imply that the protein is a ζ-class glutathione S-transferase, a maleylacetoacetate isomerase (MAAI).
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Abstract
The glutathione transferases (GSTs) are one of the most important families of detoxifying enzymes in nature. The classic activity of the GSTs is conjugation of compounds with electrophilic centers to the tripeptide glutathione (GSH), but many other activities are now associated with GSTs, including steroid and leukotriene biosynthesis, peroxide degradation, double-bond cis-trans isomerization, dehydroascorbate reduction, Michael addition, and noncatalytic "ligandin" activity (ligand binding and transport). Since the first GST structure was determined in 1991, there has been an explosion in structural data across GSTs of all three families: the cytosolic GSTs, the mitochondrial GSTs, and the membrane-associated proteins in eicosanoid and glutathione metabolism (MAPEG family). In this review, the major insights into GST structure and function will be discussed.
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Affiliation(s)
- Aaron Oakley
- School of Chemistry, University of Wollongong, Wollongong, Australia.
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28
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Meux E, Prosper P, Ngadin A, Didierjean C, Morel M, Dumarçay S, Lamant T, Jacquot JP, Favier F, Gelhaye E. Glutathione transferases of Phanerochaete chrysosporium: S-glutathionyl-p-hydroquinone reductase belongs to a new structural class. J Biol Chem 2011; 286:9162-73. [PMID: 21177852 PMCID: PMC3059006 DOI: 10.1074/jbc.m110.194548] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 12/17/2010] [Indexed: 01/24/2023] Open
Abstract
The white rot fungus Phanerochaete chrysosporium, a saprophytic basidiomycete, possesses a large number of cytosolic glutathione transferases, eight of them showing similarity to the Omega class. PcGSTO1 (subclass I, the bacterial homologs of which were recently proposed, based on their enzymatic function, to constitute a new class of glutathione transferase named S-glutathionyl-(chloro)hydroquinone reductases) and PcGSTO3 (subclass II related to mammalian homologs) have been investigated in this study. Biochemical investigations demonstrate that both enzymes are able to catalyze deglutathionylation reactions thanks to the presence of a catalytic cysteinyl residue. This reaction leads to the formation of a disulfide bridge between the conserved cysteine and the removed glutathione from their substrate. The substrate specificity of each isoform differs. In particular PcGSTO1, in contrast to PcGSTO3, was found to catalyze deglutathionylation of S-glutathionyl-p-hydroquinone substrates. The three-dimensional structure of PcGSTO1 presented here confirms the hypothesis that it belongs not only to a new biological class but also to a new structural class that we propose to name GST xi. Indeed, it shows specific features, the most striking ones being a new dimerization mode and a catalytic site that is buried due to the presence of long loops and that contains the catalytic cysteine.
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Affiliation(s)
- Edgar Meux
- From the UMR 1136 INRA-UHP “Interactions Arbres/Micro-Organismes,” IFR110 “Ecosystèmes Forestiers, Agroressources, Bioprocédés et Alimentation,”
| | - Pascalita Prosper
- the CRM2, Equipe Biocristallographie, UMR 7036 CNRS-UHP, Institut Jean Barriol, and
| | - Andrew Ngadin
- From the UMR 1136 INRA-UHP “Interactions Arbres/Micro-Organismes,” IFR110 “Ecosystèmes Forestiers, Agroressources, Bioprocédés et Alimentation,”
| | - Claude Didierjean
- the CRM2, Equipe Biocristallographie, UMR 7036 CNRS-UHP, Institut Jean Barriol, and
| | - Mélanie Morel
- From the UMR 1136 INRA-UHP “Interactions Arbres/Micro-Organismes,” IFR110 “Ecosystèmes Forestiers, Agroressources, Bioprocédés et Alimentation,”
| | - Stéphane Dumarçay
- the Laboratoire d'Études et de Recherches sur le Matériau Bois, EA UHP 4370, Nancy Université, Faculté des Sciences et Techniques, BP 70239, 54506 Vandoeuvre-les-Nancy, France
| | - Tiphaine Lamant
- From the UMR 1136 INRA-UHP “Interactions Arbres/Micro-Organismes,” IFR110 “Ecosystèmes Forestiers, Agroressources, Bioprocédés et Alimentation,”
| | - Jean-Pierre Jacquot
- From the UMR 1136 INRA-UHP “Interactions Arbres/Micro-Organismes,” IFR110 “Ecosystèmes Forestiers, Agroressources, Bioprocédés et Alimentation,”
| | - Frédérique Favier
- the CRM2, Equipe Biocristallographie, UMR 7036 CNRS-UHP, Institut Jean Barriol, and
| | - Eric Gelhaye
- From the UMR 1136 INRA-UHP “Interactions Arbres/Micro-Organismes,” IFR110 “Ecosystèmes Forestiers, Agroressources, Bioprocédés et Alimentation,”
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Structural contributions of Delta class glutathione transferase active-site residues to catalysis. Biochem J 2010; 428:25-32. [DOI: 10.1042/bj20091939] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
GST (glutathione transferase) is a dimeric enzyme recognized for biotransformation of xenobiotics and endogenous toxic compounds. In the present study, residues forming the hydrophobic substrate-binding site (H-site) of a Delta class enzyme were investigated in detail for the first time by site-directed mutagenesis and crystallographic studies. Enzyme kinetics reveal that Tyr111 indirectly stabilizes GSH binding, Tyr119 modulates hydrophobic substrate binding and Phe123 indirectly modulates catalysis. Mutations at Tyr111 and Phe123 also showed evidence for positive co-operativity for GSH and 1-chloro-2,4-dinitrobenzene respectively, strongly suggesting a role for these residues in manipulating subunit–subunit communication. In the present paper we report crystal structures of the wild-type enzyme, and two mutants, in complex with S-hexylglutathione. This study has identified an aromatic ‘zipper’ in the H-site contributing a network of aromatic π–π interactions. Several residues of the cluster directly interact with the hydrophobic substrate, whereas others indirectly maintain conformational stability of the dimeric structure through the C-terminal domain (domain II). The Y119E mutant structure shows major main-chain rearrangement of domain II. This reorganization is moderated through the ‘zipper’ that contributes to the H-site remodelling, thus illustrating a role in co-substrate binding modulation. The F123A structure shows molecular rearrangement of the H-site in one subunit, but not the other, explaining weakened hydrophobic substrate binding and kinetic co-operativity effects of Phe123 mutations. The three crystal structures provide comprehensive evidence of the aromatic ‘zipper’ residues having an impact upon protein stability, catalysis and specificity. Consequently, ‘zipper’ residues appear to modulate and co-ordinate substrate processing through permissive flexing.
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Low WY, Feil SC, Ng HL, Gorman MA, Morton CJ, Pyke J, McConville MJ, Bieri M, Mok YF, Robin C, Gooley PR, Parker MW, Batterham P. Recognition and detoxification of the insecticide DDT by Drosophila melanogaster glutathione S-transferase D1. J Mol Biol 2010; 399:358-66. [PMID: 20417639 DOI: 10.1016/j.jmb.2010.04.020] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Revised: 04/09/2010] [Accepted: 04/13/2010] [Indexed: 10/19/2022]
Abstract
GSTD1 is one of several insect glutathione S-transferases capable of metabolizing the insecticide DDT. Here we use crystallography and NMR to elucidate the binding of DDT and glutathione to GSTD1. The crystal structure of Drosophila melanogaster GSTD1 has been determined to 1.1 A resolution, which reveals that the enzyme adopts the canonical GST fold but with a partially occluded active site caused by the packing of a C-terminal helix against one wall of the binding site for substrates. This helix would need to unwind or be displaced to enable catalysis. When the C-terminal helix is removed from the model of the crystal structure, DDT can be computationally docked into the active site in an orientation favoring catalysis. Two-dimensional (1)H,(15)N heteronuclear single-quantum coherence NMR experiments of GSTD1 indicate that conformational changes occur upon glutathione and DDT binding and the residues that broaden upon DDT binding support the predicted binding site. We also show that the ancestral GSTD1 is likely to have possessed DDT dehydrochlorinase activity because both GSTD1 from D. melanogaster and its sibling species, Drosophila simulans, have this activity.
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Affiliation(s)
- Wai Yee Low
- Department of Genetics, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Melbourne, Victoria 3010, Australia
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Wrabl JO, Hilser VJ. Investigating homology between proteins using energetic profiles. PLoS Comput Biol 2010; 6:e1000722. [PMID: 20361049 PMCID: PMC2845653 DOI: 10.1371/journal.pcbi.1000722] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Accepted: 02/25/2010] [Indexed: 11/19/2022] Open
Abstract
Accumulated experimental observations demonstrate that protein stability is often preserved upon conservative point mutation. In contrast, less is known about the effects of large sequence or structure changes on the stability of a particular fold. Almost completely unknown is the degree to which stability of different regions of a protein is generally preserved throughout evolution. In this work, these questions are addressed through thermodynamic analysis of a large representative sample of protein fold space based on remote, yet accepted, homology. More than 3,000 proteins were computationally analyzed using the structural-thermodynamic algorithm COREX/BEST. Estimated position-specific stability (i.e., local Gibbs free energy of folding) and its component enthalpy and entropy were quantitatively compared between all proteins in the sample according to all-vs.-all pairwise structural alignment. It was discovered that the local stabilities of homologous pairs were significantly more correlated than those of non-homologous pairs, indicating that local stability was indeed generally conserved throughout evolution. However, the position-specific enthalpy and entropy underlying stability were less correlated, suggesting that the overall regional stability of a protein was more important than the thermodynamic mechanism utilized to achieve that stability. Finally, two different types of statistically exceptional evolutionary structure-thermodynamic relationships were noted. First, many homologous proteins contained regions of similar thermodynamics despite localized structure change, suggesting a thermodynamic mechanism enabling evolutionary fold change. Second, some homologous proteins with extremely similar structures nonetheless exhibited different local stabilities, a phenomenon previously observed experimentally in this laboratory. These two observations, in conjunction with the principal conclusion that homologous proteins generally conserved local stability, may provide guidance for a future thermodynamically informed classification of protein homology. Protein structure and function are fundamentally determined by thermodynamics. However, for technical as well as historical reasons, current evolutionary classification schemes and bioinformatics tools do not fully utilize thermodynamic information to describe or analyze proteins. In this work, we address this deficiency by computationally estimating the position-specific thermodynamic quantities of stability (ΔG), enthalpy (ΔH), and entropy (TΔS) for a large and diverse representative sample of protein structures. The sample was drawn from an expertly curated database, such that accepted evolutionary relationships existed for all protein pairs. Importantly, trivial relationships between pairs highly similar in amino acid sequence were explicitly excluded. We found that all position-specific thermodynamic quantities ΔG, ΔH, and TΔS were more similar between proteins that were evolutionarily related (i.e., homologous), and were less similar between proteins that were not evolutionarily related (i.e., non-homologous), with stability being particularly similar between homologous proteins. However, interesting statistically significant exceptions to these trends were observed, exceptions that could indicate novel processes of functional adaptation or evolutionary fold change, mediated by thermodynamics, for the proteins involved. Taken together, these results expand our understanding of the role of thermodynamics in protein evolution and suggest an organizational framework for a future thermodynamically-informed classification of protein homology.
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Affiliation(s)
- James O. Wrabl
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
| | - Vincent J. Hilser
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
- * E-mail:
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Characterization of zebrafish Esrom (Myc-binding protein 2) RCC1-like domain splice variants. Mol Cell Biochem 2010; 339:191-9. [PMID: 20143133 DOI: 10.1007/s11010-010-0385-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Accepted: 01/26/2010] [Indexed: 11/27/2022]
Abstract
PHR protein family consists of C. elegan Rpm-1/Drosophila Highwire/Zebrafish Esrom/Mouse Phr-1/Human Pam. Esrom is required for correct neurites exiting the paused state at intermediate targets as well as pteridine synthesis. This study reports the identification and characterization of two novel Esrom splice variants, named splice variants 2 (splicing out 5' 24 bp of exon 17) and 3 (splicing out 5' 24 bp of exons 17 and 18). Polypeptides encoded by 5' 24 bp of exons 17 and 18 are part of basic amino-acid-rich region inside Esrom RCC1-like domain (RLD). These two splice variants maintain the whole protein reading frame and alternative exons usage patterns are conserved with mammal. At different developmental stages and adult zebrafish tissues, abundances of these splice variants are different. Importantly, by yeast two-hybrid screen and confocal colocalization analysis, it was found that alternative splicing of exon 18 regulates Esrom RLD interaction with kinesin family member 22 and G protein beta-subunit 1. Taken together, these results suggest that Esrom RLD functions are regulated by alternative splicing at temporal and spatial-specific manner.
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Structures of yeast glutathione-S-transferase Gtt2 reveal a new catalytic type of GST family. EMBO Rep 2009; 10:1320-6. [PMID: 19851333 DOI: 10.1038/embor.2009.216] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Revised: 08/25/2009] [Accepted: 08/27/2009] [Indexed: 12/17/2022] Open
Abstract
Glutathione-S-transferases (GSTs) are ubiquitous detoxification enzymes that catalyse the conjugation of electrophilic substrates to glutathione. Here, we present the crystal structures of Gtt2, a GST of Saccharomyces cerevisiae, in apo and two ligand-bound forms, at 2.23 A, 2.20 A and 2.10 A, respectively. Although Gtt2 has the overall structure of a GST, the absence of the classic catalytic essential residues--tyrosine, serine and cysteine--distinguishes it from all other cytosolic GSTs of known structure. Site-directed mutagenesis in combination with activity assays showed that instead of the classic catalytic residues, a water molecule stabilized by Ser129 and His123 acts as the deprotonator of the glutathione sulphur atom. Furthermore, only glycine and alanine are allowed at the amino-terminus of helix-alpha1 because of stereo-hindrance. Taken together, these results show that yeast Gtt2 is a novel atypical type of cytosolic GST.
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Lerksuthirat T, Ketterman AJ. Characterization of putative hydrophobic substrate binding site residues of a Delta class glutathione transferase from Anopheles dirus. Arch Biochem Biophys 2008; 479:97-103. [DOI: 10.1016/j.abb.2008.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Revised: 08/07/2008] [Accepted: 08/08/2008] [Indexed: 10/21/2022]
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Structure of an insect epsilon class glutathione S-transferase from the malaria vector Anopheles gambiae provides an explanation for the high DDT-detoxifying activity. J Struct Biol 2008; 164:228-35. [DOI: 10.1016/j.jsb.2008.08.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2008] [Revised: 08/18/2008] [Accepted: 08/19/2008] [Indexed: 11/21/2022]
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37
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Dunker AK, Oldfield CJ, Meng J, Romero P, Yang JY, Chen JW, Vacic V, Obradovic Z, Uversky VN. The unfoldomics decade: an update on intrinsically disordered proteins. BMC Genomics 2008; 9 Suppl 2:S1. [PMID: 18831774 PMCID: PMC2559873 DOI: 10.1186/1471-2164-9-s2-s1] [Citation(s) in RCA: 386] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Our first predictor of protein disorder was published just over a decade ago in the Proceedings of the IEEE International Conference on Neural Networks (Romero P, Obradovic Z, Kissinger C, Villafranca JE, Dunker AK (1997) Identifying disordered regions in proteins from amino acid sequence. Proceedings of the IEEE International Conference on Neural Networks, 1: 90-95). By now more than twenty other laboratory groups have joined the efforts to improve the prediction of protein disorder. While the various prediction methodologies used for protein intrinsic disorder resemble those methodologies used for secondary structure prediction, the two types of structures are entirely different. For example, the two structural classes have very different dynamic properties, with the irregular secondary structure class being much less mobile than the disorder class. The prediction of secondary structure has been useful. On the other hand, the prediction of intrinsic disorder has been revolutionary, leading to major modifications of the more than 100 year-old views relating protein structure and function. Experimentalists have been providing evidence over many decades that some proteins lack fixed structure or are disordered (or unfolded) under physiological conditions. In addition, experimentalists are also showing that, for many proteins, their functions depend on the unstructured rather than structured state; such results are in marked contrast to the greater than hundred year old views such as the lock and key hypothesis. Despite extensive data on many important examples, including disease-associated proteins, the importance of disorder for protein function has been largely ignored. Indeed, to our knowledge, current biochemistry books don't present even one acknowledged example of a disorder-dependent function, even though some reports of disorder-dependent functions are more than 50 years old. The results from genome-wide predictions of intrinsic disorder and the results from other bioinformatics studies of intrinsic disorder are demanding attention for these proteins. RESULTS Disorder prediction has been important for showing that the relatively few experimentally characterized examples are members of a very large collection of related disordered proteins that are wide-spread over all three domains of life. Many significant biological functions are now known to depend directly on, or are importantly associated with, the unfolded or partially folded state. Here our goal is to review the key discoveries and to weave these discoveries together to support novel approaches for understanding sequence-function relationships. CONCLUSION Intrinsically disordered protein is common across the three domains of life, but especially common among the eukaryotic proteomes. Signaling sequences and sites of posttranslational modifications are frequently, or very likely most often, located within regions of intrinsic disorder. Disorder-to-order transitions are coupled with the adoption of different structures with different partners. Also, the flexibility of intrinsic disorder helps different disordered regions to bind to a common binding site on a common partner. Such capacity for binding diversity plays important roles in both protein-protein interaction networks and likely also in gene regulation networks. Such disorder-based signaling is further modulated in multicellular eukaryotes by alternative splicing, for which such splicing events map to regions of disorder much more often than to regions of structure. Associating alternative splicing with disorder rather than structure alleviates theoretical and experimentally observed problems associated with the folding of different length, isomeric amino acid sequences. The combination of disorder and alternative splicing is proposed to provide a mechanism for easily "trying out" different signaling pathways, thereby providing the mechanism for generating signaling diversity and enabling the evolution of cell differentiation and multicellularity. Finally, several recent small molecules of interest as potential drugs have been shown to act by blocking protein-protein interactions based on intrinsic disorder of one of the partners. Study of these examples has led to a new approach for drug discovery, and bioinformatics analysis of the human proteome suggests that various disease-associated proteins are very rich in such disorder-based drug discovery targets.
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Affiliation(s)
- A Keith Dunker
- Center for Computational Biology and Bioinformatics, Indiana University Schools of Medicine and Informatics, Indianapolis, IN 46202, USA
| | - Christopher J Oldfield
- Center for Computational Biology and Bioinformatics, Indiana University School of Informatics, Indianapolis, IN 46202, USA
| | - Jingwei Meng
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Pedro Romero
- Center for Computational Biology and Bioinformatics, Indiana University School of Informatics, Indianapolis, IN 46202, USA
| | - Jack Y Yang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jessica Walton Chen
- Center for Computational Biology and Bioinformatics, Indiana University School of Informatics, Indianapolis, IN 46202, USA
| | - Vladimir Vacic
- Center for Computational Biology and Bioinformatics, Indiana University School of Informatics, Indianapolis, IN 46202, USA
| | - Zoran Obradovic
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - Vladimir N Uversky
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Institute for Intrinsically Disordered Protein Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
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Dunker AK, Oldfield CJ, Meng J, Romero P, Yang JY, Chen JW, Vacic V, Obradovic Z, Uversky VN. The unfoldomics decade: an update on intrinsically disordered proteins. BMC Genomics 2008. [PMID: 18831774 DOI: 10.1186/1471‐2164‐9‐s2‐s1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Our first predictor of protein disorder was published just over a decade ago in the Proceedings of the IEEE International Conference on Neural Networks (Romero P, Obradovic Z, Kissinger C, Villafranca JE, Dunker AK (1997) Identifying disordered regions in proteins from amino acid sequence. Proceedings of the IEEE International Conference on Neural Networks, 1: 90-95). By now more than twenty other laboratory groups have joined the efforts to improve the prediction of protein disorder. While the various prediction methodologies used for protein intrinsic disorder resemble those methodologies used for secondary structure prediction, the two types of structures are entirely different. For example, the two structural classes have very different dynamic properties, with the irregular secondary structure class being much less mobile than the disorder class. The prediction of secondary structure has been useful. On the other hand, the prediction of intrinsic disorder has been revolutionary, leading to major modifications of the more than 100 year-old views relating protein structure and function. Experimentalists have been providing evidence over many decades that some proteins lack fixed structure or are disordered (or unfolded) under physiological conditions. In addition, experimentalists are also showing that, for many proteins, their functions depend on the unstructured rather than structured state; such results are in marked contrast to the greater than hundred year old views such as the lock and key hypothesis. Despite extensive data on many important examples, including disease-associated proteins, the importance of disorder for protein function has been largely ignored. Indeed, to our knowledge, current biochemistry books don't present even one acknowledged example of a disorder-dependent function, even though some reports of disorder-dependent functions are more than 50 years old. The results from genome-wide predictions of intrinsic disorder and the results from other bioinformatics studies of intrinsic disorder are demanding attention for these proteins. RESULTS Disorder prediction has been important for showing that the relatively few experimentally characterized examples are members of a very large collection of related disordered proteins that are wide-spread over all three domains of life. Many significant biological functions are now known to depend directly on, or are importantly associated with, the unfolded or partially folded state. Here our goal is to review the key discoveries and to weave these discoveries together to support novel approaches for understanding sequence-function relationships. CONCLUSION Intrinsically disordered protein is common across the three domains of life, but especially common among the eukaryotic proteomes. Signaling sequences and sites of posttranslational modifications are frequently, or very likely most often, located within regions of intrinsic disorder. Disorder-to-order transitions are coupled with the adoption of different structures with different partners. Also, the flexibility of intrinsic disorder helps different disordered regions to bind to a common binding site on a common partner. Such capacity for binding diversity plays important roles in both protein-protein interaction networks and likely also in gene regulation networks. Such disorder-based signaling is further modulated in multicellular eukaryotes by alternative splicing, for which such splicing events map to regions of disorder much more often than to regions of structure. Associating alternative splicing with disorder rather than structure alleviates theoretical and experimentally observed problems associated with the folding of different length, isomeric amino acid sequences. The combination of disorder and alternative splicing is proposed to provide a mechanism for easily "trying out" different signaling pathways, thereby providing the mechanism for generating signaling diversity and enabling the evolution of cell differentiation and multicellularity. Finally, several recent small molecules of interest as potential drugs have been shown to act by blocking protein-protein interactions based on intrinsic disorder of one of the partners. Study of these examples has led to a new approach for drug discovery, and bioinformatics analysis of the human proteome suggests that various disease-associated proteins are very rich in such disorder-based drug discovery targets.
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Affiliation(s)
- A Keith Dunker
- Center for Computational Biology and Bioinformatics, Indiana University Schools of Medicine and Informatics, Indianapolis, IN 46202, USA.
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Kim KJ, Park MC, Choi SJ, Oh YS, Choi EC, Cho HJ, Kim MH, Kim SH, Kim DW, Kim S, Kang BS. Determination of three-dimensional structure and residues of the novel tumor suppressor AIMP3/p18 required for the interaction with ATM. J Biol Chem 2008; 283:14032-40. [PMID: 18343821 DOI: 10.1074/jbc.m800859200] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although AIMP3/p18 is normally associated with the multi-tRNA synthetase complex via its specific interaction with methionyl-tRNA synthetase, it also works as a tumor suppressor by interacting with ATM, the upstream kinase of p53. To understand the molecular interactions of AIMP3 and the mechanisms involved, we determined the crystal structure of AIMP3 at 2.0-angstroms resolution and identified its potential sites of interaction with ATM. AIMP3 contains two distinct domains linked by a 7-amino acid (Lys57-Ser63) peptide, which contains a 3(10) helix. The 56-amino acid N-terminal domain consists of two helices into which three antiparallel beta strands are inserted, and the 111-amino acid C-terminal domain contains a bundle of five helices (Thr64-Tyr152) followed by a coiled region (Pro153-Leu169). Structural analyses revealed homologous proteins such as yeast glutamyl-tRNA synthetase, Arc1p, EF1Bgamma, and glutathione S-transferase and suggested two potential molecular binding sites. Moreover, mutations at the C-terminal putative binding site abolished the interaction between AIMP3 and ATM and the ability of AIMP3 to activate p53. Thus, this work identified the two potential molecular interaction sites of AIMP3 and determined the residues critical for its tumor-suppressive activity through the interaction with ATM.
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Affiliation(s)
- Kyung-Jin Kim
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang 790-784, Korea
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Zheng S, Deng H, Ladd T, Tomkins BL, Krell PJ, Feng Q. Cloning and characterization of two glutathione S-transferase cDNAs in the spruce budworm, Choristoneura fumiferana. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2007; 66:146-157. [PMID: 17966126 DOI: 10.1002/arch.20206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Two Choristoneura fumiferana glutathione S-transferase cDNAs were cloned from a cDNA library constructed using mRNA from the midgut cell line, CF-203. These cDNAs (CfGST2, CfGST3) encoded two structurally different proteins with a predicted molecular mass of 21 and 24 kDa, respectively, which was confirmed through protein expression in a bacterial system. Quantitative reverse-transcription PCR analyses revealed that the transcripts of these two genes were present in the epidermis, fat body, and midgut of the 6th instar larvae. CfGST2 was expressed in the fat body when the insects were close to pupal molting, while it was constantly expressed in the other two tissues during the 6th instar stage. CfGST3 gene was expressed highly and constantly in all of the tissues throughout the 6th instar stage. Immunohistochemistry analysis demonstrated that CfGST2 and CfGST3 proteins were present mainly in the fat body and epidermis and no protein was detected in the midgut. CfGST2 and CfGST3 were different from CfGST reported before (Feng et al., 1999: Insect Biochem Mol Biol 29:779-793) in amino acid sequence, expression pattern, and responsiveness to tebufenozide.
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Affiliation(s)
- Sichun Zheng
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
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Jariyapan N, Choochote W, Jitpakdi A, Harnnoi T, Siriyasatein P, Wilkinson MC, Junkum A, Bates PA. Salivary gland proteins of the human malaria vector, Anopheles dirus B (Diptera: Culicidae). Rev Inst Med Trop Sao Paulo 2007; 49:5-10. [PMID: 17384813 DOI: 10.1590/s0036-46652007000100002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2005] [Accepted: 07/14/2006] [Indexed: 11/22/2022] Open
Abstract
Salivary gland proteins of the human malaria vector, Anopheles dirus B were determined and analyzed. The amount of salivary gland proteins in mosquitoes aged between 3--10 days was approximately 1.08 +/- 0.04 microg/female and 0.1 +/- 0.05 microg/male. The salivary glands of both sexes displayed the same morphological organization as that of other anopheline mosquitoes. In females, apyrase accumulated in the distal regions, whereas alpha-glucosidase was found in the proximal region of the lateral lobes. This differential distribution of the analyzed enzymes reflects specialization of different regions for sugar and blood feeding. SDS-PAGE analysis revealed that at least seven major proteins were found in the female salivary glands, of which each morphological region contained different major proteins. Similar electrophoretic protein profiles were detected comparing unfed and blood-fed mosquitoes, suggesting that there is no specific protein induced by blood. Two-dimensional polyacrylamide gel analysis showed the most abundant salivary gland protein, with a molecular mass of approximately 35 kilodaltons and an isoelectric point of approximately 4.0. These results provide basic information that would lead to further study on the role of salivary proteins of An. dirus B in disease transmission and hematophagy.
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Affiliation(s)
- Narissara Jariyapan
- Department of Parasitology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.
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A procedure for identifying homologous alternative splicing events. BMC Bioinformatics 2007; 8:260. [PMID: 17640387 PMCID: PMC1950890 DOI: 10.1186/1471-2105-8-260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Accepted: 07/19/2007] [Indexed: 01/11/2023] Open
Abstract
Background The study of the functional role of alternative splice isoforms of a gene is a very active area of research in biology. The difficulty of the experimental approach (in particular, in its high-throughput version) leaves ample room for the development of bioinformatics tools that can provide a useful first picture of the problem. Among the possible approaches, one of the simplest is to follow classical protein function annotation protocols and annotate target alternative splice events with the information available from conserved events in other species. However, the application of this protocol requires a procedure capable of recognising such events. Here we present a simple but accurate method developed for this purpose. Results We have developed a method for identifying homologous, or equivalent, alternative splicing events, based on the combined use of neural networks and sequence searches. The procedure comprises four steps: (i) BLAST search for homologues of the two isoforms defining the target alternative splicing event; (ii) construction of all possible candidate events; (iii) scoring of the latter with a series of neural networks; and (iv) filtering of the results. When tested in a set of 473 manually annotated pairs of homologous events, our method showed a good performance, with an accuracy of 0.99, a precision of 0.98 and a sensitivity of 0.93. When no candidates were available, the specificity of our method varied between 0.81 and 0.91. Conclusion The method described in this article allows the identification of homologous alternative splicing events, with a good success rate, indicating that such method could be used for the development of functional annotation of alternative splice isoforms.
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Ma B, Chang FN. Purification and cloning of a Delta class glutathione S-transferase displaying high peroxidase activity isolated from the German cockroach Blattella germanica. FEBS J 2007; 274:1793-1803. [PMID: 17331184 DOI: 10.1111/j.1742-4658.2007.05728.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A highly active glutathione S-transferase was purified from adult German cockroaches, Blattella germanica. The purified enzyme appeared as a single band of 24 kDa by SDS/PAGE, and had a different electrophoretic mobility than, a previously identified Sigma class glutathione S-transferase (Bla g 5). Kinetic study of 1-chloro-2,4-dinitrobenzene conjugation revealed a high catalytic rate but common substrate-binding and cosubstrate-binding affinities, with V(max), k(cat), K(m) for 1-chloro-2,4-dinitrobenzene and K(m) for glutathione estimated to be 664 micromol x mg(-1) x min(-1), 545 s(-1), 0.33 mm and 0.76 mm, respectively. Interestingly, this enzyme possessed the highest activity for cumene hydroperoxide among insect glutathione S-transferases reported to date. Along with the ability to metabolize 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane and 4-hydroxynonenal, this glutathione S-transferase may play a role in defense against insecticides as well as oxidative stress. On the basis of the amino acid sequences obtained from Edman degradation and MS analyses, a 987-nucleotide cDNA clone encoding a glutathione S-transferase (BggstD1) was isolated. The longest ORF encoded a 24 614 Da protein consisting of 216 amino acid residues. The sequence had close similarities ( approximately 45-60%) to that of Delta class glutathione S-transferases, but had only 14% identity to Bla g 5. The putative amino acid sequence contained matching peptide fragments of the purified glutathione S-transferase. ELISA showed that BgGSTD1 bound to serum IgE obtained from patients with cockroach allergy, indicating that the protein may be a cockroach allergen.
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Affiliation(s)
- Bennett Ma
- Department of Drug Metabolism, Merck Research Laboratories, West Point, PA 19486, USA.
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Piromjitpong J, Wongsantichon J, Ketterman A. Differences in the subunit interface residues of alternatively spliced glutathione transferases affects catalytic and structural functions. Biochem J 2007; 401:635-44. [PMID: 16938097 PMCID: PMC1770856 DOI: 10.1042/bj20060603] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
GSTs (glutathione transferases) are multifunctional widespread enzymes. Currently there are 13 identified classes within this family. Previously most structural characterization has been reported for mammalian Alpha, Mu and Pi class GSTs. In the present study we characterize two enzymes from the insect-specific Delta class, adGSTD3-3 and adGSTD4-4. These two proteins are alternatively spliced products from the same gene and have very similar tertiary structures. Several major contributions to the dimer interface area can be separated into three regions: conserved electrostatic interactions in region 1, hydrophobic interactions in region 2 and an ionic network in region 3. The four amino acid side chains studied in region 1 interact with each other as a planar rectangle. These interactions are highly conserved among the GST classes, Delta, Sigma and Theta. The hydrophobic residues in region 2 are not only subunit interface residues but also active site residues. Overall these three regions provide important contributions to stabilization and folding of the protein. In addition, decreases in yield as well as catalytic activity changes, suggest that the mutations in these regions can disrupt the active site conformation which decreases binding affinity, alters kinetic constants and alters substrate specificity. Several of these residues have only a slight effect on the initial folding of each subunit but have more influence on the dimerization process as well as impacting upon appropriate active site conformation. The results also suggest that even splicing products from the same gene may have specific features in the subunit interface area that would preclude heterodimerization.
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Affiliation(s)
- Juthamart Piromjitpong
- Institute of Molecular Biology and Genetics, Mahidol University, Salaya Campus, Nakhon Pathom 73170, Thailand
| | - Jantana Wongsantichon
- Institute of Molecular Biology and Genetics, Mahidol University, Salaya Campus, Nakhon Pathom 73170, Thailand
| | - Albert J. Ketterman
- Institute of Molecular Biology and Genetics, Mahidol University, Salaya Campus, Nakhon Pathom 73170, Thailand
- To whom correspondence should be addressed (email )
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Romero PR, Zaidi S, Fang YY, Uversky VN, Radivojac P, Oldfield CJ, Cortese MS, Sickmeier M, LeGall T, Obradovic Z, Dunker AK. Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms. Proc Natl Acad Sci U S A 2006; 103:8390-5. [PMID: 16717195 PMCID: PMC1482503 DOI: 10.1073/pnas.0507916103] [Citation(s) in RCA: 345] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Alternative splicing of pre-mRNA generates two or more protein isoforms from a single gene, thereby contributing to protein diversity. Despite intensive efforts, an understanding of the protein structure-function implications of alternative splicing is still lacking. Intrinsic disorder, which is a lack of equilibrium 3D structure under physiological conditions, may provide this understanding. Intrinsic disorder is a common phenomenon, particularly in multicellular eukaryotes, and is responsible for important protein functions including regulation and signaling. We hypothesize that polypeptide segments affected by alternative splicing are most often intrinsically disordered such that alternative splicing enables functional and regulatory diversity while avoiding structural complications. We analyzed a set of 46 differentially spliced genes encoding experimentally characterized human proteins containing both structured and intrinsically disordered amino acid segments. We show that 81% of 75 alternatively spliced fragments in these proteins were associated with fully (57%) or partially (24%) disordered protein regions. Regions affected by alternative splicing were significantly biased toward encoding disordered residues, with a vanishingly small P value. A larger data set composed of 558 SwissProt proteins with known isoforms produced by 1,266 alternatively spliced fragments was characterized by applying the pondr vsl1 disorder predictor. Results from prediction data are consistent with those obtained from experimental data, further supporting the proposed hypothesis. Associating alternative splicing with protein disorder enables the time- and tissue-specific modulation of protein function needed for cell differentiation and the evolution of multicellular organisms.
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Affiliation(s)
- Pedro R. Romero
- *School of Informatics, Indiana University–Purdue University Indianapolis, 535 West Michigan Street, IT475, Indianapolis, IN 46202
- Department of Biochemistry and Molecular Biology and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 714 North Senate Avenue, Suite 250, Indianapolis, IN 46202
| | - Saima Zaidi
- *School of Informatics, Indiana University–Purdue University Indianapolis, 535 West Michigan Street, IT475, Indianapolis, IN 46202
| | - Ya Yin Fang
- Department of Biochemistry and Molecular Biology and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 714 North Senate Avenue, Suite 250, Indianapolis, IN 46202
| | - Vladimir N. Uversky
- Department of Biochemistry and Molecular Biology and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 714 North Senate Avenue, Suite 250, Indianapolis, IN 46202
| | - Predrag Radivojac
- School of Informatics, Indiana University, Eigenmann Hall 1005, 1900 East 10th Street, Bloomington, IN 47406; and
| | - Christopher J. Oldfield
- Department of Biochemistry and Molecular Biology and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 714 North Senate Avenue, Suite 250, Indianapolis, IN 46202
| | - Marc S. Cortese
- Department of Biochemistry and Molecular Biology and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 714 North Senate Avenue, Suite 250, Indianapolis, IN 46202
| | - Megan Sickmeier
- Department of Biochemistry and Molecular Biology and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 714 North Senate Avenue, Suite 250, Indianapolis, IN 46202
| | - Tanguy LeGall
- Department of Biochemistry and Molecular Biology and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 714 North Senate Avenue, Suite 250, Indianapolis, IN 46202
| | - Zoran Obradovic
- Center for Information Science and Technology, Temple University, 303 Wachman Hall (038-24), 1805 North Broad Street, Philadelphia, PA 19122
| | - A. Keith Dunker
- *School of Informatics, Indiana University–Purdue University Indianapolis, 535 West Michigan Street, IT475, Indianapolis, IN 46202
- Department of Biochemistry and Molecular Biology and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 714 North Senate Avenue, Suite 250, Indianapolis, IN 46202
- To whom correspondence should be addressed. E-mail:
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Wongsantichon J, Ketterman A. An intersubunit lock-and-key 'clasp' motif in the dimer interface of Delta class glutathione transferase. Biochem J 2006; 394:135-44. [PMID: 16225458 PMCID: PMC1386011 DOI: 10.1042/bj20050915] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Structural investigations of a GST (glutathione transferase), adGSTD4-4, from the malaria vector Anopheles dirus show a novel lock-and-key 'Clasp' motif in the dimer interface of the Delta class enzyme. This motif also appears to be highly conserved across several insect GST classes, but differs from a previously reported mammalian lock-and-key motif. The aromatic 'key' residue not only inserts into a hydrophobic pocket, the 'lock', of the neighbouring subunit, but also acts as part of the 'lock' for the other subunit 'key'. The 'key' residues from both subunits show aromatic ring stacking with each other in a pi-pi interaction, generating a 'Clasp' in the middle of the subunit interface. Enzyme catalytic and structural characterizations revealed that single amino acid replacements in this 'Clasp' motif impacted on catalytic efficiencies, substrate selectivity and stability. Substitutions to the 'key' residue create strong positive co-operativity for glutathione binding, with a Hill coefficient approaching 2. The lock-and-key motif in general and especially the 'Clasp' motif with the pi-pi interaction appear to play a pivotal role in subunit communication between active sites, as well as in stabilizing the quaternary structure. Evidence of allosteric effects suggests an important role for this particular intersubunit architecture in regulating catalytic activity through conformational transitions of subunits. The observation of co-operativity in the mutants also implies that glutathione ligand binding and dimerization are linked. Quaternary structural changes of all mutants suggest that subunit assembly or dimerization basically manipulates subunit communication.
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Affiliation(s)
- Jantana Wongsantichon
- Institute of Molecular Biology and Genetics, Mahidol University, Salaya Campus, 25/25 Phutthamonthol Road 4, Salaya, Nakhon Pathom 73170, Thailand
| | - Albert J. Ketterman
- Institute of Molecular Biology and Genetics, Mahidol University, Salaya Campus, 25/25 Phutthamonthol Road 4, Salaya, Nakhon Pathom 73170, Thailand
- To whom correspondence should be addressed (email )
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Vararattanavech A, Prommeenate P, Ketterman A. The structural roles of a conserved small hydrophobic core in the active site and an ionic bridge in domain I of Delta class glutathione S-transferase. Biochem J 2006; 393:89-95. [PMID: 16153184 PMCID: PMC1383667 DOI: 10.1042/bj20050555] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
GSTs (glutathione S-transferases; E.C.2.5.1.18) are a supergene family of dimeric multifunctional enzymes that have a major role in detoxification pathways. Using a GST from the mosquito Anopheles dirus (adGSTD4-4), we have characterized the enzymatic and physical properties of Leu-6, Thr-31, Leu-33, Ala-35, Glu-37, Lys-40 and Glu-42. These residues generate two motifs located in the N-terminal domain (domain I) that are functionally conserved across GST classes. The aim of this study was to understand the function of these two motifs. The first motif is a small hydrophobic core in the G-site (glutathione-binding site) wall, and the second motif contains an ionic bridge at the N-terminus of the alpha2 helix and is also part of the G-site. The mutations in the small hydrophobic core appear to have structural effects, as shown by the thermal stability, refolding rate and intrinsic fluorescence differences. In the Delta class GST, interactions form an ionic bridge motif located at the beginning of the alpha2 helix. The data suggest that electrostatic interactions in the alpha2 helix are involved in alpha-helix stabilization, and disruption of this ionic bridge interaction changes the movement of the alpha2-helix region, thereby modulating the interaction of the enzyme with substrates. These results show that the small hydrophobic core and ionic bridge have a major impact on structural stabilization, as well as being required to maintain structural conformation of the enzyme. These structural effects are also transmitted to the active site to influence substrate binding and specificity. Therefore changes in the conformation of the G-site wall in the active site appear to be capable of exerting influences on the tertiary structural organization of the whole GST protein.
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Affiliation(s)
- Ardcharaporn Vararattanavech
- *Institute of Molecular Biology and Genetics, Mahidol University, Salaya campus, 25/25 Putthamonthol Road 4, Salaya, Nakhon Pathom, 73170 Thailand
| | - Peerada Prommeenate
- †BEC Unit, National Center for Genetic Engineering and Biotechnology, 83 Moo 8, Thakham, Bangkhuntien, Bangkok 10150, Thailand
| | - Albert J. Ketterman
- *Institute of Molecular Biology and Genetics, Mahidol University, Salaya campus, 25/25 Putthamonthol Road 4, Salaya, Nakhon Pathom, 73170 Thailand
- To whom correspondence should be addressed (email )
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Wongsantichon J, Yuvaniyama J, Ketterman AJ. Crystallization and preliminary X-ray crystallographic analysis of a highly stable mutant V107A of glutathione transferase from Anopheles dirus in complex with glutathione. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:310-2. [PMID: 16511331 PMCID: PMC2197175 DOI: 10.1107/s1744309106006580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2005] [Accepted: 02/22/2006] [Indexed: 11/10/2022]
Abstract
An engineered mutant V107A of the dimeric glutathione transferase enzyme from Anopheles dirus (adgstD4-4) was cocrystallized with glutathione substrate using the hanging-drop vapour-diffusion method. The crystal diffracted to 2.47 A resolution in space group P3(2)21 (unit-cell parameters a = b = 49.4, c = 272.4 A). Although the crystal morphology differed from that previously obtained for the wild-type enzyme, the crystal packing was the same. At 318 K, the engineered mutant showed an enzyme stability that was increased by about 32-fold, while possessing a similar catalytic function to the wild type. Structural determination will provide valuable understanding of the role of Val107. This residue is in the dimeric interface and appears to contribute towards enhancing the physical properties of the entire protein.
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Affiliation(s)
- Jantana Wongsantichon
- Institute of Molecular Biology and Genetics, Mahidol University, Salaya Campus, Nakorn Pathom 73170, Thailand
| | - Jirundon Yuvaniyama
- Department of Biochemistry and Center for Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Rama 6 Road, Phayathai, Bangkok 10400, Thailand
| | - Albert J. Ketterman
- Institute of Molecular Biology and Genetics, Mahidol University, Salaya Campus, Nakorn Pathom 73170, Thailand
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Udomsinprasert R, Pongjaroenkit S, Wongsantichon J, Oakley A, Prapanthadara LA, Wilce M, Ketterman A. Identification, characterization and structure of a new Delta class glutathione transferase isoenzyme. Biochem J 2005; 388:763-71. [PMID: 15717864 PMCID: PMC1183455 DOI: 10.1042/bj20042015] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The insect GST (glutathione transferase) supergene family encodes a varied group of proteins belonging to at least six individual classes. Interest in insect GSTs has focused on their role in conferring insecticide resistance. Previously from the mosquito malaria vector Anopheles dirus, two genes encoding five Delta class GSTs have been characterized for structural as well as enzyme activities. We have obtained a new Delta class GST gene and isoenzyme from A. dirus, which we name adGSTD5-5. The adGSTD5-5 isoenzyme was identified and was only detectably expressed in A. dirus adult females. A putative promoter analysis suggests that this GST has an involvement in oogenesis. The enzyme displayed little activity for classical GST substrates, although it possessed the greatest activity for DDT [1,1,1-trichloro-2,2-bis-(p-chlorophenyl)ethane] observed for Delta GSTs. However, GST activity was inhibited or enhanced in the presence of various fatty acids, suggesting that the enzyme may be modulated by fatty acids. We obtained a crystal structure for adGSTD5-5 and compared it with other Delta GSTs, which showed that adGSTD5-5 possesses an elongated and more polar active-site topology.
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Affiliation(s)
- Rungrutai Udomsinprasert
- *Institute of Molecular Biology and Genetics, Mahidol University, Salaya Campus, 25/25 Putthamonthol Road 4, Salaya, Nakon Pathom 73170, Thailand
| | | | - Jantana Wongsantichon
- *Institute of Molecular Biology and Genetics, Mahidol University, Salaya Campus, 25/25 Putthamonthol Road 4, Salaya, Nakon Pathom 73170, Thailand
| | - Aaron J. Oakley
- ‡Department of Pharmacology/Crystallography Centre, University of Western Australia, Crawley 6009, Australia
| | - La-aied Prapanthadara
- §Research Institute for Health Sciences, Chiangmai University, Chiangmai 50200, Thailand
| | - Matthew C. J. Wilce
- ‡Department of Pharmacology/Crystallography Centre, University of Western Australia, Crawley 6009, Australia
| | - Albert J. Ketterman
- *Institute of Molecular Biology and Genetics, Mahidol University, Salaya Campus, 25/25 Putthamonthol Road 4, Salaya, Nakon Pathom 73170, Thailand
- To whom correspondence should be addressed (email )
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50
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Stetefeld J, Ruegg MA. Structural and functional diversity generated by alternative mRNA splicing. Trends Biochem Sci 2005; 30:515-21. [PMID: 16023350 DOI: 10.1016/j.tibs.2005.07.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2005] [Revised: 06/22/2005] [Accepted: 07/01/2005] [Indexed: 12/25/2022]
Abstract
Alternative mRNA splicing is becoming increasingly recognized as an important mechanism for the generation of structural and functional diversity in proteins. Recent estimations predict that approximately 50% of all eukaryotic proteins can be alternatively spliced. Several lines of evidence suggest that alternative mRNA splicing results in small changes in protein structure and is likely to fine-tune the function and specificity of the affected protein. However, knowledge of how alternative splicing regulates cellular processes on the molecular level is still limited. It is only recently that structures of alternatively spliced proteins have been solved. These studies have shown that alternative splicing affects the structure not only in the vicinity of the splice site but also at long distance.
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Affiliation(s)
- Jörg Stetefeld
- Biozentrum, University Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.
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