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Jonak K, Suppanz I, Bender J, Chacinska A, Warscheid B, Topf U. Ageing-dependent thiol oxidation reveals early oxidation of proteins with core proteostasis functions. Life Sci Alliance 2024; 7:e202302300. [PMID: 38383455 PMCID: PMC10881836 DOI: 10.26508/lsa.202302300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/23/2024] Open
Abstract
Oxidative post-translational modifications of protein thiols are well recognized as a readily occurring alteration of proteins, which can modify their function and thus control cellular processes. The development of techniques enabling the site-specific assessment of protein thiol oxidation on a proteome-wide scale significantly expanded the number of known oxidation-sensitive protein thiols. However, lacking behind are large-scale data on the redox state of proteins during ageing, a physiological process accompanied by increased levels of endogenous oxidants. Here, we present the landscape of protein thiol oxidation in chronologically aged wild-type Saccharomyces cerevisiae in a time-dependent manner. Our data determine early-oxidation targets in key biological processes governing the de novo production of proteins, protein folding, and degradation, and indicate a hierarchy of cellular responses affected by a reversible redox modification. Comparison with existing datasets in yeast, nematode, fruit fly, and mouse reveals the evolutionary conservation of these oxidation targets. To facilitate accessibility, we integrated the cross-species comparison into the newly developed OxiAge Database.
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Affiliation(s)
- Katarzyna Jonak
- https://ror.org/034tvp782 Laboratory of Molecular Basis of Aging and Rejuvenation, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Ida Suppanz
- CIBSS Centre for Integrative Biological Signalling Research, University of Freiburg, Freiburg, Germany
| | - Julian Bender
- https://ror.org/00fbnyb24 Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | | | - Bettina Warscheid
- CIBSS Centre for Integrative Biological Signalling Research, University of Freiburg, Freiburg, Germany
- https://ror.org/00fbnyb24 Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Ulrike Topf
- https://ror.org/034tvp782 Laboratory of Molecular Basis of Aging and Rejuvenation, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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2
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Hoang T, Jeong C, Jang SH, Lee C. Tyr76 is essential for the cold adaptation of a class II glutaredoxin 4 with a heat-labile structure from the Arctic bacterium Sphingomonas sp. FEBS Open Bio 2023; 13:500-510. [PMID: 36680400 PMCID: PMC9989929 DOI: 10.1002/2211-5463.13560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/12/2023] [Accepted: 01/19/2023] [Indexed: 01/22/2023] Open
Abstract
Glutaredoxins (Grxs) are small proteins that share a well-conserved thioredoxin (Trx)-fold and participate in many biological processes. This study examined the cold adaptation mechanism of a Fe-S cluster binding class II Grx4 (SpGrx4) from the psychrophilic Arctic bacterium Sphingomonas sp. PAMC 26621. Three polar residues close to the cis-proline residue (P73) of SpGrx4 form a hydrogen bond network (Q74-S67-Y76) with the cis-proline loop main chain. The hydroxyl group of S67 or Y76 or both is replaced in similar Grxs depending on the temperature of the habitat. Mutants with reduced hydrogen bonds (S67A, Q74A, Y76F, and S67A/Y76W) were more susceptible to urea-induced unfolding and more flexible than the wild-type (WT). By contrast, Y76W, with a bulky indole group, was the most stable. These mutants showed higher melting temperatures than WT as a consequence of increased hydrophobic interactions. These results suggest that the tyrosine residue, Y76, is preferred for the cold adaptation of SpGrx4 with a heat-labile structure despite the rigid cis-proline loop, due to hydrogen bond formation. An aromatic residue on β3 (cis-proline plus3) modulates the stability-flexibility of the cis-proline loop for temperature adaptation of prokaryotic class II Grx4 members via hydrogen bonds and hydrophobic interactions.
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Affiliation(s)
- Trang Hoang
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - ChanSu Jeong
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - Sei-Heon Jang
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - ChangWoo Lee
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
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3
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Lennicke C, Cochemé HM. Redox metabolism: ROS as specific molecular regulators of cell signaling and function. Mol Cell 2021; 81:3691-3707. [PMID: 34547234 DOI: 10.1016/j.molcel.2021.08.018] [Citation(s) in RCA: 302] [Impact Index Per Article: 100.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/02/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022]
Abstract
Redox reactions are intrinsically linked to energy metabolism. Therefore, redox processes are indispensable for organismal physiology and life itself. The term reactive oxygen species (ROS) describes a set of distinct molecular oxygen derivatives produced during normal aerobic metabolism. Multiple ROS-generating and ROS-eliminating systems actively maintain the intracellular redox state, which serves to mediate redox signaling and regulate cellular functions. ROS, in particular hydrogen peroxide (H2O2), are able to reversibly oxidize critical, redox-sensitive cysteine residues on target proteins. These oxidative post-translational modifications (PTMs) can control the biological activity of numerous enzymes and transcription factors (TFs), as well as their cellular localization or interactions with binding partners. In this review, we describe the diverse roles of redox regulation in the context of physiological cellular metabolism and provide insights into the pathophysiology of diseases when redox homeostasis is dysregulated.
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Affiliation(s)
- Claudia Lennicke
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Helena M Cochemé
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK.
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4
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Roret T, Zhang B, Moseler A, Dhalleine T, Gao XH, Couturier J, Lemaire SD, Didierjean C, Johnson MK, Rouhier N. Atypical Iron-Sulfur Cluster Binding, Redox Activity and Structural Properties of Chlamydomonas reinhardtii Glutaredoxin 2. Antioxidants (Basel) 2021; 10:antiox10050803. [PMID: 34069657 PMCID: PMC8161271 DOI: 10.3390/antiox10050803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/10/2021] [Accepted: 05/14/2021] [Indexed: 12/03/2022] Open
Abstract
Glutaredoxins (GRXs) are thioredoxin superfamily members exhibiting thiol-disulfide oxidoreductase activity and/or iron-sulfur (Fe-S) cluster binding capacities. These properties are determined by specific structural factors. In this study, we examined the capacity of the class I Chlamydomonas reinhardtii GRX2 recombinant protein to catalyze both protein glutathionylation and deglutathionylation reactions using a redox sensitive fluorescent protein as a model protein substrate. We observed that the catalytic cysteine of the CPYC active site motif of GRX2 was sufficient for catalyzing both reactions in the presence of glutathione. Unexpectedly, spectroscopic characterization of the protein purified under anaerobiosis showed the presence of a [2Fe-2S] cluster despite having a presumably inadequate active site signature, based on past mutational analyses. The spectroscopic characterization of cysteine mutated variants together with modeling of the Fe–S cluster-bound GRX homodimer from the structure of an apo-GRX2 indicate the existence of an atypical Fe–S cluster environment and ligation mode. Overall, the results further delineate the biochemical and structural properties of conventional GRXs, pointing to the existence of multiple factors more complex than anticipated, sustaining the capacity of these proteins to bind Fe–S clusters.
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Affiliation(s)
- Thomas Roret
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France; (T.R.); (A.M.); (T.D.); (J.C.)
| | - Bo Zhang
- Department of Chemistry and Centre for Metalloenzyme Studies, University of Georgia, Athens, GA 30602, USA; (B.Z.); (M.K.J.)
| | - Anna Moseler
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France; (T.R.); (A.M.); (T.D.); (J.C.)
| | - Tiphaine Dhalleine
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France; (T.R.); (A.M.); (T.D.); (J.C.)
| | - Xing-Huang Gao
- Department of Genetics, Case Western Reserve University, Cleveland, OH 44106, USA;
| | - Jérémy Couturier
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France; (T.R.); (A.M.); (T.D.); (J.C.)
| | - Stéphane D. Lemaire
- Institut de Biologie Paris-Seine, Laboratoire de Biologie Computationnelle et Quantitative, Sorbonne Université, CNRS, UMR7238, 75006 Paris, France;
- Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Sorbonne Université, CNRS, UMR8226, 75006 Paris, France
| | | | - Michael K. Johnson
- Department of Chemistry and Centre for Metalloenzyme Studies, University of Georgia, Athens, GA 30602, USA; (B.Z.); (M.K.J.)
| | - Nicolas Rouhier
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France; (T.R.); (A.M.); (T.D.); (J.C.)
- Correspondence: ; Tel.: +33-372-745-157
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5
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Quantitative assessment of the determinant structural differences between redox-active and inactive glutaredoxins. Nat Commun 2020; 11:1725. [PMID: 32265442 PMCID: PMC7138851 DOI: 10.1038/s41467-020-15441-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/04/2020] [Indexed: 11/08/2022] Open
Abstract
Class I glutaredoxins are enzymatically active, glutathione-dependent oxidoreductases, whilst class II glutaredoxins are typically enzymatically inactive, Fe-S cluster-binding proteins. Enzymatically active glutaredoxins harbor both a glutathione-scaffold site for reacting with glutathionylated disulfide substrates and a glutathione-activator site for reacting with reduced glutathione. Here, using yeast ScGrx7 as a model protein, we comprehensively identified and characterized key residues from four distinct protein regions, as well as the covalently bound glutathione moiety, and quantified their contribution to both interaction sites. Additionally, we developed a redox-sensitive GFP2-based assay, which allowed the real-time assessment of glutaredoxin structure-function relationships inside living cells. Finally, we employed this assay to rapidly screen multiple glutaredoxin mutants, ultimately enabling us to convert enzymatically active and inactive glutaredoxins into each other. In summary, we have gained a comprehensive understanding of the mechanistic underpinnings of glutaredoxin catalysis and have elucidated the determinant structural differences between the two main classes of glutaredoxins. Glutaredoxins play a central role in numerous biological processes including cellular redox homeostasis and Fe-S cluster biogenesis. Here the authors establish the molecular basis for glutaredoxin redox catalysis through comprehensive biochemical and structural analyses.
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6
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Janssen-Heininger Y, Reynaert NL, van der Vliet A, Anathy V. Endoplasmic reticulum stress and glutathione therapeutics in chronic lung diseases. Redox Biol 2020; 33:101516. [PMID: 32249209 PMCID: PMC7251249 DOI: 10.1016/j.redox.2020.101516] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/20/2020] [Accepted: 03/20/2020] [Indexed: 02/07/2023] Open
Affiliation(s)
- Yvonne Janssen-Heininger
- Department of Pathology and Laboratory Medicine, University of Vermont, Larner College of Medicine, Burlington, VT, 05405, USA.
| | - Niki L Reynaert
- Department of Respiratory Medicine and School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center, Maastricht, the Netherlands
| | - Albert van der Vliet
- Department of Pathology and Laboratory Medicine, University of Vermont, Larner College of Medicine, Burlington, VT, 05405, USA
| | - Vikas Anathy
- Department of Pathology and Laboratory Medicine, University of Vermont, Larner College of Medicine, Burlington, VT, 05405, USA
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7
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Khattri RB, Morris DL, Bilinovich SM, Manandhar E, Napper KR, Sweet JW, Modarelli DA, Leeper TC. Identifying Ortholog Selective Fragment Molecules for Bacterial Glutaredoxins by NMR and Affinity Enhancement by Modification with an Acrylamide Warhead. Molecules 2019; 25:E147. [PMID: 31905878 PMCID: PMC6983068 DOI: 10.3390/molecules25010147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 12/30/2022] Open
Abstract
Illustrated here is the development of a new class of antibiotic lead molecules targeted at Pseudomonas aeruginosa glutaredoxin (PaGRX). This lead was produced to (a) circumvent efflux-mediated resistance mechanisms via covalent inhibition while (b) taking advantage of species selectivity to target a fundamental metabolic pathway. This work involved four components: a novel workflow for generating protein specific fragment hits via independent nuclear magnetic resonance (NMR) measurements, NMR-based modeling of the target protein structure, NMR guided docking of hits, and synthetic modification of the fragment hit with a vinyl cysteine trap moiety, i.e., acrylamide warhead, to generate the chimeric lead. Reactivity of the top warhead-fragment lead suggests that the ortholog selectivity observed for a fragment hit can translate into a substantial kinetic advantage in the mature warhead lead, which bodes well for future work to identify potent, species specific drug molecules targeted against proteins heretofore deemed undruggable.
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Affiliation(s)
- Ram B. Khattri
- Department of Physiology and Functional genomics, University of Florida, Gainesville, FL 32610, USA;
| | - Daniel L. Morris
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA; (D.L.M.); (K.R.N.); (J.W.S.); (D.A.M.)
| | - Stephanie M. Bilinovich
- Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI 48824, USA;
| | | | - Kahlilah R. Napper
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA; (D.L.M.); (K.R.N.); (J.W.S.); (D.A.M.)
| | - Jacob W. Sweet
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA; (D.L.M.); (K.R.N.); (J.W.S.); (D.A.M.)
| | - David A. Modarelli
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA; (D.L.M.); (K.R.N.); (J.W.S.); (D.A.M.)
| | - Thomas C. Leeper
- Department of Chemistry and Biochemistry, Kennesaw State University, GA 30144, USA
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8
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Chia SB, Elko EA, Aboushousha R, Manuel AM, van de Wetering C, Druso JE, van der Velden J, Seward DJ, Anathy V, Irvin CG, Lam YW, van der Vliet A, Janssen-Heininger YMW. Dysregulation of the glutaredoxin/ S-glutathionylation redox axis in lung diseases. Am J Physiol Cell Physiol 2019; 318:C304-C327. [PMID: 31693398 DOI: 10.1152/ajpcell.00410.2019] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Glutathione is a major redox buffer, reaching millimolar concentrations within cells and high micromolar concentrations in airways. While glutathione has been traditionally known as an antioxidant defense mechanism that protects the lung tissue from oxidative stress, glutathione more recently has become recognized for its ability to become covalently conjugated to reactive cysteines within proteins, a modification known as S-glutathionylation (or S-glutathiolation or protein mixed disulfide). S-glutathionylation has the potential to change the structure and function of the target protein, owing to its size (the addition of three amino acids) and charge (glutamic acid). S-glutathionylation also protects proteins from irreversible oxidation, allowing them to be enzymatically regenerated. Numerous enzymes have been identified to catalyze the glutathionylation/deglutathionylation reactions, including glutathione S-transferases and glutaredoxins. Although protein S-glutathionylation has been implicated in numerous biological processes, S-glutathionylated proteomes have largely remained unknown. In this paper, we focus on the pathways that regulate GSH homeostasis, S-glutathionylated proteins, and glutaredoxins, and we review methods required toward identification of glutathionylated proteomes. Finally, we present the latest findings on the role of glutathionylation/glutaredoxins in various lung diseases: idiopathic pulmonary fibrosis, asthma, and chronic obstructive pulmonary disease.
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Affiliation(s)
- Shi B Chia
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont
| | - Evan A Elko
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont
| | - Reem Aboushousha
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont
| | - Allison M Manuel
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont
| | - Cheryl van de Wetering
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont
| | - Joseph E Druso
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont
| | - Jos van der Velden
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont
| | - David J Seward
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont
| | - Vikas Anathy
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont
| | - Charles G Irvin
- Department of Medicine, University of Vermont, Burlington, Vermont
| | - Ying-Wai Lam
- Department of Biology, University of Vermont, Burlington, Vermont
| | - Albert van der Vliet
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont
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9
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Maghool S, La Fontaine S, Maher MJ. High-resolution crystal structure of the reduced Grx1 from Saccharomyces cerevisiae. Acta Crystallogr F Struct Biol Commun 2019; 75:392-396. [PMID: 31045569 PMCID: PMC6497100 DOI: 10.1107/s2053230x19003327] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 03/07/2019] [Indexed: 11/10/2022] Open
Abstract
Grx1, a cytosolic thiol-disulfide oxidoreductase, actively maintains cellular redox homeostasis using glutathione substrates (reduced, GSH, and oxidized, GSSG). Here, the crystallization of reduced Grx1 from the yeast Saccharomyces cerevisiae (yGrx1) in space group P212121 and its structure solution and refinement to 1.22 Å resolution are reported. To study the structure-function relationship of yeast Grx1, the crystal structure of reduced yGrx1 was compared with the existing structures of the oxidized and glutathionylated forms. These comparisons revealed structural differences in the conformations of residues neighbouring the Cys27-Cys30 active site which accompany alterations in the redox status of the protein.
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Affiliation(s)
- Shadi Maghool
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Sharon La Fontaine
- School of Life and Environmental Sciences, Deakin University, Melbourne, Victoria, Australia
| | - Megan J. Maher
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
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10
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Abdalla M, Eltayb WA, Yousif A. Comparison of structures among Saccharomyces cerevisiae Grxs proteins. Genes Environ 2018; 40:17. [PMID: 30186535 PMCID: PMC6120076 DOI: 10.1186/s41021-018-0104-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 07/12/2018] [Indexed: 11/11/2022] Open
Abstract
Glutaredoxins (Grxs) comprise a group of glutathione (GSH)-dependent oxidoreductase enzymes that respond to oxidative stress and sustain redox homeostasis. Saccharomyces cerevisiae Grx has a similar interaction patterns through its residues between the residues and the environment. The glutaredoxin domain covers 100% of the entire mature Grx1 and Grx8, while the glutaredoxin domain covers ~ 52% of the entire mature Grx6 and Grx7, which have approximately 74 additional amino acids in their N-terminal regions, whereas Grx3 and Grx4 have two functional domains: glutaredoxin and thioredoxin. We have presented the prediction of disordered regions within these protein sequences. Multiple sequence alignment combined with a phylogenetic tree enabled us to specify the key residues contributing to the differences between Saccharomyces cerevisiae Grxs and the proportion symmetry.
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Affiliation(s)
- Mohnad Abdalla
- 1Faculty of Science and Technology, Omdurman Islamic University, Omdurman, Sudan.,2School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 People's Republic of China
| | - Wafa Ali Eltayb
- 2School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 People's Republic of China.,3Faculty of Science and Technology, Shendi University, Shendi, Nher Anile Sudan
| | - Aadil Yousif
- 4Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
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11
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Abdalla M, Eltayb WA, El-Arabey AA, Mo R, Dafaalla TIM, Hamouda HI, Bhat EA, Awadasseid A, Ali HAA. Structure analysis of yeast glutaredoxin Grx6 protein produced in Escherichia coli. Genes Environ 2018; 40:15. [PMID: 30123389 PMCID: PMC6091153 DOI: 10.1186/s41021-018-0103-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/05/2018] [Indexed: 12/20/2022] Open
Abstract
Background Grx6 is a yeast Golgi/endoplasmic reticulum protein involved in iron-sulfur binding that belongs to monothiol glutaredoxin-protein family. Grx6 has been biochemically characterized previously. Grx6 contains a conserved cysteine residue (Cys-136). Depending on the active-site sequences, Grxs can be classified to classic dithiol Grxs with a CXXC motif known as classes II and monothiol Grxs with a CXXS motif known as classes I, and Grx6 belongs to the class I with a CSYS motif. Results Our results showed how the loop between the N-terminal and C-terminal can affect the stability. When Grx6 was incubated with FeSO4·7H2O and (NH4)2Fe(SO4)2·6H2O, a disulfide bond was formed between the cysteine 136 and glutathione, and the concentration of dimer and tetramer was increased. The results presented various levels of stability of Grx6 with mutant and deleted amino acids. We also highlighted the difference between the monomer and dimer forms of the Grx6, in addition to comparison of the Fe-S cluster positions among holo forms of poplar Grx-C1, human Grx2 and Saccharomyces cerevisiae Grx6. Conclusions In this paper, we used a combination of spectroscopic and proteomic techniques to analyse the sequence and to determine the affected mutations and deletions in the stability of Grx6. Our results have increased the knowledge about the differences between monomer and dimer structures in cellular processes and proteins whose roles and functions depend on YCA1 in yeast. Electronic supplementary material The online version of this article (10.1186/s41021-018-0103-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mohnad Abdalla
- 1Faculty of Science and Technology, Omdurman Islamic University, Khartoum, Sudan.,2School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 People's Republic of China.,3Qingdao Institute of Bioenergy and Bioprocess Technology, Qingdao Shi, Shandong Sheng 266000 People's Republic of China
| | - Wafa Ali Eltayb
- 2School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 People's Republic of China.,4Faculty of Science and Technology, Shendi University, Shendi, Nher Anile Sudan
| | - Amr Ahmed El-Arabey
- 2School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 People's Republic of China
| | - Raihan Mo
- 2School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 People's Republic of China
| | - T I M Dafaalla
- 5College of Education, Sinnar University, 11147 Sinnar, Sudan
| | - Hamed I Hamouda
- 3Qingdao Institute of Bioenergy and Bioprocess Technology, Qingdao Shi, Shandong Sheng 266000 People's Republic of China
| | - Eijaz Ahmed Bhat
- School of Biotechnology and Graduate School of Biochemistry, Yeungnam, 280, Daehak-ro, Gyeongsan-si, Gyeongsangbuk-do 712-749 South Korea
| | - Annoor Awadasseid
- 7Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, 116044 China
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12
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Chi CB, Tang Y, Zhang J, Dai YN, Abdalla M, Chen Y, Zhou CZ. Structural and Biochemical Insights into the Multiple Functions of Yeast Grx3. J Mol Biol 2018. [PMID: 29524511 DOI: 10.1016/j.jmb.2018.02.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The yeast Saccharomyces cerevisiae monothiol glutaredoxin Grx3 plays a key role in cellular defense against oxidative stress and more importantly, cooperates with BolA-like iron repressor of activation protein Fra2 to regulate the localization of the iron-sensing transcription factor Aft2. The interplay among Grx3, Fra2 and Aft2 responsible for the regulation of iron homeostasis has not been clearly described. Here we solved the crystal structures of the Trx domain (Grx3Trx) and Grx domain (Grx3Grx) of Grx3 in addition to the solution structure of Fra2. Structural analyses and activity assays indicated that the Trx domain also contributes to the glutathione S-transferase activity of Grx3, via an inter-domain disulfide bond between Cys37 and Cys176. NMR titration and pull-down assays combined with surface plasmon resonance experiments revealed that Fra2 could form a noncovalent heterodimer with Grx3 via an interface between the helix-turn-helix motif of Fra2 and the C-terminal segment of Grx3Grx, different from the previously identified covalent heterodimer mediated by Fe-S cluster. Comparative affinity assays indicated that the interaction between Fra2 and Aft2 is much stronger than that between Grx3 and Aft2, or Aft2 toward its target DNA. These structural and biochemical analyses enabled us to propose a model how Grx3 executes multiple functions to coordinate the regulation of Aft2-controlled iron metabolism.
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Affiliation(s)
- Chang-Biao Chi
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China; Key Laboratory of Structural Biology, Chinese Academy of Science, Hefei, Anhui, 230027, People's Republic of China
| | - YaJun Tang
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China; Key Laboratory of Structural Biology, Chinese Academy of Science, Hefei, Anhui, 230027, People's Republic of China.
| | - Jiahai Zhang
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China; Key Laboratory of Structural Biology, Chinese Academy of Science, Hefei, Anhui, 230027, People's Republic of China
| | - Ya-Nan Dai
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China; Key Laboratory of Structural Biology, Chinese Academy of Science, Hefei, Anhui, 230027, People's Republic of China
| | - Mohnad Abdalla
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China; Key Laboratory of Structural Biology, Chinese Academy of Science, Hefei, Anhui, 230027, People's Republic of China
| | - Yuxing Chen
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China; Key Laboratory of Structural Biology, Chinese Academy of Science, Hefei, Anhui, 230027, People's Republic of China
| | - Cong-Zhao Zhou
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China; Key Laboratory of Structural Biology, Chinese Academy of Science, Hefei, Anhui, 230027, People's Republic of China.
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13
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Glutaredoxin catalysis requires two distinct glutathione interaction sites. Nat Commun 2017; 8:14835. [PMID: 28374771 PMCID: PMC5382279 DOI: 10.1038/ncomms14835] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 02/02/2017] [Indexed: 01/15/2023] Open
Abstract
Glutaredoxins are key players in cellular redox homoeostasis and exert a variety of essential functions ranging from glutathione-dependent catalysis to iron metabolism. The exact structure–function relationships and mechanistic differences among glutaredoxins that are active or inactive in standard enzyme assays have so far remained elusive despite numerous kinetic and structural studies. Here, we elucidate the enzymatic mechanism showing that glutaredoxins require two distinct glutathione interaction sites for efficient redox catalysis. The first site interacts with the glutathione moiety of glutathionylated disulfide substrates. The second site activates glutathione as the reducing agent. We propose that the requirement of two distinct glutathione interaction sites for the efficient reduction of glutathionylated disulfide substrates explains the deviating structure–function relationships, activities and substrate preferences of different glutaredoxin subfamilies as well as thioredoxins. Our model also provides crucial insights for the design or optimization of artificial glutaredoxins, transition-state inhibitors and glutaredoxin-coupled redox sensors. Glutaredoxins have important roles in redox processes. Here the authors show that the enzymatic activity of glutaredoxins requires two distinct glutathione interactions sites, one recognizing the glutathione disulfide substrate and one activating glutathione as a reducing agent.
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14
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Abdalla M, Dai YN, Chi CB, Cheng W, Cao DD, Zhou K, Ali W, Chen Y, Zhou CZ. Crystal structure of yeast monothiol glutaredoxin Grx6 in complex with a glutathione-coordinated [2Fe-2S] cluster. Acta Crystallogr F Struct Biol Commun 2016; 72:732-737. [PMID: 27710937 PMCID: PMC5053157 DOI: 10.1107/s2053230x16013418] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/20/2016] [Indexed: 01/10/2023] Open
Abstract
Glutaredoxins (Grxs) constitute a superfamily of proteins that perform diverse biological functions. The Saccharomyces cerevisiae glutaredoxin Grx6 not only serves as a glutathione (GSH)-dependent oxidoreductase and as a GSH transferase, but also as an essential [2Fe-2S]-binding protein. Here, the dimeric structure of the C-terminal domain of Grx6 (holo Grx6C), bridged by one [2Fe-2S] cluster coordinated by the active-site Cys136 and two external GSH molecules, is reported. Structural comparison combined with multiple-sequence alignment demonstrated that holo Grx6C is similar to the [2Fe-2S] cluster-incorporated dithiol Grxs, which share a highly conserved [2Fe-2S] cluster-binding pattern and dimeric conformation that is distinct from the previously identified [2Fe-2S] cluster-ligated monothiol Grxs.
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Affiliation(s)
- Mohnad Abdalla
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Ya-Nan Dai
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Chang-Biao Chi
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Wang Cheng
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Dong-Dong Cao
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Kang Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Wafa Ali
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Yuxing Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
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15
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Khattri RB, Morris DL, Davis CM, Bilinovich SM, Caras AJ, Panzner MJ, Debord MA, Leeper TC. An NMR-Guided Screening Method for Selective Fragment Docking and Synthesis of a Warhead Inhibitor. Molecules 2016; 21:molecules21070846. [PMID: 27438815 PMCID: PMC6274284 DOI: 10.3390/molecules21070846] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/20/2016] [Accepted: 06/22/2016] [Indexed: 02/07/2023] Open
Abstract
Selective hits for the glutaredoxin ortholog of Brucella melitensis are determined using STD NMR and verified by trNOE and (15)N-HSQC titration. The most promising hit, RK207, was docked into the target molecule using a scoring function to compare simulated poses to experimental data. After elucidating possible poses, the hit was further optimized into the lead compound by extension with an electrophilic acrylamide warhead. We believe that focusing on selectivity in this early stage of drug discovery will limit cross-reactivity that might occur with the human ortholog as the lead compound is optimized. Kinetics studies revealed that lead compound 5 modified with an ester group results in higher reactivity than an acrylamide control; however, after modification this compound shows little selectivity for bacterial protein versus the human ortholog. In contrast, hydrolysis of compound 5 to the acid form results in a decrease in the activity of the compound. Together these results suggest that more optimization is warranted for this simple chemical scaffold, and opens the door for discovery of drugs targeted against glutaredoxin proteins-a heretofore untapped reservoir for antibiotic agents.
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Affiliation(s)
- Ram B Khattri
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA.
| | - Daniel L Morris
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA.
| | - Caroline M Davis
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA.
| | - Stephanie M Bilinovich
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Andrew J Caras
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA.
| | - Matthew J Panzner
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA.
| | - Michael A Debord
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA.
| | - Thomas C Leeper
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA.
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16
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Netto LES, de Oliveira MA, Tairum CA, da Silva Neto JF. Conferring specificity in redox pathways by enzymatic thiol/disulfide exchange reactions. Free Radic Res 2016; 50:206-45. [DOI: 10.3109/10715762.2015.1120864] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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17
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Yenugudhati D, Prakash D, Kumar AK, Kumar RSS, Yennawar NH, Yennawar HP, Ferry JG. Structural and Biochemical Characterizations of Methanoredoxin from Methanosarcina acetivorans, a Glutaredoxin-Like Enzyme with Coenzyme M-Dependent Protein Disulfide Reductase Activity. Biochemistry 2015; 55:313-21. [PMID: 26684934 DOI: 10.1021/acs.biochem.5b00823] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Glutaredoxins (GRXs) are thiol-disulfide oxidoreductases abundant in prokaryotes, although little is understood of these enzymes from the domain Archaea. The numerous characterized GRXs from the domain Bacteria utilize a diversity of low-molecular-weight thiols in addition to glutathione as reductants. We report here the biochemical and structural properties of a GRX-like protein named methanoredoxin (MRX) from Methanosarcina acetivorans of the domain Archaea. MRX utilizes coenzyme M (CoMSH) as reductant for insulin disulfide reductase activity, which adds to the diversity of thiol protectants in prokaryotes. Cell-free extracts of M. acetivorans displayed CoMS-SCoM reductase activity that complements the CoMSH-dependent activity of MRX. The crystal structure exhibits a classic thioredoxin-glutaredoxin fold comprising three α-helices surrounding four antiparallel β-sheets. A pocket on the surface contains a CVWC motif, identifying the active site with architecture similar to GRXs. Although it is a monomer in solution, the crystal lattice has four monomers in a dimer of dimers arrangement. A cadmium ion is found within the active site of each monomer. Two such ions stabilize the N-terminal tails and dimer interfaces. Our modeling studies indicate that CoMSH and glutathione (GSH) bind to the active site of MRX similar to the binding of GSH in GRXs, although there are differences in the amino acid composition of the binding motifs. The results, combined with our bioinformatic analyses, show that MRX represents a class of GRX-like enzymes present in a diversity of methane-producing Archaea.
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Affiliation(s)
- Deepa Yenugudhati
- Department of Biochemistry and Molecular Biology, ‡Huck Institutes of Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Divya Prakash
- Department of Biochemistry and Molecular Biology, ‡Huck Institutes of Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Adepu K Kumar
- Department of Biochemistry and Molecular Biology, ‡Huck Institutes of Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - R Siva Sai Kumar
- Department of Biochemistry and Molecular Biology, ‡Huck Institutes of Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Neela H Yennawar
- Department of Biochemistry and Molecular Biology, ‡Huck Institutes of Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Hemant P Yennawar
- Department of Biochemistry and Molecular Biology, ‡Huck Institutes of Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - James G Ferry
- Department of Biochemistry and Molecular Biology, ‡Huck Institutes of Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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18
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Lee EH, Kim HY, Hwang KY. The GSH- and GSSG-bound structures of glutaredoxin from Clostridium oremlandii. Arch Biochem Biophys 2014; 564:20-5. [PMID: 25218089 DOI: 10.1016/j.abb.2014.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 08/25/2014] [Accepted: 09/01/2014] [Indexed: 12/21/2022]
Abstract
Glutaredoxin (Grx) is a major redox enzyme that reduces disulfide bonds using glutathione (GSH) as an electron donor. The anaerobic bacterium Clostridium oremlandii possesses a selenocysteine-containing Grx (cGrx1) and a cysteine-containing homolog (cGrx2). Here, the crystal structure of the GSSG-bound form of cGrx2 was determined for the first time at a resolution of 1.95Å. In addition, its monothiol variant cGrx2/C15S in complex with GSH was also determined at a resolution of 1.58Å. cGrx2 is a monomeric protein with an overall structure that consists of the typical thioredoxin fold composed of four α-helices and four β-strands. Two ligands, GSH and GSSG, share a conserved binding site consisting of CPYC, TVP, and CDD motifs. The cysteinyl and γ-glutamyl moieties show similar binding interactions in the two structures, whereas the glycine moiety shows different interactions. Interestingly, the structures revealed that only one GSH moiety of GSSG is sufficient for its binding to the protein. The GSSG-bound structure of cGrx2 was obtained as an oxidized form with a disulfide bond at the CPYC motif. Comparison of the GSH-binding mode in cGrx2 to other known Grxs revealed similarities as well as some diversity.
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Affiliation(s)
- Eun Hye Lee
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Hwa-Young Kim
- Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu, Republic of Korea.
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea.
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19
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Tang Y, Zhang J, Yu J, Xu L, Wu J, Zhou CZ, Shi Y. Structure-Guided Activity Enhancement and Catalytic Mechanism of Yeast Grx8. Biochemistry 2014; 53:2185-96. [DOI: 10.1021/bi401293s] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- YaJun Tang
- Hefei National Laboratory
for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Jiahai Zhang
- Hefei National Laboratory
for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Jiang Yu
- Hefei National Laboratory
for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Ling Xu
- Hefei National Laboratory
for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Jihui Wu
- Hefei National Laboratory
for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Cong-Zhao Zhou
- Hefei National Laboratory
for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Yunyu Shi
- Hefei National Laboratory
for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
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20
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Yogavel M, Tripathi T, Gupta A, Banday MM, Rahlfs S, Becker K, Belrhali H, Sharma A. Atomic resolution crystal structure of glutaredoxin 1 from Plasmodium falciparum and comparison with other glutaredoxins. ACTA ACUST UNITED AC 2013; 70:91-100. [PMID: 24419382 DOI: 10.1107/s1399004713025285] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 09/11/2013] [Indexed: 12/30/2022]
Abstract
Glutaredoxins (Grxs) are redox proteins that use glutathione ((γ)Glu-Cys-Gly; GSH) as a cofactor. Plasmodium falciparum has one classic dithiol (CXXC) glutaredoxin (glutaredoxin 1; PfGrx1) and three monothiol (CXXS) Grx-like proteins (GLPs), which have five residue insertions prior to the active-site Cys. Here, the crystal structure of PfGrx1 has been determined by the sulfur single-wavelength anomalous diffraction (S-SAD) method utilizing intrinsic protein and solvent S atoms. Several residues were modelled with alternate conformations, and an alternate position was refined for the active-site Cys29 owing to radiation damage. The GSH-binding site is occupied by water polygons and buffer molecules. Structural comparison of PfGrx1 with other Grxs and Grx-like proteins revealed that the GSH-binding motifs (CXXC/CXXS, TVP, CDD, Lys26 and Gln/Arg63) are structurally conserved. Both the monothiol and dithiol Grxs possess three conserved water molecules; two of these were located in the GSH-binding site. PfGrx1 has several polar and charged amino-acid substitutions that provide structurally important additional hydrogen bonds and salt bridges missing in other Grxs.
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Affiliation(s)
- Manickam Yogavel
- Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Road, New Delhi 110 067, India
| | - Timir Tripathi
- Department of Biochemistry, North-Eastern Hill University, Shillong 792 022, India
| | - Ankita Gupta
- Department of Biochemistry, North-Eastern Hill University, Shillong 792 022, India
| | - Mudassir Meraj Banday
- Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Road, New Delhi 110 067, India
| | - Stefan Rahlfs
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Katja Becker
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Hassan Belrhali
- European Molecular Biology Laboratory, 6 Rue Jules Horowitz, BP 181, 38042 Grenoble, France
| | - Amit Sharma
- Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Road, New Delhi 110 067, India
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21
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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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22
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Deponte M. Glutathione catalysis and the reaction mechanisms of glutathione-dependent enzymes. Biochim Biophys Acta Gen Subj 2013; 1830:3217-66. [DOI: 10.1016/j.bbagen.2012.09.018] [Citation(s) in RCA: 625] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 09/25/2012] [Indexed: 12/12/2022]
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23
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Yadav S, Kushwaha HR, Kumar K, Verma PK. Comparative structural modeling of a monothiol GRX from chickpea: Insight in iron–sulfur cluster assembly. Int J Biol Macromol 2012; 51:266-73. [DOI: 10.1016/j.ijbiomac.2012.05.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 04/27/2012] [Accepted: 05/11/2012] [Indexed: 01/12/2023]
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24
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Roos G, Messens J. Protein sulfenic acid formation: from cellular damage to redox regulation. Free Radic Biol Med 2011; 51:314-26. [PMID: 21605662 DOI: 10.1016/j.freeradbiomed.2011.04.031] [Citation(s) in RCA: 187] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 03/31/2011] [Accepted: 04/17/2011] [Indexed: 01/17/2023]
Abstract
Protein sulfenic acid formation has long been regarded as unwanted damage caused by reactive oxygen species (ROS). However, over the past 10 years, accumulating evidence has shown that the reversible oxidation of cysteine thiol groups to sulfenic acid functions as a redox-based signal transduction mechanism. Here, we review the mechanisms of sulfenic acid formation by ROS. We present some of the most important roles played by sulfenic acids in living cells as well as the pathways that regulate sulfenic acid formation. We highlight the experimental tools that have been developed to study the cellular sulfenome and show how computational approaches might help to better understand the mechanisms of sulfenic acid formation.
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Affiliation(s)
- Goedele Roos
- Department of Molecular and Cellular Interactions, Flanders Institute for Biotechnology, VIB, B-1050 Brussels, Belgium
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25
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Li WF, Yu J, Ma XX, Teng YB, Luo M, Tang YJ, Zhou CZ. Structural basis for the different activities of yeast Grx1 and Grx2. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:1542-7. [DOI: 10.1016/j.bbapap.2010.04.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Revised: 03/24/2010] [Accepted: 04/13/2010] [Indexed: 01/01/2023]
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26
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Li L, Cheng N, Hirschi KD, Wang X. Structure of Arabidopsis chloroplastic monothiol glutaredoxin AtGRXcp. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:725-32. [PMID: 20516625 PMCID: PMC2879357 DOI: 10.1107/s0907444910013119] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Accepted: 04/08/2010] [Indexed: 01/13/2023]
Abstract
The structure of Arabidopsis monothiol glutaredoxin AtGRXcp has been determined and reveals unique structural features of monothiol glutaredoxins, key residues for their interaction with glutathione and structural determinants for their distinct biochemical properties. Monothiol glutaredoxins (Grxs) play important roles in maintaining redox homeostasis in living cells and are conserved across species. Arabidopsis thaliana monothiol glutaredoxin AtGRXcp is critical for protection from oxidative stress in chloroplasts. The crystal structure of AtGRXcp has been determined at 2.4 Å resolution. AtGRXcp has a glutaredoxin/thioredoxin-like fold with distinct structural features that differ from those of dithiol Grxs. The structure reveals that the putative active-site motif CGFS is well defined and is located on the molecular surface and that a long groove extends to both sides of the catalytic Cys97. Structural comparison and molecular modeling suggest that glutathione can bind in this groove and form extensive interactions with conserved charged residues including Lys89, Arg126 and Asp152. Further comparative studies reveal that a unique loop with five additional residues adjacent to the active-site motif may be a key structural feature of monothiol Grxs and may influence their function. This study provides the first structural information on plant CGFS-type monothiol Grxs, allowing a better understanding of the redox-regulation mechanism mediated by these plant Grxs.
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Affiliation(s)
- Lenong Li
- Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401, USA
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27
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Luo M, Jiang YL, Ma XX, Tang YJ, He YX, Yu J, Zhang RG, Chen Y, Zhou CZ. Structural and Biochemical Characterization of Yeast Monothiol Glutaredoxin Grx6. J Mol Biol 2010; 398:614-22. [DOI: 10.1016/j.jmb.2010.03.029] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 03/14/2010] [Accepted: 03/17/2010] [Indexed: 10/19/2022]
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28
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Iversen R, Andersen PA, Jensen KS, Winther JR, Sigurskjold BW. Thiol-disulfide exchange between glutaredoxin and glutathione. Biochemistry 2010; 49:810-20. [PMID: 19968277 DOI: 10.1021/bi9015956] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Glutaredoxins are ubiquitous thiol-disulfide oxidoreductases which catalyze the reduction of glutathione-protein mixed disulfides. Belonging to the thioredoxin family, they contain a conserved active site CXXC motif. The N-proximal active site cysteine can form a mixed disulfide with glutathione or an intramolecular disulfide with the C-proximal cysteine. The C-proximal cysteine is not known to be involved in the catalytic mechanism. The stability of the mixed disulfide with glutathione has been investigated in detail using a mutant variant of yeast glutaredoxin 1, in which the C-proximal active site cysteine has been replaced with serine. The exchange reaction between the reduced protein and oxidized glutathione leading to formation of the mixed disulfide could readily be monitored by isothermal titration calorimetry (ITC) due to the enthalpic contributions from the noncovalent interactions and the protonation of glutathione thiolate. An algorithm for the analysis of this type of reaction by ITC was developed and showed that the interaction is enthalpy driven with a large entropy penalty. The applicability of the method was verified by a mass spectrometry-based approach, which gave a standard reduction potential of -295 mV for the mixed disulfide. In another set of experiments, the pK(a) value of the active site cysteine was determined. In line with what has been observed for other glutaredoxins, this cysteine was found to have a very low pK(a) value. The glutathionylation of glutaredoxin was shown to have a substantial effect on the thermal stability of the protein as revealed by differential scanning calorimetry.
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Affiliation(s)
- Rasmus Iversen
- Department of Biology, University of Copenhagen, Copenhagen Biocenter, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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29
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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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Kaur J, Bachhawat AK. Gln-222 in transmembrane domain 4 and Gln-526 in transmembrane domain 9 are critical for substrate recognition in the yeast high affinity glutathione transporter, Hgt1p. J Biol Chem 2009; 284:23872-84. [PMID: 19589778 PMCID: PMC2749159 DOI: 10.1074/jbc.m109.029728] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Revised: 07/02/2009] [Indexed: 11/06/2022] Open
Abstract
Hgt1p, a member of the oligopeptide transporter family, is a high affinity glutathione transporter from the yeast Saccharomyces cerevisiae. We have explored the role of polar or charged residues in the putative transmembrane domains of Hgt1p to obtain insights into the structural features of Hgt1p that govern its substrate specificity. A total of 22 charged and polar residues in the predicted transmembrane domains and other conserved regions were subjected to alanine mutagenesis. Functional characterization of these 22 mutants identified 11 mutants which exhibited significant loss in functional activity. All 11 mutants except T114A had protein expression levels comparable with wild type, and all except E744A were proficient in trafficking to the cell surface. Kinetic analyses revealed differential contributions toward the functional activity of Hgt1p by these residues and identified Asn-124 in transmembrane domain 1 (TMD1), Gln-222 in TMD4, Gln-526 in TMD9, and Glu-544, Arg-554, and Lys-562 in the intracellular loop region 537-568 containing the highly conserved proline-rich motif to be essential for the transport activity of the protein. Furthermore, mutants Q222A and Q526A exhibited a nearly 4- and 8-fold increase in the K(m) for glutathione. Interestingly, although Gln-222 is widely conserved among other functionally characterized oligopeptide transporter family members including those having a different substrate specificity, Gln-526 is present only in Hgt1p and Pgt1, the only two known high affinity glutathione transporters. These results provide the first insights into the substrate recognition residues of a high affinity glutathione transporter and on residues/helices involved in substrate translocation in the structurally uncharacterized oligopeptide transporter family.
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Affiliation(s)
- Jaspreet Kaur
- From the Institute of Microbial Technology, Sector 39-A, Chandigarh 160 036, India
| | - Anand K. Bachhawat
- From the Institute of Microbial Technology, Sector 39-A, Chandigarh 160 036, India
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Bao R, Zhang Y, Lou X, Zhou CZ, Chen Y. Structural and kinetic analysis of Saccharomyces cerevisiae thioredoxin Trx1: Implications for the catalytic mechanism of GSSG reduced by the thioredoxin system. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1218-23. [DOI: 10.1016/j.bbapap.2009.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2009] [Revised: 03/28/2009] [Accepted: 04/01/2009] [Indexed: 10/20/2022]
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Gallogly MM, Starke DW, Mieyal JJ. Mechanistic and kinetic details of catalysis of thiol-disulfide exchange by glutaredoxins and potential mechanisms of regulation. Antioxid Redox Signal 2009; 11:1059-81. [PMID: 19119916 PMCID: PMC2842129 DOI: 10.1089/ars.2008.2291] [Citation(s) in RCA: 169] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Glutaredoxins are small, heat-stable proteins that exhibit a characteristic thioredoxin fold and a CXXC/S active-site motif. A variety of glutathione (GSH)-dependent catalytic activities have been attributed to the glutaredoxins, including reduction of ribonucleotide reductase, arsenate, and dehydroascorbate; assembly of iron sulfur cluster complexes; and protein glutathionylation and deglutathionylation. Catalysis of reversible protein glutathionylation by glutaredoxins has been implicated in regulation of redox signal transduction and sulfhydryl homeostasis in numerous contexts in health and disease. This forum review is presented in two parts. Part I is focused primarily on the mechanism of the deglutathionylation reaction catalyzed by prototypical dithiol glutaredoxins, especially human Grx1 and Grx2. Grx-catalyzed protein deglutathionylation proceeds by a nucleophilic, double-displacement mechanism in which rate enhancement is attributed to special reactivity of the low pK(a) cysteine at its active site, and to increased nucleophilicity of the second substrate, GSH. Glutaredoxins (and Grx domains) have been identified in most organisms, and many exhibit deglutathionylation or other activities or both. Further characterization according to glutathionyl selectivity, physiological substrates, and intracellular roles may lead to subclassification of this family of enzymes. Part II presents potential mechanisms for in vivo regulation of Grx activity, providing avenues for future studies.
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Affiliation(s)
- Molly M Gallogly
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106-4965, USA
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Visualization and orchestration of the dynamic molecular society in cells. Cell Res 2009; 19:152-5. [PMID: 19153596 DOI: 10.1038/cr.2009.7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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Zhang ZR, Perrett S. Novel glutaredoxin activity of the yeast prion protein Ure2 reveals a native-like dimer within fibrils. J Biol Chem 2009; 284:14058-67. [PMID: 19321443 DOI: 10.1074/jbc.m901189200] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ure2 is the protein determinant of the Saccharomyces cerevisiae prion [URE3]. Ure2 has structural similarity to glutathione transferases, protects cells against heavy metal and oxidant toxicity in vivo, and shows glutathione-dependent peroxidase activity in vitro. Here we report that Ure2 (which has no cysteine residues) also shows thiol-disulfide oxidoreductase activity similar to that of glutaredoxin enzymes. This demonstrates that disulfide reductase activity can be independent of the classical glutaredoxin CXXC/CXXS motif or indeed an intrinsic catalytic cysteine residue. The kinetics of the glutaredoxin activity of Ure2 showed positive cooperativity for the substrate glutathione in both the soluble native state and in amyloid-like fibrils, indicating native-like dimeric structure within Ure2 fibrils. Characterization of the glutaredoxin activity of Ure2 sheds light on its ability to protect yeast from heavy metal ion and oxidant toxicity and suggests a role in reversible protein glutathionylation signal transduction. Observation of allosteric enzyme behavior within amyloid-like Ure2 fibrils not only provides insight into the molecular structure of the fibrils but also has implications for the mechanism of [URE3] prion formation.
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Affiliation(s)
- Zai-Rong Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
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Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Gilge JL, Fisher M, Chai YC. The effect of oxidant and the non-oxidant alteration of cellular thiol concentration on the formation of protein mixed-disulfides in HEK 293 cells. PLoS One 2008; 3:e4015. [PMID: 19107210 PMCID: PMC2603474 DOI: 10.1371/journal.pone.0004015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Accepted: 11/24/2008] [Indexed: 02/02/2023] Open
Abstract
Cellular molecules possess various mechanisms in responding to oxidant stress. In terms of protein responses, protein S-glutathionylation is a unique post-translational modification of protein reactive cysteines forming disulfides with glutathione molecules. This modification has been proposed to play roles in antioxidant, regulatory and signaling in cells under oxidant stress. Recently, the increased level of protein S-glutathionylation has been linked with the development of diseases. In this report, specific S-glutathionylated proteins were demonstrated in human embryonic kidney 293 cells treated with two different oxidative reagents: diamide and hydrogen peroxide. Diamide is a chemical oxidizing agent whereas hydrogen peroxide is a physiological oxidant. Under the experimental conditions, these two oxidants decreased glutathione concentration without toxicity. S-glutathionylated proteins were detected by immunoblotting and glutathione concentrations were determined by high performance liquid chromatography. We further show the effect of alteration of the cellular thiol pool on the amount of protein S-glutathionylation in oxidant-treated cells. Cellular thiol concentrations were altered either by a specific way using buthionine sulfoximine, a specific inhibitor of glutathione biosynthesis or by a non-specific way, incubating cells in cystine-methionine deficient media. Cells only treated with either buthionine sulfoximine or cystine-methionine deficient media did not induce protein S-glutathionylation, even though both conditions decreased 65% of cellular glutathione. Moreover, the amount of protein S-glutathionylation under both conditions in the presence of oxidants was not altered when compared to the amount observed in regular media with oxidants present. Protein S-glutathionylation is a dynamic reaction which depends on the rate of adding and removing glutathione. Phenylarsine oxide, which specifically forms a covalent adduct with vicinal thiols, was used to determine the possible role of vicinal thiols in the amount of glutathionylation. Our data shows phenylarsine oxide did not change glutathione concentrations, but it did enhance the amount of glutathionylation in oxidant-treated cells.
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Affiliation(s)
- Jasen Lee Gilge
- Department of Chemistry, John Carroll University, University Height, Ohio, United States of America
| | - Michael Fisher
- Department of Chemistry, John Carroll University, University Height, Ohio, United States of America
| | - Yuh-Cherng Chai
- Department of Chemistry, John Carroll University, University Height, Ohio, United States of America
- * E-mail:
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Elgán TH, Berndt KD. Quantifying Escherichia coli Glutaredoxin-3 Substrate Specificity Using Ligand-induced Stability. J Biol Chem 2008; 283:32839-47. [DOI: 10.1074/jbc.m804019200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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