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Wu M, Deng C, Lo TH, Chan KY, Li X, Wong CM. Peroxiredoxin, Senescence, and Cancer. Cells 2022; 11:cells11111772. [PMID: 35681467 PMCID: PMC9179887 DOI: 10.3390/cells11111772] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 05/26/2022] [Accepted: 05/26/2022] [Indexed: 02/08/2023] Open
Abstract
Peroxiredoxins are multifunctional enzymes that play a key role in protecting cells from stresses and maintaining the homeostasis of many cellular processes. Peroxiredoxins were firstly identified as antioxidant enzymes that can be found in all living organisms. Later studies demonstrated that peroxiredoxins also act as redox signaling regulators, chaperones, and proinflammatory factors and play important roles in oxidative defense, redox signaling, protein folding, cycle cell progression, DNA integrity, inflammation, and carcinogenesis. The versatility of peroxiredoxins is mainly based on their unique active center cysteine with a wide range of redox states and the ability to switch between low- and high-molecular-weight species for regulating their peroxidase and chaperone activities. Understanding the molecular mechanisms of peroxiredoxin in these processes will allow the development of new approaches to enhance longevity and to treat various cancers. In this article, we briefly review the history of peroxiredoxins, summarize recent advances in our understanding of peroxiredoxins in aging- and cancer-related biological processes, and discuss the future perspectives of using peroxiredoxins in disease diagnostics and treatments.
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Relevance of peroxiredoxins in pathogenic microorganisms. Appl Microbiol Biotechnol 2021; 105:5701-5717. [PMID: 34258640 DOI: 10.1007/s00253-021-11360-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 12/19/2022]
Abstract
The oxidative and nitrosative responses generated by animals and plants are important defenses against infection and establishment of pathogenic microorganisms such as bacteria, fungi, and protozoa. Among distinct oxidant species, hydroperoxides are a group of chemically diverse compounds that comprise small hydrophilic molecules, such as hydrogen peroxide and peroxynitrite, and bulky hydrophobic species, such as organic hydroperoxides. Peroxiredoxins (Prx) are ubiquitous enzymes that use a highly reactive cysteine residue to decompose hydroperoxides and can also perform other functions, like molecular chaperone and phospholipase activities, contributing to microbial protection against the host defenses. Prx are present in distinct cell compartments and, in some cases, they can be secreted to the extracellular environment. Despite their high abundance, Prx expression can be further increased in response to oxidative stress promoted by host defense systems, by treatment with hydroperoxides or by antibiotics. In consequence, some isoforms have been described as virulence factors, highlighting their importance in pathogenesis. Prx are very diverse and are classified into six different classes (Prx1-AhpC, BCP-PrxQ, Tpx, Prx5, Prx6, and AhpE) based on structural and biochemical features. Some groups are absent in hosts, while others present structural peculiarities that differentiate them from the host's isoforms. In this context, the intrinsic characteristics of these enzymes may aid the development of new drugs to combat pathogenic microorganisms. Additionally, since some isoforms are also found in the extracellular environment, Prx emerge as attractive targets for the production of diagnostic tests and vaccines. KEY POINTS: • Peroxiredoxins are front-line defenses against host oxidative and nitrosative stress. • Functional and structural peculiarities differ pathogen and host enzymes. • Peroxiredoxins are potential targets to microbicidal drugs.
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Bolduc J, Koruza K, Luo T, Malo Pueyo J, Vo TN, Ezeriņa D, Messens J. Peroxiredoxins wear many hats: Factors that fashion their peroxide sensing personalities. Redox Biol 2021; 42:101959. [PMID: 33895094 PMCID: PMC8113037 DOI: 10.1016/j.redox.2021.101959] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/07/2021] [Accepted: 03/25/2021] [Indexed: 02/07/2023] Open
Abstract
Peroxiredoxins (Prdxs) sense and assess peroxide levels, and signal through protein interactions. Understanding the role of the multiple structural and post-translational modification (PTM) layers that tunes the peroxiredoxin specificities is still a challenge. In this review, we give a tabulated overview on what is known about human and bacterial peroxiredoxins with a focus on structure, PTMs, and protein-protein interactions. Armed with numerous cellular and atomic level experimental techniques, we look at the future and ask ourselves what is still needed to give us a clearer view on the cellular operating power of Prdxs in both stress and non-stress conditions.
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Affiliation(s)
- Jesalyn Bolduc
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Katarina Koruza
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Ting Luo
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Julia Malo Pueyo
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Trung Nghia Vo
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Daria Ezeriņa
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Joris Messens
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium.
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Himiyama T, Tsuchiya Y, Yonezawa Y, Nakamura T. Rebuilding Ring-Type Assembly of Peroxiredoxin by Chemical Modification. Bioconjug Chem 2020; 32:153-160. [PMID: 33334100 DOI: 10.1021/acs.bioconjchem.0c00587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Direct control of the protein quaternary structure (QS) is challenging owing to the complexity of the protein structure. As a protein with a characteristic QS, peroxiredoxin from Aeropyrum pernix K1 (ApPrx) forms a decamer, wherein five dimers associate to form a ring. Here, we disrupted and reconstituted ApPrx QS via amino acid mutations and chemical modifications targeting hot spots for protein assembly. The decameric QS of an ApPrx* mutant, wherein all cysteine residues in wild-type ApPrx were mutated to serine, was destructed to dimers via an F80C mutation. The dimeric ApPrx*F80C mutant was then modified with a small molecule and successfully assembled as a decamer. Structural analysis confirmed that an artificially installed chemical moiety potentially facilitates suitable protein-protein interactions to rebuild a native structure. Rebuilding of dodecamer was also achieved through an additional amino acid mutation. This study describes a facile method to regulate the protein assembly state.
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Affiliation(s)
- Tomoki Himiyama
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka 563-8577, Japan.,DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Ikeda, Osaka 563-8577, Japan
| | - Yuko Tsuchiya
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
| | - Yasushige Yonezawa
- High Pressure Protein Research Center, Institute of Advanced Technology, Kindai University, Kinokawa, Wakayama 649-6493, Japan
| | - Tsutomu Nakamura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka 563-8577, Japan.,DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Ikeda, Osaka 563-8577, Japan
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5
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Himiyama T, Nakamura T. Disassembly of the ring-type decameric structure of peroxiredoxin from Aeropyrum pernix K1 by amino acid mutation. Protein Sci 2020; 29:1138-1147. [PMID: 32022337 DOI: 10.1002/pro.3837] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/23/2020] [Accepted: 01/28/2020] [Indexed: 12/13/2022]
Abstract
The quaternary structure of peroxiredoxin from Aeropyrum pernix K1 (ApPrx) is a decamer, in which five homodimers are assembled in a pentagonal ring through hydrophobic interactions. In this study, we determined the amino acid (AA) residues of ApPrx crucial for forming the decamer using AA mutations. The ApPrx0Cys mutant, wherein all cysteine residues were mutated to serine, was prepared as a model protein to remove the influence of the redox states of the cysteines on its assembling behavior. The boundary between each homodimer of ApPrx0Cys contains characteristic aromatic AA residues forming hydrophobic interactions: F46, F80, W88, W210, and W211. We found that a single mutation of F46, F80, or W210 to alanine completely disassembled the ApPrx0Cys decamer to homodimers, which was clarified by gel-filtration chromatography and dynamic light scattering measurements. F46A, F80A, and W210A mutants lacked only one aromatic ring compared with ApPrx0Cys, indicating that the assembly is very sensitive to the surface structure of the protein. X-ray structures revealed two mechanisms of disassembly of the ApPrx decamer: loss of hydrophobicity between homodimers and flip of the arm domain. The AA residues targeted in this study are well conserved in ring-type Prx proteins, suggesting the importance of these residues in the assembly. This study demonstrates the sensitivity and modifiability of peroxiredoxin assembly by a simple AA mutation.
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Affiliation(s)
- Tomoki Himiyama
- National Institute of Advanced Industrial Science and Technology, Ikeda, Japan.,DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Ikeda, Japan
| | - Tsutomu Nakamura
- National Institute of Advanced Industrial Science and Technology, Ikeda, Japan.,DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Ikeda, Japan
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Aljannat MAK, Oldfield NJ, Albasri HM, Dorrington LKG, Ohri RL, Wooldridge KG, Turner DPJ. The moonlighting peroxiredoxin-glutaredoxin in Neisseria meningitidis binds plasminogen via a C-terminal lysine residue and contributes to survival in a whole blood model. Microb Pathog 2019; 139:103890. [PMID: 31765768 DOI: 10.1016/j.micpath.2019.103890] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 11/20/2019] [Accepted: 11/22/2019] [Indexed: 01/24/2023]
Abstract
Neisseria meningitidis is a human-restricted bacterium that can invade the bloodstream and cross the blood-brain barrier resulting in life-threatening sepsis and meningitis. Meningococci express a cytoplasmic peroxiredoxin-glutaredoxin (Prx5-Grx) hybrid protein that has also been identified on the bacterial surface. Here, recombinant Prx5-Grx was confirmed as a plasminogen (Plg)-binding protein, in an interaction which could be inhibited by the lysine analogue ε-aminocapronic acid. rPrx5-Grx derivatives bearing a substituted C-terminal lysine residue (rPrx5-GrxK244A), but not the active site cysteine residue (rPrx5-GrxC185A) or the sub-terminal rPrx5-GrxK230A lysine residue, exhibited significantly reduced Plg-binding. The absence of Prx5-Grx did not significantly reduce the ability of whole meningococcal cells to bind Plg, but under hydrogen peroxide-mediated oxidative stress, the N. meningitidis Δpxn5-grx mutant survived significantly better than the wild-type or complemented strains. Significantly, using human whole blood as a model of meningococcal bacteremia, it was found that the N. meningitidis Δpxn5-grx mutant had a survival defect compared with the parental or complemented strain, confirming an important role for Prx5-Grx in meningococcal pathogenesis.
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Affiliation(s)
- Mahab A K Aljannat
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Neil J Oldfield
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Hibah M Albasri
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | | | - Radhica L Ohri
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Karl G Wooldridge
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - David P J Turner
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
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Su T, Si M, Zhao Y, Liu Y, Yao S, Che C, Chen C. A thioredoxin-dependent peroxiredoxin Q from Corynebacterium glutamicum plays an important role in defense against oxidative stress. PLoS One 2018; 13:e0192674. [PMID: 29438446 PMCID: PMC5811025 DOI: 10.1371/journal.pone.0192674] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 01/29/2018] [Indexed: 02/07/2023] Open
Abstract
Peroxiredoxin Q (PrxQ) that belonged to the cysteine-based peroxidases has long been identified in numerous bacteria, but the information on the physiological and biochemical functions of PrxQ remain largely lacking in Corynebacterium glutamicum. To better systematically understand PrxQ, we reported that PrxQ from model and important industrial organism C. glutamicum, encoded by the gene ncgl2403 annotated as a putative PrxQ, played important roles in adverse stress resistance. The lack of C. glutamicum prxQ gene resulted in enhanced cell sensitivity, increased ROS accumulation, and elevated protein carbonylation levels under adverse stress conditions. Accordingly, PrxQ-mediated resistance to adverse stresses mainly relied on the degradation of ROS. The physiological roles of PrxQ in resistance to adverse stresses were corroborated by its induced expression under adverse stresses, regulated directly by the stress-responsive ECF-sigma factor SigH. Through catalytical kinetic activity, heterodimer formation, and bacterial two-hybrid analysis, we proved that C. glutamicum PrxQ catalytically eliminated peroxides by exclusively receiving electrons from thioredoxin (Trx)/thioredoxin reductase (TrxR) system and had a broad range of oxidizing substrates, but a better efficiency for peroxynitrite and cumene hydroperoxide (CHP). Site-directed mutagenesis confirmed that the conserved Cys49 and Cys54 are the peroxide oxidation site and the resolving Cys residue, respectively. It was also discovered that C. glutamicum PrxQ mainly existed in monomer whether under its native state or functional state. Based on these results, a catalytic model of PrxQ is being proposed. Moreover, our result that C. glutamicum PrxQ can prevent the damaging effects of adverse stresses by acting as thioredoxin-dependent monomeric peroxidase could be further applied to improve the survival ability and robustness of the important bacterium during fermentation process.
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Affiliation(s)
- Tao Su
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Meiru Si
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Yunfeng Zhao
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Yan Liu
- School of Geography And Tourism, Qufu Normal University, Rizhao, Shandong, China
| | - Shumin Yao
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Chengchuan Che
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Can Chen
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
- * E-mail:
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8
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Abstract
SIGNIFICANCE Mitochondrial glutathione fulfills crucial roles in a number of processes, including iron-sulfur cluster biosynthesis and peroxide detoxification. Recent Advances: Genetically encoded fluorescent probes for the glutathione redox potential (EGSH) have permitted extensive new insights into the regulation of mitochondrial glutathione redox homeostasis. These probes have revealed that the glutathione pools of the mitochondrial matrix and intermembrane space (IMS) are highly reduced, similar to the cytosolic glutathione pool. The glutathione pool of the IMS is in equilibrium with the cytosolic glutathione pool due to the presence of porins that allow free passage of reduced glutathione (GSH) and oxidized glutathione (GSSG) across the outer mitochondrial membrane. In contrast, limited transport of glutathione across the inner mitochondrial membrane ensures that the matrix glutathione pool is kinetically isolated from the cytosol and IMS. CRITICAL ISSUES In contrast to the situation in the cytosol, there appears to be extensive crosstalk between the mitochondrial glutathione and thioredoxin systems. Further, both systems appear to be intimately involved in the removal of reactive oxygen species, particularly hydrogen peroxide (H2O2), produced in mitochondria. However, a detailed understanding of these interactions remains elusive. FUTURE DIRECTIONS We postulate that the application of genetically encoded sensors for glutathione in combination with novel H2O2 probes and conventional biochemical redox state assays will lead to fundamental new insights into mitochondrial redox regulation and reinvigorate research into the physiological relevance of mitochondrial redox changes. Antioxid. Redox Signal. 27, 1162-1177.
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Affiliation(s)
- Gaetano Calabrese
- 1 Institute of Biochemistry, University of Cologne , Cologne, Germany
| | - Bruce Morgan
- 2 Department of Cellular Biochemistry, University of Kaiserslautern , Kaiserslautern, Germany
| | - Jan Riemer
- 1 Institute of Biochemistry, University of Cologne , Cologne, Germany
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Angelucci F, Miele AE, Ardini M, Boumis G, Saccoccia F, Bellelli A. Typical 2-Cys peroxiredoxins in human parasites: Several physiological roles for a potential chemotherapy target. Mol Biochem Parasitol 2016; 206:2-12. [PMID: 27002228 DOI: 10.1016/j.molbiopara.2016.03.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 03/16/2016] [Accepted: 03/17/2016] [Indexed: 01/07/2023]
Abstract
Peroxiredoxins (Prxs) are ubiquitary proteins able to play multiple physiological roles, that include thiol-dependent peroxidase, chaperone holdase, sensor of H2O2, regulator of H2O2-dependent signal cascades, and modulator of the immune response. Prxs have been found in a great number of human pathogens, both eukaryotes and prokaryotes. Gene knock-out studies demonstrated that Prxs are essential for the survival and virulence of at least some of the pathogens tested, making these proteins potential drug targets. However, the multiplicity of roles played by Prxs constitutes an unexpected obstacle to drug development. Indeed, selective inhibitors of some of the functions of Prxs are known (namely of the peroxidase and holdase functions) and are here reported. However, it is often unclear which function is the most relevant in each pathogen, hence which one is most desirable to inhibit. Indeed there are evidences that the main physiological role of Prxs may not be the same in different parasites. We here review which functions of Prxs have been demonstrated to be relevant in different human parasites, finding that the peroxidase and chaperone activities figure prominently, whereas other known functions of Prxs have rarely, if ever, been observed in parasites, or have largely escaped detection thus far.
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Affiliation(s)
- Francesco Angelucci
- Department of Health, Life and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Adriana Erica Miele
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Matteo Ardini
- Department of Health, Life and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Giovanna Boumis
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Fulvio Saccoccia
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Andrea Bellelli
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy.
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Berndt C, Schwenn JD, Lillig CH. The specificity of thioredoxins and glutaredoxins is determined by electrostatic and geometric complementarity. Chem Sci 2015; 6:7049-7058. [PMID: 29861944 PMCID: PMC5947528 DOI: 10.1039/c5sc01501d] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 09/08/2015] [Indexed: 02/06/2023] Open
Abstract
Thiol-disulfide oxidoreductases from the thioredoxin (Trx) family of proteins have a broad range of well documented functions and possess distinct substrate specificities. The mechanisms and characteristics that control these specificities are key to the understanding of both the reduction of catalytic disulfides as well as allosteric disulfides (thiol switches). Here, we have used the catalytic disulfide of E. coli 3'-phosphoadenosine 5'-phosphosulfate (PAPS) reductase (PR) that forms between the single active site thiols of two monomers during the reaction cycle as a model system to investigate the mechanisms of Trx and Grx protein specificity. Enzyme kinetics, ΔE'0 determination, and structural analysis of various Trx and Grx family members suggested that the redox potential does not determine specificity nor efficiency of the redoxins as reductant for PR. Instead, the efficiency of PR with various redoxins correlated strongly to the extent of a negative electric field of the redoxins reaching into the solvent outside the active site, and electrostatic and geometric complementary contact surfaces. These data suggest that, in contrast to common assumption, the composition of the active site motif is less important for substrate specificity than other amino acids in or even outside the immediate contact area.
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Affiliation(s)
- Carsten Berndt
- From the Department of Neurology , Medical Faculty , Heinrich-Heine Universität , Merowingerplatz 1a , 40225 Düsseldorf , Germany
| | - Jens-Dirk Schwenn
- Biochemistry of Plants , Ruhr-Universität Bochum , Universitätsstraße 150 , 44780 Bochum , Germany
| | - Christopher Horst Lillig
- Institute for Medical Biochemistry and Molecular Biology , Universitätsmedizin Greifswald , Ernst-Moritz-Arndt Universität , Ferdinand Sauerbruch Straße , DE-17475 Greifswald , Germany . ; ; Tel: +49 3834 86 5407
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Staudacher V, Djuika CF, Koduka J, Schlossarek S, Kopp J, Büchler M, Lanzer M, Deponte M. Plasmodium falciparum antioxidant protein reveals a novel mechanism for balancing turnover and inactivation of peroxiredoxins. Free Radic Biol Med 2015; 85:228-36. [PMID: 25952724 DOI: 10.1016/j.freeradbiomed.2015.04.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 04/20/2015] [Accepted: 04/24/2015] [Indexed: 12/12/2022]
Abstract
Life under aerobic conditions has shaped peroxiredoxins (Prx) as ubiquitous thiol-dependent hydroperoxidases and redox sensors. Structural features that balance the catalytically active or inactive redox states of Prx, and, therefore, their hydroperoxidase or sensor function, have so far been analyzed predominantly for Prx1-type enzymes. Here we identify and characterize two modulatory residues of the Prx5-type model enzyme PfAOP from the malaria parasite Plasmodium falciparum. Gain- and loss-of-function mutants reveal a correlation between the enzyme parameters and the inactivation susceptibility of PfAOP with the size of residue 109 and the presence or absence of a catalytically relevant but nonessential cysteine residue. Based on our kinetic data and the crystal structure of PfAOP(L109M), we suggest a novel mechanism for balancing the hydroperoxidase activity and inactivation susceptibility of Prx5-type enzymes. Our study provides unexpected insights into Prx structure-function relationships and contributes to our understanding of what makes Prx good enzymes or redox sensors.
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Affiliation(s)
- Verena Staudacher
- Department of Parasitology, Ruprecht-Karls University, D-69120 Heidelberg, Germany
| | - Carine F Djuika
- Department of Parasitology, Ruprecht-Karls University, D-69120 Heidelberg, Germany
| | - Joshua Koduka
- Department of Parasitology, Ruprecht-Karls University, D-69120 Heidelberg, Germany
| | - Sarah Schlossarek
- Department of Parasitology, Ruprecht-Karls University, D-69120 Heidelberg, Germany
| | - Jürgen Kopp
- Biochemistry Center (BZH), Ruprecht-Karls University, D-69120 Heidelberg, Germany; Cellnetworks Excellence Cluster, Ruprecht-Karls University, D-69120 Heidelberg, Germany
| | - Marleen Büchler
- Department of Parasitology, Ruprecht-Karls University, D-69120 Heidelberg, Germany
| | - Michael Lanzer
- Department of Parasitology, Ruprecht-Karls University, D-69120 Heidelberg, Germany
| | - Marcel Deponte
- Department of Parasitology, Ruprecht-Karls University, D-69120 Heidelberg, Germany.
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Banerjee M, Raghavan PS, Ballal A, Rajaram H, Apte SK. Oxidative stress management in the filamentous, heterocystous, diazotrophic cyanobacterium, Anabaena PCC7120. PHOTOSYNTHESIS RESEARCH 2013; 118:59-70. [PMID: 24122336 DOI: 10.1007/s11120-013-9929-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 09/23/2013] [Indexed: 05/26/2023]
Abstract
Reactive oxygen species (ROS) are inevitably generated as by-products of respiratory/photosynthetic electron transport in oxygenic photoautotrophs. Unless effectively scavenged, these ROS can damage all cellular components. The filamentous, heterocystous, nitrogen-fixing strains of the cyanobacterium, Anabaena, serve as naturally abundant contributors of nitrogen biofertilizers in tropical rice paddy fields. Anabaena strains are known to tolerate several abiotic stresses, such as heat, UV, gamma radiation, desiccation, etc., that are known to generate ROS. ROS are detoxified by specific antioxidant enzymes like superoxide dismutases (SOD), catalases and peroxiredoxins. The genome of Anabaena PCC7120 encodes two SODs, two catalases and seven peroxiredoxins, indicating the presence of an elaborate antioxidant enzymatic machinery to defend its cellular components from ROS. This article summarizes recent findings and depicts important perspectives in oxidative stress management in Anabaena PCC7120.
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Affiliation(s)
- Manisha Banerjee
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400 085, India
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Djuika CF, Fiedler S, Schnölzer M, Sanchez C, Lanzer M, Deponte M. Plasmodium falciparum antioxidant protein as a model enzyme for a special class of glutaredoxin/glutathione-dependent peroxiredoxins. Biochim Biophys Acta Gen Subj 2013; 1830:4073-90. [DOI: 10.1016/j.bbagen.2013.04.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 04/15/2013] [Accepted: 04/16/2013] [Indexed: 01/06/2023]
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15
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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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16
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Gretes MC, Poole LB, Karplus PA. Peroxiredoxins in parasites. Antioxid Redox Signal 2012; 17:608-33. [PMID: 22098136 PMCID: PMC3373223 DOI: 10.1089/ars.2011.4404] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 11/18/2011] [Indexed: 12/11/2022]
Abstract
SIGNIFICANCE Parasite survival and virulence relies on effective defenses against reactive oxygen and nitrogen species produced by the host immune system. Peroxiredoxins (Prxs) are ubiquitous enzymes now thought to be central to such defenses and, as such, have potential value as drug targets and vaccine antigens. RECENT ADVANCES Plasmodial and kinetoplastid Prx systems are the most extensively studied, yet remain inadequately understood. For many other parasites our knowledge is even less well developed. Through parasite genome sequencing efforts, however, the key players are being discovered and characterized. Here we describe what is known about the biochemistry, regulation, and cell biology of Prxs in parasitic protozoa, helminths, and fungi. At least one Prx is found in each parasite with a sequenced genome, and a notable theme is the common patterns of expression, localization, and functionality among sequence-similar Prxs in related species. CRITICAL ISSUES The nomenclature of Prxs from parasites is in a state of disarray, causing confusion and making comparative inferences difficult. Here we introduce a systematic Prx naming convention that is consistent between organisms and informative about structural and evolutionary relationships. FUTURE DIRECTIONS The new nomenclature should stimulate the crossfertilization of ideas among parasitologists and with the broader redox research community. The diverse parasite developmental stages and host environments present complex systems in which to explore the variety of roles played by Prxs, with a view toward parlaying what is learned into novel therapies and vaccines that are urgently needed.
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Affiliation(s)
- Michael C. Gretes
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, Oregon
| | - Leslie B. Poole
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - P. Andrew Karplus
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, Oregon
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17
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Harrison A, Bakaletz LO, Munson RS. Haemophilus influenzae and oxidative stress. Front Cell Infect Microbiol 2012; 2:40. [PMID: 22919631 PMCID: PMC3417577 DOI: 10.3389/fcimb.2012.00040] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 03/13/2012] [Indexed: 12/16/2022] Open
Abstract
Haemophilus influenzae is a commensal of the human upper respiratory tract. H. influenzae can, however, move out of its commensal niche and cause multiple respiratory tract diseases. Such diseases include otitis media in young children, as well as exacerbations of chronic obstructive pulmonary disease (COPD), sinusitis, conjunctivitis, and bronchitis. During the course of colonization and infection, H. influenzae must withstand oxidative stress generated by multiple reactive oxygen species produced endogenously, by other co-pathogens and by host cells. H. influenzae has, therefore, evolved multiple mechanisms that protect the cell against oxygen-generated stresses. In this review, we will describe these systems relative to the well-described systems in Escherichia coli. Moreover, we will compare how H. influenzae combats the effect of oxidative stress as a necessary phenotype for its roles as both a successful commensal and pathogen.
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Affiliation(s)
- Alistair Harrison
- The Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus OH, USA. alistair.harrison@ nationwidechildrens.org
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18
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A novel glutaredoxin domain-containing peroxiredoxin ‘All1541’ protects the N2-fixing cyanobacterium Anabaena PCC 7120 from oxidative stress. Biochem J 2012; 442:671-80. [DOI: 10.1042/bj20111877] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Prxs (peroxiredoxins) are ubiquitous thiol-based peroxidases that detoxify toxic peroxides. The Anabaena PCC 7120 genome harbours seven genes/ORFs (open reading frames) which have homology with Prxs. One of these (all1541) was identified to encode a novel Grx (glutaredoxin) domain-containing Prx by bioinformatic analysis. A recombinant N-terminal histidine-tagged All1541 protein was overexpressed in Escherichia coli and purified. Analysis with the protein alkylating agent AMS (4-acetamido-4′-maleimidyl-stilbene-2,2′-disulfonate) showed All1541 to form an intra-molecular disulfide bond. The All1541 protein used glutathione (GSH) more efficiently than Trx (thioredoxin) to detoxify H2O2. Deletion of the Grx domain from All1541 resulted in loss of GSH-dependent peroxidase activity. Employing site-directed mutagenesis, the cysteine residues at positions 50 and 75 were identified as peroxidatic and resolving cysteine residues respectively, whereas both the cysteine residues within the Grx domain (positions 181 and 184) were shown to be essential for GSH-dependent peroxidase activity. On the basis of these data, a reaction mechanism has been proposed for All1541. In vitro All1541 protein protected plasmid DNA from oxidative damage. In Anabaena PCC 7120, all1541 was transcriptionally activated under oxidative stress. Recombinant Anabaena PCC 7120 strain overexpressing All1541 protein showed superior oxidative stress tolerance to H2O2 as compared with the wild-type strain. The results suggest that the glutathione-dependent peroxidase All1541 plays an important role in protecting Anabaena from oxidative stress.
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Reeves SA, Parsonage D, Nelson KJ, Poole LB. Kinetic and thermodynamic features reveal that Escherichia coli BCP is an unusually versatile peroxiredoxin. Biochemistry 2011; 50:8970-81. [PMID: 21910476 DOI: 10.1021/bi200935d] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In Escherichia coli, bacterioferritin comigratory protein (BCP) is a peroxiredoxin (Prx) that catalyzes the reduction of H(2)O(2) and organic hydroperoxides. This protein, along with plant PrxQ, is a founding member of one of the least studied subfamilies of Prxs. Recent structural data have suggested that proteins in the BCP/PrxQ group can exist as monomers or dimers; we report here that, by analytical ultracentrifugation, both oxidized and reduced E. coli BCP behave as monomers in solution at concentrations as high as 200 μM. Unexpectedly, thioredoxin (Trx1)-dependent peroxidase assays conducted by stopped-flow spectroscopy demonstrated that V(max,app) increases with increasing Trx1 concentrations, indicating a nonsaturable interaction (K(m) > 100 μM). At a physiologically reasonable Trx1 concentration of 10 μM, the apparent K(m) value for H(2)O(2) is ~80 μM, and overall, the V(max)/K(m) for H(2)O(2), which remains constant at the various Trx1 concentrations (consistent with a ping-pong mechanism), is ~1.3 × 10(4) M(-1) s(-1). Our kinetic analyses demonstrated that BCP can utilize a variety of reducing substrates, including Trx1, Trx2, Grx1, and Grx3. BCP exhibited a high redox potential of -145.9 ± 3.2 mV, the highest to date observed for a Prx. Moreover, BCP exhibited a broad peroxide specificity, with comparable rates for H(2)O(2) and cumene hydroperoxide. We determined a pK(a) of ~5.8 for the peroxidatic cysteine (Cys45) using both spectroscopic and activity titration data. These findings support an important role for BCP in interacting with multiple substrates and remaining active under highly oxidizing cellular conditions, potentially serving as a defense enzyme of last resort.
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Affiliation(s)
- Stacy A Reeves
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA
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20
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Hall A, Nelson K, Poole LB, Karplus PA. Structure-based insights into the catalytic power and conformational dexterity of peroxiredoxins. Antioxid Redox Signal 2011; 15:795-815. [PMID: 20969484 PMCID: PMC3125576 DOI: 10.1089/ars.2010.3624] [Citation(s) in RCA: 251] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 10/01/2010] [Accepted: 10/24/2010] [Indexed: 12/25/2022]
Abstract
Peroxiredoxins (Prxs), some of nature's dominant peroxidases, use a conserved Cys residue to reduce peroxides. They are highly expressed in organisms from all kingdoms, and in eukaryotes they participate in hydrogen peroxide signaling. Seventy-two Prx structures have been determined that cover much of the diversity of the family. We review here the current knowledge and show that Prxs can be effectively classified by a structural/evolutionary organization into six subfamilies followed by specification of a 1-Cys or 2-Cys mechanism, and for 2-Cys Prxs, the structural location of the resolving Cys. We visualize the varied catalytic structural transitions and highlight how they differ depending on the location of the resolving Cys. We also review new insights into the question of how Prxs are such effective catalysts: the enzyme activates not only the conserved Cys thiolate but also the peroxide substrate. Moreover, the hydrogen-bonding network created by the four residues conserved in all Prx active sites stabilizes the transition state of the peroxidatic S(N)2 displacement reaction. Strict conservation of the peroxidatic active site along with the variation in structural transitions provides a fascinating picture of how the diverse Prxs function to break down peroxide substrates rapidly.
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Affiliation(s)
- Andrea Hall
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, Oregon
| | - Kimberly Nelson
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Leslie B. Poole
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - P. Andrew Karplus
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, Oregon
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21
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Meng EC, Babbitt PC. Topological variation in the evolution of new reactions in functionally diverse enzyme superfamilies. Curr Opin Struct Biol 2011; 21:391-7. [PMID: 21458983 PMCID: PMC3551608 DOI: 10.1016/j.sbi.2011.03.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 03/05/2011] [Accepted: 03/09/2011] [Indexed: 10/18/2022]
Abstract
In functionally diverse enzyme superfamilies (SFs), conserved structural and active site features reflect catalytic capabilities 'hard-wired' in each SF architecture. Overlaid on this foundation, evolutionary changes in active site machinery, structural topology and other aspects of structural organization and interactions support the emergence of new reactions, mechanisms, and substrate specificity. This review connects topological with functional variation in each of the haloalkanoic acid dehalogenase (HAD) and vicinal oxygen chelate fold (VOC) SFs and a set of redox-active thioredoxin (Trx)-fold SFs to illustrate a few of the varied themes nature has used to evolve new functions from a limited set of structural scaffolds.
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Affiliation(s)
- Elaine C. Meng
- Department of Pharmaceutical Chemistry, University of California, M/S 2240, 600 16th Street, San Francisco, CA 94158-2517, USA,
| | - Patricia C. Babbitt
- Department of Pharmaceutical Chemistry, University of California, M/S 2240, 600 16th Street, San Francisco, CA 94158-2517, USA,
- Department of Bioengineering and Therapeutic Sciences, University of California, M/S 2250, 1700 4 Street, San Francisco, CA 94158-2330, USA
- California Institute for Quantitative Biosciences, University of California, San Francisco
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22
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Nelson KJ, Knutson ST, Soito L, Klomsiri C, Poole LB, Fetrow JS. Analysis of the peroxiredoxin family: using active-site structure and sequence information for global classification and residue analysis. Proteins 2011; 79:947-64. [PMID: 21287625 PMCID: PMC3065352 DOI: 10.1002/prot.22936] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Revised: 10/13/2010] [Accepted: 10/25/2010] [Indexed: 12/25/2022]
Abstract
Peroxiredoxins (Prxs) are a widespread and highly expressed family of cysteine-based peroxidases that react very rapidly with H₂O₂, organic peroxides, and peroxynitrite. Correct subfamily classification has been problematic because Prx subfamilies are frequently not correlated with phylogenetic distribution and diverge in their preferred reductant, oligomerization state, and tendency toward overoxidation. We have developed a method that uses the Deacon Active Site Profiler (DASP) tool to extract functional-site profiles from structurally characterized proteins to computationally define subfamilies and to identify new Prx subfamily members from GenBank(nr). For the 58 literature-defined Prx test proteins, 57 were correctly assigned, and none were assigned to the incorrect subfamily. The >3500 putative Prx sequences identified were then used to analyze residue conservation in the active site of each Prx subfamily. Our results indicate that the existence and location of the resolving cysteine vary in some subfamilies (e.g., Prx5) to a greater degree than previously appreciated and that interactions at the A interface (common to Prx5, Tpx, and higher order AhpC/Prx1 structures) are important for stabilization of the correct active-site geometry. Interestingly, this method also allows us to further divide the AhpC/Prx1 into four groups that are correlated with functional characteristics. The DASP method provides more accurate subfamily classification than PSI-BLAST for members of the Prx family and can now readily be applied to other large protein families.
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Affiliation(s)
- Kimberly J. Nelson
- Department of Biochemistry, Wake Forest University Health Sciences, Medical Center Blvd., Winston-Salem NC 27157
| | - Stacy T. Knutson
- Departments of Physics and Computer Science, Wake Forest University, Winston-Salem, NC 27109
| | - Laura Soito
- Department of Biochemistry, Wake Forest University Health Sciences, Medical Center Blvd., Winston-Salem NC 27157
| | - Chananat Klomsiri
- Department of Biochemistry, Wake Forest University Health Sciences, Medical Center Blvd., Winston-Salem NC 27157
| | - Leslie B. Poole
- Department of Biochemistry, Wake Forest University Health Sciences, Medical Center Blvd., Winston-Salem NC 27157
| | - Jacquelyn S. Fetrow
- Departments of Physics and Computer Science, Wake Forest University, Winston-Salem, NC 27109
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23
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Pedone E, Limauro D, D’Ambrosio K, De Simone G, Bartolucci S. Multiple catalytically active thioredoxin folds: a winning strategy for many functions. Cell Mol Life Sci 2010; 67:3797-814. [PMID: 20625793 PMCID: PMC11115506 DOI: 10.1007/s00018-010-0449-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 06/23/2010] [Accepted: 06/28/2010] [Indexed: 10/19/2022]
Abstract
The Thioredoxin (Trx) fold is a versatile protein scaffold consisting of a four-stranded β-sheet surrounded by three α-helices. Various insertions are possible on this structural theme originating different proteins, which show a variety of functions and specificities. During evolution, the assembly of different Trx fold domains has been used many times to build new multi-domain proteins able to perform a large number of catalytic functions. To clarify the interaction mode of the different Trx domains within a multi-domain structure and how their combination can affect catalytic performances, in this review, we report on a structural and functional analysis of the most representative proteins containing more than one catalytically active Trx domain: the eukaryotic protein disulfide isomerases (PDIs), the thermophilic protein disulfide oxidoreductases (PDOs) and the hybrid peroxiredoxins (Prxs).
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Affiliation(s)
- Emilia Pedone
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Naples, Italy
| | - Danila Limauro
- Dipartimento di Biologia Strutturale e Funzionale, Università degli Studi di Napoli “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, 80126 Naples, Italy
| | - Katia D’Ambrosio
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Naples, Italy
| | - Giuseppina De Simone
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Naples, Italy
| | - Simonetta Bartolucci
- Dipartimento di Biologia Strutturale e Funzionale, Università degli Studi di Napoli “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, 80126 Naples, Italy
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24
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D'Ambrosio K, Limauro D, Pedone E, Galdi I, Pedone C, Bartolucci S, De Simone G. Insights into the catalytic mechanism of the Bcp family: functional and structural analysis of Bcp1 from Sulfolobus solfataricus. Proteins 2009; 76:995-1006. [PMID: 19338062 DOI: 10.1002/prot.22408] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Bcps constitute a group of antioxidant enzymes, belonging to the Prx family, that are widely distributed in bacteria, plants, and fungi. These proteins can contain two conserved cysteines within the CXXXXC motif. Recent studies demonstrated that though the role of the first cysteine is well defined, being the catalytic peroxidatic cysteine in all the members of this protein family, data on the function of the second cysteine are controversial and require further investigation. In this article, we report on the functional and structural characterization of Bcp1, an archaeal Bcp isolated from Sulfolobus solfataricus, which presents two conserved cysteine residues at positions 45 and 50. Functional studies revealed that this enzyme performs the catalytic reaction using an atypical 2-Cys mechanism, where Cys45 is the peroxidatic and Cys50 is the resolving cysteine. The X-ray structure of the double mutant C45S/C50S, representative of the fully reduced enzyme state, was determined at a resolution of 2.15 A, showing a Trx fold similar to that of other Prxs. Superposition with a structural homologue in the oxidized state provided, for the first time, a detailed description of the structural rearrangement necessary for a member of the Bcp family to perform the catalytic reaction. From this structural analysis, it emerges that a significant conformational change from a fully folded, to a locally unfolded form is required to form the intramolecular disulfide bond upon oxidation, according to the proposed reaction mechanism. Two residues, namely Arg53 and Asp54, which could play a role in this rearrangement, were also identified.
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Affiliation(s)
- Katia D'Ambrosio
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Naples, Italy
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25
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An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations. PLoS Comput Biol 2009; 5:e1000541. [PMID: 19851441 PMCID: PMC2757866 DOI: 10.1371/journal.pcbi.1000541] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Accepted: 09/21/2009] [Indexed: 01/08/2023] Open
Abstract
The group of proteins that contain a thioredoxin (Trx) fold is huge and diverse. Assessment of the variation in catalytic machinery of Trx fold proteins is essential in providing a foundation for understanding their functional diversity and predicting the function of the many uncharacterized members of the class. The proteins of the Trx fold class retain common features-including variations on a dithiol CxxC active site motif-that lead to delivery of function. We use protein similarity networks to guide an analysis of how structural and sequence motifs track with catalytic function and taxonomic categories for 4,082 representative sequences spanning the known superfamilies of the Trx fold. Domain structure in the fold class is varied and modular, with 2.8% of sequences containing more than one Trx fold domain. Most member proteins are bacterial. The fold class exhibits many modifications to the CxxC active site motif-only 56.8% of proteins have both cysteines, and no functional groupings have absolute conservation of the expected catalytic motif. Only a small fraction of Trx fold sequences have been functionally characterized. This work provides a global view of the complex distribution of domains and catalytic machinery throughout the fold class, showing that each superfamily contains remnants of the CxxC active site. The unifying context provided by this work can guide the comparison of members of different Trx fold superfamilies to gain insight about their structure-function relationships, illustrated here with the thioredoxins and peroxiredoxins.
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26
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Barranco-Medina S, Lázaro JJ, Dietz KJ. The oligomeric conformation of peroxiredoxins links redox state to function. FEBS Lett 2009; 583:1809-16. [PMID: 19464293 DOI: 10.1016/j.febslet.2009.05.029] [Citation(s) in RCA: 173] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2009] [Revised: 05/08/2009] [Accepted: 05/12/2009] [Indexed: 12/25/2022]
Abstract
Protein-protein associations, i.e. formation of permanent or transient protein complexes, are essential for protein functionality and regulation within the cellular context. Peroxiredoxins (Prx) undergo major redox-dependent conformational changes and the dynamics are linked to functional switches. While a large number of investigations have addressed the principles and functions of Prx oligomerization, understanding of the diverse in vivo roles of this conserved redox-dependent feature of Prx is slowly emerging. The review summarizes studies on Prx oligomerization, its tight connection to the redox state, and the knowledge and hypotheses on its physiological function in the cell as peroxidase, chaperone, binding partner, enzyme activator and/or redox sensor.
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27
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Rouhier N, Koh CS, Gelhaye E, Corbier C, Favier F, Didierjean C, Jacquot JP. Redox based anti-oxidant systems in plants: Biochemical and structural analyses. Biochim Biophys Acta Gen Subj 2008; 1780:1249-60. [DOI: 10.1016/j.bbagen.2007.12.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Revised: 12/11/2007] [Accepted: 12/17/2007] [Indexed: 12/18/2022]
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28
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Gama F, Bréhélin C, Gelhaye E, Meyer Y, Jacquot JP, Rey P, Rouhier N. Functional analysis and expression characteristics of chloroplastic Prx IIE. PHYSIOLOGIA PLANTARUM 2008; 133:599-610. [PMID: 18422870 DOI: 10.1111/j.1399-3054.2008.01097.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Peroxiredoxins (Prxs) are ubiquitous thiol-dependent peroxidases capable of eliminating a variety of peroxides through reactive catalytic cysteines, which are regenerated by reducing systems. Based on amino acid sequences and their mode of catalysis, five groups of thiol peroxidases have been distinguished in plants, and type II Prx is one of them with representatives in many sub-cellular compartments. The mature form of poplar chloroplastic Prx IIE was expressed as a recombinant protein in Escherichia coli. The protein is able to reduce H2O2 and tert-butyl hydroperoxide and is regenerated by both glutaredoxin (Grx) and thioredoxin (Trx) systems. Nevertheless, compared with Trxs, Grxs, and more especially chloroplastic Grx S12, are far more efficient reductants towards Prx IIE. The expression of Prx IIE at both the mRNA and protein levels as a function of organ type and abiotic stress conditions was investigated. Western blot analysis revealed that Prx IIE gene is constitutively expressed in Arabidopsis thaliana, mostly in young and mature leaves and in flowers. Under photo-oxidative treatment and water deficit, almost no change was observed in the abundance of Prx IIE in A. thaliana, while the level of Prx Q (one of the two other chloroplastic Prxs with 2-Cys Prx) increased in response to both stresses, indicating that plastidic members of the Prx family exhibit specific patterns of expression under stress.
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Affiliation(s)
- Filipe Gama
- Unité Mixte de Recherches 1136 INRA UHP (Interactions Arbres Microorganismes), IFR 110 Génomique Ecophysiologie et Ecologie Fonctionnelles, Université Henri Poincaré BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France
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29
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Smeets A, Marchand C, Linard D, Knoops B, Declercq JP. The crystal structures of oxidized forms of human peroxiredoxin 5 with an intramolecular disulfide bond confirm the proposed enzymatic mechanism for atypical 2-Cys peroxiredoxins. Arch Biochem Biophys 2008; 477:98-104. [PMID: 18489898 DOI: 10.1016/j.abb.2008.04.036] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Revised: 04/21/2008] [Accepted: 04/22/2008] [Indexed: 10/22/2022]
Abstract
Peroxiredoxin 5 (PRDX5) belongs to the PRDX superfamily of thiol-dependent peroxidases able to reduce hydrogen peroxide, alkyl hydroperoxides and peroxynitrite. PRDX5 is classified in the atypical 2-Cys subfamily of PRDXs. In this subfamily, the oxidized form of the enzyme is characterized by the presence of an intramolecular disulfide bridge between the peroxidatic and the resolving cysteine residues. We report here three crystal forms in which this intramolecular disulfide bond is indeed observed. The structures are characterized by the expected local unfolding of the peroxidatic loop, but also by the unfolding of the resolving loop. A new type of interface between PRDX molecules is described. The three crystal forms were not oxidized in the same way and the influence of the oxidizing conditions is discussed.
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Affiliation(s)
- Aude Smeets
- Unit of Structural Chemistry (CSTR), Université catholique de Louvain, 1, place Louis Pasteur, B-1348 Louvain-la-Neuve, Belgium
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30
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Smeets A, Loumaye E, Clippe A, Rees JF, Knoops B, Declercq JP. The crystal structure of the C45S mutant of annelid Arenicola marina peroxiredoxin 6 supports its assignment to the mechanistically typical 2-Cys subfamily without any formation of toroid-shaped decamers. Protein Sci 2008; 17:700-10. [PMID: 18359859 DOI: 10.1110/ps.073399308] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The peroxiredoxins (PRDXs) define a superfamily of thiol-dependent peroxidases able to reduce hydrogen peroxide, alkyl hydroperoxides, and peroxynitrite. Besides their cytoprotective antioxidant function, PRDXs have been implicated in redox signaling and chaperone activity, the latter depending on the formation of decameric high-molecular-weight structures. PRDXs have been mechanistically divided into three major subfamilies, namely typical 2-Cys, atypical 2-Cys, and 1-Cys PRDXs, based on the number and position of cysteines involved in the catalysis. We report the structure of the C45S mutant of annelid worm Arenicola marina PRDX6 in three different crystal forms determined at 1.6, 2.0, and 2.4 A resolution. Although A. marina PRDX6 was cloned during the search of annelid homologs of mammalian 1-Cys PRDX6s, the crystal structures support its assignment to the mechanistically typical 2-Cys PRDX subfamily. The protein is composed of two distinct domains: a C-terminal domain and an N-terminal domain exhibiting a thioredoxin fold. The subunits are associated in dimers compatible with the formation of intersubunit disulfide bonds between the peroxidatic and the resolving cysteine residues in the wild-type enzyme. The packing of two crystal forms is very similar, with pairs of dimers associated as tetramers. The toroid-shaped decamers formed by dimer association and observed in most typical 2-Cys PRDXs is not present. Thus, A. marina PRDX6 presents structural features of typical 2-Cys PRDXs without any formation of toroid-shaped decamers, suggesting that it should function more like a cytoprotective antioxidant enzyme or a modulator of peroxide-dependent cell signaling rather than a molecular chaperone.
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Affiliation(s)
- Aude Smeets
- Unit of Structural Chemistry (CSTR), Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
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31
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Abstract
Peroxiredoxins (Prxs) are ubiquitous proteins that use an active site Cys residue to reduce hydroperoxides. Structural studies since the first Prx structure was determined in 1998 have produced 35 crystal structures of wild type and mutant Prxs with at least one representative structure from each of the five major evolutionary subfamilies of Prxs. These structures have yielded a great deal of knowledge about Prx structure and structure-function relations, revealing fascinating variations in quaternary structure and details of the fully-folded and locally-unfolded conformations that are involved in the catalytic cycle of all Prxs.
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Affiliation(s)
- P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
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32
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Abstract
Peroxiredoxins carry out the efficient reduction of a typically broad range of peroxide substrates through an absolutely conserved, activated cysteine residue within a highly conserved active site pocket structure. Though details of reductive recycling after cysteine sulfenic acid formation at the active site vary among members of different Prx classes, local unfolding around the active site cysteine is likely generally required in these proteins for disulfide bond formation with a second resolving cysteine and/or for access of the reductant to the oxidized active site. The conformational change associated with the catalytic cycle and the redox-dependent decamer formation occurring in at least some typical 2-Cys Prxs have interesting implications in the interplay between active site loop dynamics, oligomerization state, catalytic efficiency and propensity toward inactivation during turnover in these important antioxidant enzymes.
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Affiliation(s)
- Leslie B Poole
- Department of Biochemistry, Center for Structural Biology, BGTC, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
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33
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Abstract
Peroxiredoxins compose a superfamily of peroxidases ubiquitously found throughout evolution in prokaryotes, archaea and eukaryotes. These enzymes contain a conserved catalytic peroxidatic cysteine (Cp) in the N-terminal region of the protein. The residues surrounding Cp and the catalytic site appear also to be well conserved. Peroxiredoxins can be classified either into three subfamilies according to their catalytic mechanism or into five subfamilies according to sequence homology. Notably, the number of peroxiredoxin genes increased during evolution. In eukaryotes, the higher number of genes coding for peroxiredoxin family members is due to the existence of different isoforms targeted to different subcellular compartments but is probably due also to the acquisition of new functions. Indeed, it has been postulated that the antioxidant protective role of peroxiredoxins, which is particularly critical in prokaryotes, in yeasts and in parasitic eukaryotes, may have evolved to a modulatory role in hydrogen peroxide signaling in plants and animals.
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Affiliation(s)
- Bernard Knoops
- Laboratory of Cell Biology, Institut des Sciences de la Vie, Université catholique de Louvain, Louvain-la-Neuve, Belgium
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34
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35
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Noguera-Mazon V, Krimm I, Walker O, Lancelin JM. Protein-protein interactions within peroxiredoxin systems. PHOTOSYNTHESIS RESEARCH 2006; 89:277-90. [PMID: 17089212 DOI: 10.1007/s11120-006-9106-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Accepted: 09/11/2006] [Indexed: 05/12/2023]
Abstract
Peroxiredoxin systems in plants were demonstrated involved in crucial roles related to reactive oxygenated species (ROS) metabolism and the linked cell signalling to ROS. Peroxiredoxins function as peroxidasic systems that combine at least a reactivating reductant agent like thioredoxins, and sometimes glutaredoxins and glutathion. In the past three years a number of peroxiredoxin structures were solved by crystallography in different experimental crystallisation conditions. The structures have revealed a significant propensity of peroxiredoxins for oligomerism that was confirmed by biophysical studies in solution using NMR and other methods as analytical ultra-centrifugation. These studies showed that quaternary structures of peroxiredoxins involve specific protein-protein interaction interfaces that rely upon the peroxiredoxin types and/or their redox conditions. The protein-protein interactions with the reactivating redoxins essentially lead to transient unstable complexes. We review herein the different protein-protein interactions characterized or deduced from those reports.
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Affiliation(s)
- Valérie Noguera-Mazon
- Sciences Analytiques, ANABIO - RMN et Spectrométrie de Masse Biomoléculaires, CNRS UMR 5180, Université Claude Bernard - Lyon 1, Domaine Scientifique de La Doua, Ecole Supérieure de Chimie Physique Electronique de Lyon, F-69622, Villeurbanne, France
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36
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Håkansson KO, Østergaard H, Winther JR. Crystallization of mutant forms of glutaredoxin Grx1p from yeast. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:920-2. [PMID: 16946480 PMCID: PMC2242864 DOI: 10.1107/s1744309106031216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2006] [Accepted: 08/08/2006] [Indexed: 11/10/2022]
Abstract
Glutaredoxin Grx1p from yeast was crystallized both as an independent protein and in a protein fusion with His-tagged yellow fluorescent protein (rxYFP). A glutathionylated C30S mutant of the 12 kDa Grx1p was crystallized in two different forms in PEG 4000 at low pH. These orthorhombic and monoclinic forms diffract to 2.0 A (synchrotron radiation) and 2.7 A (rotating-anode generator), respectively. In contrast, rxYFP-Grx1p formed crystals at high pH in MgSO(4) which diffract synchrotron radiation to 2.7 A.
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Affiliation(s)
- Kjell O Håkansson
- Institute of Molecular Biology, August Krogh Building, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen O, Denmark.
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37
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Noguera-Mazon V, Lemoine J, Walker O, Rouhier N, Salvador A, Jacquot JP, Lancelin JM, Krimm I. Glutathionylation induces the dissociation of 1-Cys D-peroxiredoxin non-covalent homodimer. J Biol Chem 2006; 281:31736-42. [PMID: 16916801 DOI: 10.1074/jbc.m602188200] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
1-Cys peroxiredoxins (1-Cys Prxs) are antioxidant enzymes that catalyze the reduction of hydroperoxides into alcohols using a strictly conserved cysteine. 1-Cys B-Prxs, homologous to human PrxVI, were recently shown to be reactivated by glutathione S-transferase (GST) pi via the formation of a GST-Prx heterodimer and Prx glutathionylation. In contrast, 1-Cys D-Prxs, homologous to human PrxV, are reactivated by the glutaredoxin-glutathione system through an unknown mechanism. To investigate the mechanistic events that mediate the 1-Cys D-Prx regeneration, interaction of the Prx with glutathione was studied by mass spectrometry and NMR. This work reveals that the Prx can be glutathionylated on its active site cysteine. Evidences are reported that the glutathionylation of 1-Cys D-Prx induces the dissociation of the Prx non-covalent homodimer, which can be recovered by reduction with dithiothreitol. This work demonstrates for the first time the existence of a redox-dependent dimer-monomer switch in the Prx family, similar to the decamer-dimer switch for the 2-Cys Prxs.
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Affiliation(s)
- Valérie Noguera-Mazon
- CNRS, Unité Mixte de Recherche, 5180 Sciences Analytiques,Ecole Supérieure Chimie PhysiqueElectronique de Lyon, Domaine Scientifique de la Doua, Université Claude Bernard, Lyon1, 69622 Villeurbanne, France
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38
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Rouhier N, Gama F, Wingsle G, Gelhaye E, Gans P, Jacquot JP. Engineering functional artificial hybrid proteins between poplar peroxiredoxin II and glutaredoxin or thioredoxin. Biochem Biophys Res Commun 2006; 341:1300-8. [PMID: 16476584 DOI: 10.1016/j.bbrc.2006.01.099] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2006] [Accepted: 01/21/2006] [Indexed: 11/21/2022]
Abstract
The existence of natural peroxiredoxin-glutaredoxin hybrid enzymes in several bacteria is in line with previous findings indicating that poplar peroxiredoxin II can use glutaredoxin as an electron donor. This peroxiredoxin remains however unique since it also uses thioredoxin with a quite good efficiency. Based on the existing fusions, we have created artificial enzymes containing a poplar peroxiredoxin module linked to glutaredoxin or thioredoxin modules. The recombinant fusion enzymes folded properly into non-covalently bound homodimers or homotetramers. Two of the three protein constructs exhibit peroxidase activity, a reaction where the two modules need to function together, but they also display enzymatic activities specific of each module. In addition, mass spectrometry analyses indicate that the Prx module can be both glutathiolated or overoxidized in vitro. This is discussed in the light of the Prx reactivity.
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Affiliation(s)
- Nicholas Rouhier
- UMR 1136 Interactions Arbres Mircoorganismes INRA-UHP, IFR 110 GEEF, Faculté des Sciences, 54506 Vandouevre-les-Nancy Cedex, France.
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39
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Smeets A, Evrard C, Landtmeters M, Marchand C, Knoops B, Declercq JP. Crystal structures of oxidized and reduced forms of human mitochondrial thioredoxin 2. Protein Sci 2005; 14:2610-21. [PMID: 16195549 PMCID: PMC2253300 DOI: 10.1110/ps.051632905] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Mammalian thioredoxin 2 is a mitochondrial isoform of highly evolutionary conserved thioredoxins. Thioredoxins are small ubiquitous protein-disulfide oxidoreductases implicated in a large variety of biological functions. In mammals, thioredoxin 2 is encoded by a nuclear gene and is targeted to mitochondria by a N-terminal mitochondrial presequence. Recently, mitochondrial thioredoxin 2 was shown to interact with components of the mitochondrial respiratory chain and to play a role in the control of mitochondrial membrane potential, regulating mitochondrial apoptosis signaling pathway. Here we report the first crystal structures of a mammalian mitochondrial thioredoxin 2. Crystal forms of reduced and oxidized human thioredoxin 2 are described at 2.0 and 1.8 A resolution. Though the folding is rather similar to that of human cytosolic/nuclear thioredoxin 1, important differences are observed during the transition between the oxidized and the reduced states of human thioredoxin 2, compared with human thioredoxin 1. In spite of the absence of the Cys residue implicated in dimer formation in human thioredoxin 1, dimerization still occurs in the crystal structure of human thioredoxin 2, mainly mediated by hydrophobic contacts, and the dimers are associated to form two-dimensional polymers. Interestingly, the structure of human thioredoxin 2 reveals possible interaction domains with human peroxiredoxin 5, a substrate protein of human thioredoxin 2 in mitochondria.
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Affiliation(s)
- Aude Smeets
- Unit of Structural Chemistry (CSTR), Université catholique de Louvain, 1 place Louis Pasteur, B-1348 Louvain-la-Neuve, Belgium
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40
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Noguera V, Walker O, Rouhier N, Jacquot JP, Krimm I, Lancelin JM. NMR Reveals a Novel Glutaredoxin–Glutaredoxin Interaction Interface. J Mol Biol 2005; 353:629-41. [PMID: 16181638 DOI: 10.1016/j.jmb.2005.08.035] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2005] [Revised: 08/01/2005] [Accepted: 08/17/2005] [Indexed: 11/25/2022]
Abstract
Glutaredoxins (Grx) represent a large family of glutathione (GSH)-dependent oxidoreductases that catalyse the reduction of disulfides or glutathione mixed disulfide. Grx domains from pathogenic bacteria and plant Grxs have been recently reported to target specific peroxiredoxins (Prxs). The specificity that triggers the interaction between Grx and Prx is poorly understood and is only based on the structure of Haemophilus influenzae Prx-Grx hybrid (hyPrx5). We report here an NMR study of the Populus tremula Grx C4 that targets a P.tremula D-type II Prx. We show that Grx C4 specifically self-associates in a monomer-dimer equilibrium with an apparent K(d) of ca 2.6 mM. Grx C4 homodimer was docked under experimental restraints. The results reveal a novel Grx-Grx interface that is unrelated to the hyPrx5 Grx-Grx dimer interface. Chemical-shift perturbations and 15N spin-relaxation measurements show that the auto-association surface comprises both the active site and the GSH binding site. Reduced GSH is demonstrated to bind reduced Grx with a K(d) of ca 8.6 mM. The potential biological significance of the new Grx-Grx interaction interface is discussed.
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Affiliation(s)
- Valerie Noguera
- RMN Biomoléculaire, Université Claude Bernard, Lyon 1, CNRS UMR 5180 Sciences Analytiques, ESCPE-Lyon, 69622 Villeurbanne, France
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41
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Mizohata E, Sakai H, Fusatomi E, Terada T, Murayama K, Shirouzu M, Yokoyama S. Crystal structure of an archaeal peroxiredoxin from the aerobic hyperthermophilic crenarchaeon Aeropyrum pernix K1. J Mol Biol 2005; 354:317-29. [PMID: 16214169 DOI: 10.1016/j.jmb.2005.09.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2005] [Revised: 08/31/2005] [Accepted: 09/06/2005] [Indexed: 10/25/2022]
Abstract
Peroxiredoxins (Prxs) are thiol-dependent peroxidases that catalyze the detoxification of various peroxide substrates such as H2O2, peroxinitrite, and hydroperoxides, and control some signal transduction in eukaryotic cells. Prxs are found in all cellular organisms and represent an enormous superfamily. Recent genome sequencing projects and biochemical studies have identified a novel subfamily, the archaeal Prxs. Their primary sequences are similar to those of the 1-Cys Prxs, which use only one cysteine residue in catalysis, while their catalytic properties resemble those of the typical 2-Cys Prxs, which utilize two cysteine residues from adjacent monomers within a dimer in catalysis. We present here the X-ray crystal structure of an archaeal Prx from the aerobic hyperthermophilic crenarchaeon, Aeropyrum pernix K1, determined at 2.3 A resolution (Rwork of 17.8% and Rfree of 23.0%). The overall subunit arrangement of the A.pernix archaeal Prx is a toroid-shaped pentamer of homodimers, or an (alpha2)5 decamer, as observed in the previously reported crystal structures of decameric Prxs. The basic folding topology and the peroxidatic active site structure are essentially the same as those of the 1-Cys Prx, hORF6, except that the C-terminal extension of the A.pernix archaeal Prx forms a unique helix with its flanking loops. The thiol group of the peroxidatic cysteine C50 is overoxidized to sulfonic acid. Notably, the resolving cysteine C213 forms the intra-monomer disulfide bond with the third cysteine, C207, which should be a unique structural characteristic in the many archaeal Prxs that retain two conserved cysteine residues in the C-terminal region. The conformational flexibility near the intra-monomer disulfide linkage might be necessary for the dramatic structural rearrangements that occur in the catalytic cycle.
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Affiliation(s)
- Eiichi Mizohata
- RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
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42
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Rhee SG, Chae HZ, Kim K. Peroxiredoxins: a historical overview and speculative preview of novel mechanisms and emerging concepts in cell signaling. Free Radic Biol Med 2005; 38:1543-52. [PMID: 15917183 DOI: 10.1016/j.freeradbiomed.2005.02.026] [Citation(s) in RCA: 1034] [Impact Index Per Article: 54.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2005] [Revised: 02/21/2005] [Accepted: 02/23/2005] [Indexed: 12/20/2022]
Abstract
The observation that purified yeast glutamine synthetase is rapidly inactivated in a thiol-containing buffer yet retains activity in crude extracts containing the same thiol led to our discovery of an enzyme that protects against oxidation in a thiol-containing system. This novel antioxidant enzyme was shown to reduce hydroperoxides and, more recently, peroxynitrite with the use of electrons provided by a physiological thiol like thioredoxin. It defined a family of proteins, present in organisms from all kingdoms, that was named peroxiredoxin (Prx). All Prx enzymes contain a conserved Cys residue that undergoes a cycle of peroxide-dependent oxidation and thiol-dependent reduction during catalysis. Mammalian cells express six isoforms of Prx (Prx I to VI), which are classified into three subgroups (2-Cys, atypical 2-Cys, and 1-Cys) based on the number and position of Cys residues that participate in catalysis. The relative abundance of Prx enzymes in mammalian cells appears to protect cellular components by removing the low levels of peroxides produced as a result of normal cellular metabolism. During catalysis, the active site cysteine is occasionally overoxidized to cysteine sulfinic acid. Contrary to the general belief that oxidation to the sulfinic state is an irreversible process in cells, studies on the fate of the overoxidized Prx species revealed a mechanism by which the catalytically active thiol form is recovered. This sulfinic reduction is a slow, ATP-dependent process that is specific to 2-Cys Prx isoforms. This reversible overoxidation may represent an adaptation unique to eukaryotic cells that accommodates the intracellular messenger function of H(2)O(2), but experimental validation of such speculation is yet to come.
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Affiliation(s)
- Sue Goo Rhee
- Laboratory of Cell Signaling, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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43
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Murphy TF, Kirkham C, Sethi S, Lesse AJ. Expression of a peroxiredoxin-glutaredoxin by Haemophilus influenzae in biofilms and during human respiratory tract infection. ACTA ACUST UNITED AC 2005; 44:81-9. [PMID: 15780580 DOI: 10.1016/j.femsim.2004.12.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2004] [Revised: 10/28/2004] [Accepted: 12/05/2004] [Indexed: 11/25/2022]
Abstract
Evidence is mounting that nontypeable Haemophilus influenzae grows as a biofilm in the middle ear of children with otitis media and the airways of adults with chronic obstructive pulmonary disease. To begin to assess antigens expressed by H. influenzae in biofilms, cell envelopes of bacteria grown as a biofilm were compared to those grown planktonically. A approximately 30kDa peroxiredoxin-glutaredoxin was present in greater abundance during growth in biofilms. Mutants deficient in expression of peroxiredoxin-glutaredoxin were constructed by homologous recombination in four clinical isolates. The mutants showed a 25-50% reduction in biofilm formation compared to the corresponding parent strains. To study in vivo expression of peroxiredoxin-glutaredoxin during human respiratory tract infection, paired pre- and post-exacerbation serum from adults with chronic obstructive pulmonary disease and H. influenzae in sputum were assayed using an enzyme-linked immunosorbent assay and purified recombinant peroxiredoxin-glutaredoxin. Eight from 18 (44.4%) paired serum samples showed a significant increase in antibody to peroxiredoxin-glutaredoxin from pre- to post-infection. These results indicate that (1) peroxiredoxin-glutaredoxin is present in greater abundance in H. influenzae biofilms compared to planktonically grown bacteria; (2) peroxiredoxin-glutaredoxin is involved in biofilm formation by H. influenzae and the degree of involvement varies among strains; and (3) peroxiredoxin-glutaredoxin is expressed by H. influenzae during infection of the human respiratory tract and is recognized by the human immune system.
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Affiliation(s)
- Timothy F Murphy
- Division of Infectious Diseases, University at Buffalo, State University of New York, Buffalo, NY, USA.
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44
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Dombrecht B, Heusdens C, Beullens S, Verreth C, Mulkers E, Proost P, Vanderleyden J, Michiels J. Defence of Rhizobium etli bacteroids against oxidative stress involves a complexly regulated atypical 2-Cys peroxiredoxin. Mol Microbiol 2005; 55:1207-21. [PMID: 15686565 DOI: 10.1111/j.1365-2958.2005.04457.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In general, oxidative stress, the consequence of an aerobic lifestyle, induces bacterial antioxidant defence enzymes. Here we report on a peroxiredoxin of Rhizobium etli, prxS, strongly expressed under microaerobic conditions and during the symbiotic interaction with Phaseolus vulgaris. The microaerobic induction of the prxS-rpoN2 operon is mediated by the alternative sigma factor RpoN and the enhancer-binding protein NifA. The RpoN-dependent promoter is also active under low-nitrogen conditions through the enhancer-binding protein NtrC. An additional symbiosis-specific weak promoter is located between prxS and rpoN2. Constitutive expression of prxS confers enhanced survival and growth to R. etli in the presence of H2O2. Single prxS mutants are not affected in their symbiotic abilities or defence response against oxidative stress under free-living conditions. In contrast, a prxS katG double mutant has a significantly reduced (>40%) nitrogen fixation capacity, suggesting a functional redundancy between PrxS and KatG, a bifunctional catalase-peroxidase. In vitro assays demonstrate the reduction of PrxS protein by DTT and thioredoxin. PrxS displays substrate specificity towards H2O2 (Km = 62 microM) over alkyl hydroperoxides (Km > 1 mM). Peroxidase activity is abolished in both the peroxidatic (C56) and resolving (C156) cysteine PrxS mutants, while the conserved C81 residue is required for proper folding of the protein. Resolving of the R. etli PrxS peroxidatic cysteine is probably an intramolecular process and intra- and intersubunit associations were observed. Taken together, our data support, for the first time, a role for an atypical 2-Cys peroxiredoxin against oxidative stress in R. etli bacteroids.
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Affiliation(s)
- Bruno Dombrecht
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, 3001 Heverlee, Belgium
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45
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Li S, Peterson NA, Kim MY, Kim CY, Hung LW, Yu M, Lekin T, Segelke BW, Lott JS, Baker EN. Crystal Structure of AhpE from Mycobacterium tuberculosis, a 1-Cys peroxiredoxin. J Mol Biol 2005; 346:1035-46. [PMID: 15701515 DOI: 10.1016/j.jmb.2004.12.046] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2004] [Revised: 12/15/2004] [Accepted: 12/20/2004] [Indexed: 11/29/2022]
Abstract
All living systems require protection against the damaging effects of reactive oxygen species. The genome of Mycobacterium tuberculosis, the cause of TB, encodes a number of peroxidases that are thought to be active against organic and inorganic peroxides, and are likely to play a key role in the ability of this organism to survive within the phagosomes of macrophages. The open reading frame Rv2238c in M.tuberculosis encodes a 153-residue protein AhpE, which is a peroxidase of the 1-Cys peroxiredoxin (Prx) family. The crystal structure of AhpE, determined at 1.87 A resolution (R(cryst)=0.179, R(free)=0.210), reveals a compact single-domain protein with a thioredoxin fold. AhpE forms both dimers and octamers; a tightly-associated dimer and a ring-like octamer, generated by crystallographic 4-fold symmetry. In this native structure, the active site Cys45 is in its oxidized, sulfenic acid (S-O-H) state. A second crystal form of AhpE, obtained after soaking in sodium bromide and refined at 1.90 A resolution (R(cryst)=0.242, R(free)=0.286), reveals the reduced structure. In this structure, a conformational change in an external loop, in two of the four molecules in the asymmetric unit, allows Arg116 to stabilise the Cys45 thiolate ion, and concomitantly closes a surface channel. This channel is identified as the likely binding site for a physiological reductant, and the conformational change is inferred to be important for the reaction cycle of AhpE.
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Affiliation(s)
- Simon Li
- Centre of Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
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46
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Sarma GN, Nickel C, Rahlfs S, Fischer M, Becker K, Karplus PA. Crystal structure of a novel Plasmodium falciparum 1-Cys peroxiredoxin. J Mol Biol 2005; 346:1021-34. [PMID: 15701514 DOI: 10.1016/j.jmb.2004.12.022] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2004] [Revised: 12/07/2004] [Accepted: 12/08/2004] [Indexed: 12/22/2022]
Abstract
Plasmodium falciparum, the causative agent of malaria, is sensitive to oxidative stress and therefore the family of antioxidant enzymes, peroxiredoxins (Prxs) represent a target for antimalarial drug design. We present here the 1.8 A resolution crystal structure of P.falciparum antioxidant protein, PfAOP, a Prx that in terms of sequence groups with mammalian PrxV. The structure is compared to all 11 known Prx structures to gain maximal insight into its properties. We describe the common Prx fold and show that the dimeric PfAOP can be mechanistically categorized as a 1-Cys Prx. In the active site the peroxidatic Cys is over-oxidized to cysteine sulfonic acid, making this the first Prx structure seen in that state. Now with structures of Prxs in Cys-sulfenic, -sulfinic and -sulfonic acid oxidation states known, the structural steps involved in peroxide binding and over-oxidation are suggested. We also describe that PfAOP has an alpha-aneurism (a one residue insertion), a feature that appears characteristic of the PrxV-like group. In terms of crystallographic methodology, we enhance the information content of the model by identifying bound water sites based on peak electron densities, and we use that information to infer that the oxidized active site has suboptimal interactions that may influence catalysis. The dimerization interface of PfAOP is representative of an interface that is widespread among Prxs, and has sequence-dependent variation in geometry. The interface differences and the structural features (like the alpha-aneurism) may be used as markers to better classify Prxs and study their evolution.
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Affiliation(s)
- Ganapathy N Sarma
- Department of Biochemistry and Biophysics, Oregon State University, 2011 ALS, Corvallis, OR 97331-7305, USA
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47
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Woo JR, Kim SJ, Jeong W, Cho YH, Lee SC, Chung YJ, Rhee SG, Ryu SE. Structural basis of cellular redox regulation by human TRP14. J Biol Chem 2004; 279:48120-5. [PMID: 15355959 DOI: 10.1074/jbc.m407079200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Thioredoxin-related protein 14 (TRP14) is involved in regulating tumor necrosis factor-alpha-induced signaling pathways in a different manner from human thioredoxin 1 (Trx1). Here, we report the crystal structure of human TRP14 determined at 1.8-A resolutions. The structure reveals a typical thioredoxin fold with characteristic structural features that account for the substrate specificity of the protein. The surface of TRP14 in the vicinity of the active site includes an extended loop and an additional alpha-helix, and the distribution of charged residues in the surface is different from Trx1. The distinctive dipeptide between the redox-active cysteines contributes to stabilizing the thiolate anion of the active site cysteine 43, increasing reactivity of the cysteine toward substrates. These structural differences in the active site suggest that TRP14 has evolved to regulate cellular redox signaling by recognizing a distinctive group of substrates that would complement the group of proteins regulated by Trx1.
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Affiliation(s)
- Joo Rang Woo
- Center for Cellular Switch Protein Structure and Systemic Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, 52 Euh-eun-dong, Yuseong-gu, Daejeon 305-806, Korea
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48
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Evrard C, Capron A, Marchand C, Clippe A, Wattiez R, Soumillion P, Knoops B, Declercq JP. Crystal structure of a dimeric oxidized form of human peroxiredoxin 5. J Mol Biol 2004; 337:1079-90. [PMID: 15046979 DOI: 10.1016/j.jmb.2004.02.017] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2003] [Revised: 01/27/2004] [Accepted: 02/04/2004] [Indexed: 12/25/2022]
Abstract
Peroxiredoxin 5 is the last discovered mammalian member of an ubiquitous family of peroxidases widely distributed among prokaryotes and eukaryotes. Mammalian peroxiredoxin 5 has been recently classified as an atypical 2-Cys peroxiredoxin due to the presence of a conserved peroxidatic N-terminal cysteine (Cys47) and an unconserved resolving C-terminal cysteine residue (Cys151) forming an intramolecular disulfide intermediate in the oxidized enzyme. We have recently reported the crystal structure of human peroxiredoxin 5 in its reduced form. Here, a new crystal form of human peroxiredoxin 5 is described at 2.0 A resolution. The asymmetric unit contains three polypeptide chains. Surprisingly, beside two reduced chains, the third one is oxidized although the enzyme was crystallized under initial reducing conditions in the presence of 1 mM 1,4-dithio-dl-threitol. The oxidized polypeptide chain forms an homodimer with a symmetry-related one through intermolecular disulfide bonds between Cys47 and Cys151. The formation of these disulfide bonds is accompanied by the partial unwinding of the N-terminal parts of the alpha2 helix, which, in the reduced form, contains the peroxidatic Cys47 and the alpha6 helix, which is sequentially close to the resolving residue Cys151. In each monomer of the oxidized chain, the C-terminal part including the alpha6 helix is completely reorganized and is isolated from the rest of the protein on an extended arm. In the oxidized dimer, the arm belonging to the first monomer now appears at the surface of the second subunit and vice versa.
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Affiliation(s)
- Christine Evrard
- Unit of Structural Chemistry (CSTR), Université catholique de Louvain, 1 place Louis Pasteur, B-1348 Louvain-la-Neuve, Belgium
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Rouhier N, Gelhaye E, Gualberto JM, Jordy MN, De Fay E, Hirasawa M, Duplessis S, Lemaire SD, Frey P, Martin F, Manieri W, Knaff DB, Jacquot JP. Poplar peroxiredoxin Q. A thioredoxin-linked chloroplast antioxidant functional in pathogen defense. PLANT PHYSIOLOGY 2004; 134:1027-38. [PMID: 14976238 PMCID: PMC389925 DOI: 10.1104/pp.103.035865] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2003] [Revised: 12/02/2003] [Accepted: 12/04/2003] [Indexed: 05/18/2023]
Abstract
Peroxiredoxins are ubiquitous thioredoxin- or glutaredoxin-dependent peroxidases, the function of which is to destroy peroxides. Peroxiredoxin Q, one of the four plant subtypes, is a homolog of the bacterial bacterioferritin comigratory proteins. We show here that the poplar (Populus tremula x Populus tremuloides) protein acts as a monomer with an intramolecular disulfide bridge between two conserved cysteines. A wide range of electron donors and substrates was tested. Unlike type II peroxiredoxin, peroxiredoxin Q cannot use the glutaredoxin or cyclophilin isoforms tested, but various cytosolic, chloroplastic, and mitochondrial thioredoxins are efficient electron donors with no marked specificities. The redox midpoint potential of the peroxiredoxin Q catalytic disulfide is -325 mV at pH 7.0, explaining why the wild-type protein is reduced by thioredoxin but not by glutaredoxin. Additional evidence that thioredoxin serves as a donor comes from the formation of heterodimers between peroxiredoxin Q and monocysteinic mutants of spinach (Spinacia oleracea) thioredoxin m. Peroxiredoxin Q can reduce various alkyl hydroperoxides, but with a better efficiency for cumene hydroperoxide than hydrogen peroxide and tertiary butyl hydroperoxide. The use of immunolocalization and of a green fluorescence protein fusion construct indicates that the transit sequence efficiently targets peroxiredoxin Q to the chloroplasts and especially to those of the guard cells. The expression of this protein and of type II peroxiredoxin is modified in response to an infection by two races of Melampsora larici-populina, the causative agent of the poplar rust. In the case of an hypersensitive response, the peroxiredoxin expression increased, whereas it decreased during a compatible interaction.
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Affiliation(s)
- Nicolas Rouhier
- Unité Mixte de Recherche Institut National de la Recherche Agronomique-Université Henri Poincaré 1136, Interactions Arbres/Micro-Organismes, Université Henri Poincaré, Faculté des Sciences, BP 239, 54506 Vandoeuvre cedex France
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Cha MK, Hong SK, Lee DS, Kim IH. Vibrio cholerae thiol peroxidase-glutaredoxin fusion is a 2-Cys TSA/AhpC subfamily acting as a lipid hydroperoxide reductase. J Biol Chem 2003; 279:11035-41. [PMID: 14702341 DOI: 10.1074/jbc.m312657200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Recently, novel hybrid thiol peroxidase (TPx) proteins fused with a glutaredoxin (Grx) were found from some pathogenic bacteria, cyanobacteria, and anaerobic sulfur-oxidizing phototroph. The phylogenic tree analysis that was constructed from the aligned sequences showed two major branches. Haemophilus influenzae TPx.Grx was grouped in one branch as a 1-Cys subfamily of the thiol-specific antioxident protein/AhpC family. Most TPx.Grx proteins, including Vibrio cholerae TPx.Grx, were grouped in the 2-Cys subfamily. To explain the existence of two subgroups in novel hybrid TPx proteins, we have compared the kinetics given by V. cholerae TPx.Grx, H. influenzae TPx.Grx, their separated TPx domains, and a set of mutants devoid of the redox-active cysteines. The kinetic study described here demonstrates clearly that V. cholerae TPx.Grx is a 2-Cys TPx subfamily. For the first time, we also demonstrate the lipid peroxidase activity of V. cholerae TPx.Grx fusion and suggest the in vivo function of 2-Cys TPx.Grx fusion serving as a lipid peroxidase.
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Affiliation(s)
- Mee-Kyung Cha
- Department of Biochemistry, Paichai University, Taejon 302-735, Republic of Korea
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