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Rahaman H, Herojit K, Singh LR, Haobam R, Fisher AB. Structural and Functional Diversity of the Peroxiredoxin 6 Enzyme Family. Antioxid Redox Signal 2024; 40:759-775. [PMID: 37463006 DOI: 10.1089/ars.2023.0287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Significance: Peroxiredoxins (Prdxs) with a single peroxidative cysteine (CP) in a conserved motif PXXX(T/S)XXCP within its thioredoxin fold, have been classified as the peroxiredoxin 6 (Prdx6 ) family. All Prdxs can reduce H2O2 and short chain hydroperoxides while Prdx6 in addition, can reduce phospholipid hydroperoxides (PLOOH) due to its ability to interact with peroxidized phospholipid substrate. The single CP of Prdx6 uses various external electron donors including glutathione thioredoxin, and ascorbic acid for resolution of its peroxidized state and, therefore, its peroxidase activity. Prdx6 proteins also exhibit Ca2+-independent phospholipase A2 (PLA2), lysophosphatidylcholine acyltransferase (LPCAT), and chaperone activities that depend on cellular localization and the oxidation and oligomerisation states of the protein. Thus, Prdx6 is a "moonlighting" enzyme. Recent Advance: Physiologically, Prdx6s have been reported to play an important role in protection against oxidative stress, repair of peroxidized cell membranes, mammalian lung surfactant turnover, activation of some NADPH oxidases, the regulation of seed germination in plants, as an indicator of cellular levels of reactive O2 species through Nrf-Klf9 activation, and possibly in male fertility, regulation of cell death through ferroptosis, cancer metastasis, and oxidative stress-related signalling pathways. Critical Issues: This review outlines Prdx6 enzyme unique structural features and explores its wide range of physiological functions. Yet, existing structural data falls short of fully revealing all of human Prdx6 multifunctional roles. Further endeavour is required to bridge this gap in its understanding. Although there are wide variations in both the structure and function of Prdx6 family members in various organisms, all Prdx6 proteins show the unique a long C-terminal extension that is also seen in Prdx1, but not in other Prdxs. Future Directions: As research data continues to accumulate, the potential for detailed insights into the role of C-terminal of Prdx6 in its oligomerisation and activities. There is a need for thorough exploration of structural characteristics of the various biological functions. Additionally, uncovering the interacting partners of Prdx6 and understanding its involvement in signalling pathways will significantly contribute to a more profound comprehension of its role.
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Affiliation(s)
- Hamidur Rahaman
- Department of Biotechnology, Manipur University, Imphal, India
| | - Khundrakpam Herojit
- Department of Biotechnology, Manipur University, Imphal, India
- Department of Biotechnology, Mangolnganbi College, Ningthoukhong, India
| | | | - Reena Haobam
- Department of Biotechnology, Manipur University, Imphal, India
| | - Aron B Fisher
- Institute for Environmental Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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2
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Troussicot L, Burmann BM, Molin M. Structural determinants of multimerization and dissociation in 2-Cys peroxiredoxin chaperone function. Structure 2021; 29:640-654. [PMID: 33945778 DOI: 10.1016/j.str.2021.04.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/31/2021] [Accepted: 04/14/2021] [Indexed: 12/19/2022]
Abstract
Peroxiredoxins (PRDXs) are abundant peroxidases present in all kingdoms of life. Recently, they have been shown to also carry out additional roles as molecular chaperones. To address this emerging supplementary function, this review focuses on structural studies of 2-Cys PRDX systems exhibiting chaperone activity. We provide a detailed understanding of the current knowledge of structural determinants underlying the chaperone function of PRDXs. Specifically, we describe the mechanisms which may modulate their quaternary structure to facilitate interactions with client proteins and how they are coordinated with the functions of other molecular chaperones. Following an overview of PRDX molecular architecture, we outline structural details of the presently best-characterized peroxiredoxins exhibiting chaperone function and highlight common denominators. Finally, we discuss the remarkable structural similarities between 2-Cys PRDXs, small HSPs, and J-domain-independent Hsp40 holdases in terms of their functions and dynamic equilibria between low- and high-molecular-weight oligomers.
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Affiliation(s)
- Laura Troussicot
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Göteborg, Sweden
| | - Björn M Burmann
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Göteborg, Sweden.
| | - Mikael Molin
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden; Department of Biology and Biological Engineering, Chalmers University of Technology, 405 30 Göteborg, Sweden.
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3
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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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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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Stroobants S, Van Molle I, Saidi Q, Jonckheere K, Maes D, Peeters E. Structure of the Prx6-subfamily 1-Cys peroxiredoxin from Sulfolobus islandicus. Acta Crystallogr F Struct Biol Commun 2019; 75:428-434. [PMID: 31204689 PMCID: PMC6572100 DOI: 10.1107/s2053230x19006472] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 05/07/2019] [Indexed: 11/28/2022] Open
Abstract
Aerobic thermoacidophilic archaea belonging to the genus Sulfolobus harbor peroxiredoxins, thiol-dependent peroxidases that assist in protecting the cells from oxidative damage. Here, the crystal structure of the 1-Cys peroxiredoxin from Sulfolobus islandicus, named 1-Cys SiPrx, is presented. A 2.75 Å resolution data set was collected from a crystal belonging to space group P212121, with unit-cell parameters a = 86.8, b = 159.1, c = 189.3 Å, α = β = γ = 90°. The structure was solved by molecular replacement using the homologous Aeropyrum pernix peroxiredoxin (ApPrx) structure as a search model. In the crystal structure, 1-Cys SiPrx assembles into a ring-shaped decamer composed of five homodimers. This quaternary structure corresponds to the oligomeric state of the protein in solution, as observed by size-exclusion chromatography. 1-Cys SiPrx harbors only a single cysteine, which is the peroxidatic cysteine, and lacks both of the cysteines that are highly conserved in the C-terminal arm domain in other archaeal Prx6-subfamily proteins such as ApPrx and that are involved in the association of dimers into higher-molecular-weight decamers and dodecamers. It is thus concluded that the Sulfolobus Prx6-subfamily protein undergoes decamerization independently of arm-domain cysteines.
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Affiliation(s)
- Sander Stroobants
- Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Inge Van Molle
- Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Queen Saidi
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Karl Jonckheere
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Dominique Maes
- Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
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Himiyama T, Oshima M, Uegaki K, Nakamura T. Distinct molecular assembly of homologous peroxiredoxins from Pyrococcus horikoshii and Thermococcus kodakaraensis. J Biochem 2019; 166:89-95. [DOI: 10.1093/jb/mvz013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/20/2019] [Indexed: 11/14/2022] Open
Abstract
Abstract
Peroxiredoxins from Pyrococcus horikoshii (PhPrx) and Thermococcus kodakaraensis (TkPrx) are highly homologous proteins sharing 196 of the 216 residues. We previously reported a pentagonal ring-type decameric structure of PhPrx. Here, we present the crystal structure of TkPrx. Despite their homology, unlike PhPrx, the quaternary structure of TkPrx was found to be a dodecamer comprised of six homodimers arranged in a hexagonal ring-type assembly. The possibility of the redox-dependent conversion of the molecular assembly, which had been observed in PhPrx, was excluded for TkPrx based on the crystal structure of a mutant in which all of the cysteine residues were substituted with serine. The monomer structures of the dodecameric TkPrx and decameric PhPrx coincided well, but there was a slight difference in the relative orientation of the two domains. Molecular assembly of PhPrx and TkPrx in solution evaluated by gel-filtration chromatography was consistent with the crystallographic results. For both PhPrx and TkPrx, the gel-filtration elution volume slightly increased with a decrease in the protein concentration, suggesting the existence of an equilibrium state between the decameric/dodecameric ring and lower-order assembly. This structural assembly difference between highly homologous Prxs suggests a significant influence of quaternary structure on function, worthy of further exploration.
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Affiliation(s)
- Tomoki Himiyama
- National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka, Japan
- DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), 1-8-31 Midorigaoka, Ikeda, Osaka, Japan
| | - Maki Oshima
- National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka, Japan
| | - Koichi Uegaki
- National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka, Japan
- Faculty of Agriculture, Kindai University, 3327-204 Nakamachi, Nara, Nara, Japan
| | - Tsutomu Nakamura
- National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka, Japan
- DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), 1-8-31 Midorigaoka, Ikeda, Osaka, Japan
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7
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Liu W, Liu A, Gao H, Wang Q, Wang L, Warkentin E, Rao Z, Michel H, Peng G. Structural properties of the peroxiredoxin AhpC2 from the hyperthermophilic eubacterium Aquifex aeolicus. Biochim Biophys Acta Gen Subj 2018; 1862:2797-2805. [DOI: 10.1016/j.bbagen.2018.08.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/18/2018] [Accepted: 08/23/2018] [Indexed: 11/25/2022]
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Feld K, Geissel F, Liedgens L, Schumann R, Specht S, Deponte M. Tyrosine substitution of a conserved active-site histidine residue activates Plasmodium falciparum peroxiredoxin 6. Protein Sci 2018; 28:100-110. [PMID: 30056630 DOI: 10.1002/pro.3490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/27/2018] [Accepted: 07/27/2018] [Indexed: 01/05/2023]
Abstract
Peroxiredoxins efficiently remove hydroperoxides and peroxynitrite in pro- and eukaryotes. However, isoforms of one subfamily of peroxiredoxins, the so-called Prx6-type enzymes, usually have very low activities in standard peroxidase assays in vitro. In contrast to other peroxiredoxins, Prx6 homologues share a conserved histidyl residue at the bottom of the active site. Here we addressed the role of this histidyl residue for redox catalysis using the Plasmodium falciparum homologue PfPrx6 as a model enzyme. Steady-state kinetics with tert-butyl hydroperoxide (tBuOOH) revealed that the histidyl residue is nonessential for Prx6 catalysis and that a replacement with tyrosine can even increase the enzyme activity four- to six-fold in vitro. Stopped-flow kinetics with reduced PfPrx6WT , PfPrx6C128A , and PfPrx6H39Y revealed a preference for H2 O2 as an oxidant with second order rate constants for H2 O2 and tBuOOH around 2.5 × 107 M-1 s-1 and 3 × 106 M-1 s-1 , respectively. Differences between the oxidation kinetics of PfPrx6WT , PfPrx6C128A , and PfPrx6H39Y were observed during a slower second-reaction phase. Our kinetic data support the interpretation that the reductive half-reaction is the rate-limiting step for PfPrx6 catalysis in steady-state measurements. Whether the increased activity of PfPrx6H39Y is caused by a facilitated enzyme reduction because of a destabilization of the fully folded enzyme conformation remains to be analyzed. In summary, the conserved histidyl residue of Prx6-type enzymes is non-essential for catalysis, PfPrx6 is rapidly oxidized by hydroperoxides, and the gain-of-function mutant PfPrx6H39Y might provide a valuable tool to address the influence of conformational changes on the reactivity of Prx6 homologues.
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Affiliation(s)
- Kristina Feld
- Department of Parasitology, Ruprecht-Karls University, D-69120, Heidelberg, Germany
| | - Fabian Geissel
- Faculty of Chemistry/Biochemistry, TU Kaiserslautern, D-67663, Kaiserslautern, Germany
| | - Linda Liedgens
- Department of Parasitology, Ruprecht-Karls University, D-69120, Heidelberg, Germany.,Faculty of Chemistry/Biochemistry, TU Kaiserslautern, D-67663, Kaiserslautern, Germany
| | - Robin Schumann
- Faculty of Chemistry/Biochemistry, TU Kaiserslautern, D-67663, Kaiserslautern, Germany
| | - Sandra Specht
- Department of Parasitology, Ruprecht-Karls University, D-69120, Heidelberg, Germany.,Faculty of Chemistry/Biochemistry, TU Kaiserslautern, D-67663, Kaiserslautern, Germany
| | - Marcel Deponte
- Department of Parasitology, Ruprecht-Karls University, D-69120, Heidelberg, Germany.,Faculty of Chemistry/Biochemistry, TU Kaiserslautern, D-67663, Kaiserslautern, Germany
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