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Sylvestre-Gonon E, Morette L, Viloria M, Mathiot S, Boutilliat A, Favier F, Rouhier N, Didierjean C, Hecker A. Biochemical and Structural Insights on the Poplar Tau Glutathione Transferase GSTU19 and 20 Paralogs Binding Flavonoids. Front Mol Biosci 2022; 9:958586. [PMID: 36032685 PMCID: PMC9412104 DOI: 10.3389/fmolb.2022.958586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/22/2022] [Indexed: 12/04/2022] Open
Abstract
Glutathione transferases (GSTs) constitute a widespread superfamily of enzymes notably involved in xenobiotic detoxification and/or in specialized metabolism. Populus trichocarpa genome (V4.1 assembly, Phytozome 13) consists of 74 genes coding for full-length GSTs and ten likely pseudogenes. These GSTs are divided into 11 classes, in which the tau class (GSTU) is the most abundant with 54 isoforms. PtGSTU19 and 20, two paralogs sharing more than 91% sequence identity (95% of sequence similarity), would have diverged from a common ancestor of P. trichocarpa and P. yatungensis species. These enzymes display the distinctive glutathione (GSH)-conjugation and peroxidase activities against model substrates. The resolution of the crystal structures of these proteins revealed significant structural differences despite their high sequence identity. PtGSTU20 has a well-defined deep pocket in the active site whereas the bottom of this pocket is disordered in PtGSTU19. In a screen of potential ligands, we were able to identify an interaction with flavonoids. Some of them, previously identified in poplar (chrysin, galangin, and pinocembrin), inhibited GSH-conjugation activity of both enzymes with a more pronounced effect on PtGSTU20. The crystal structures of PtGSTU20 complexed with these molecules provide evidence for their potential involvement in flavonoid transport in P. trichocarpa.
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Affiliation(s)
| | - Laura Morette
- Université de Lorraine, INRAE, IAM, Nancy, France
- Université de Lorraine, CNRS, CRM2, Nancy, France
| | | | | | | | | | | | - Claude Didierjean
- Université de Lorraine, CNRS, CRM2, Nancy, France
- *Correspondence: Claude Didierjean, ; Arnaud Hecker,
| | - Arnaud Hecker
- Université de Lorraine, INRAE, IAM, Nancy, France
- *Correspondence: Claude Didierjean, ; Arnaud Hecker,
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2
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Chikunova A, Ubbink M. The roles of highly conserved, non‐catalytic residues in class A β‐lactamases. Protein Sci 2022; 31:e4328. [PMID: 35634774 PMCID: PMC9112487 DOI: 10.1002/pro.4328] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/03/2022] [Accepted: 04/20/2022] [Indexed: 11/12/2022]
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Kortheerakul C, Kageyama H, Waditee-Sirisattha R. Molecular and functional insights into glutathione S-transferase genes associated with salt stress in Halothece sp. PCC7418. PLANT, CELL & ENVIRONMENT 2021; 44:3583-3596. [PMID: 34347891 DOI: 10.1111/pce.14161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/22/2021] [Accepted: 07/25/2021] [Indexed: 06/13/2023]
Abstract
Evolution and function of glutathione S-transferase (GST) in primordial oxygenic phototrophs such as cyanobacteria are poorly understood. In this study, we identified and functionally characterized the GST gene family in the halotolerant cyanobacterium Halothece sp. PCC7418. Four putative Halothece-GSTs had very low homology, which implies evolutionary divergence. Of these, H0647, H0729 and H3557 were differentially expressed by oxidative stress whereas H3557 was highly and specifically upregulated under salt stress. In vitro analysis revealed that the recombinant H3557 exhibited GST activity toward 1-chloro-2, 4-dinitrobenzene (CDNB) and glutathione (GSH). H3557 displayed a broad range of activity at pH 6.5-10.5. Kinetic parameters showed the apparent Km for CDNB and GSH was 0.14 and 0.75 mM, respectively. H3557 remained catalytically active in the presence of NaCl. Structural modelling supported that H3557 is salt-adaptive enzyme with highly acidic residues on the protein surface. The vital function of H3557 in heterologous expression system was evaluated. The H3557-expressing cells were more tolerant to H2 O2 -induced oxidative stress compared with other GST-expressing cells and conferred salt tolerance. Taken together, the findings of this study provide insights into the molecular and cellular functions of GST in cyanobacteria, particularly under salt stress, which is less understood compared with other species.
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Affiliation(s)
- Chananwat Kortheerakul
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- The Chemical Approaches for Food Applications Research Group, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Hakuto Kageyama
- Department of Chemistry, Faculty of Science and Technology, Meijo University, Nagoya, Japan
- Graduate School of Environmental and Human Sciences, Meijo University, Nagoya, Japan
| | - Rungaroon Waditee-Sirisattha
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- The Chemical Approaches for Food Applications Research Group, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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Di Matteo A, Federici L, Masulli M, Carletti E, Santorelli D, Cassidy J, Paradisi F, Di Ilio C, Allocati N. Structural Characterization of the Xi Class Glutathione Transferase From the Haloalkaliphilic Archaeon Natrialba magadii. Front Microbiol 2019; 10:9. [PMID: 30713525 PMCID: PMC6345682 DOI: 10.3389/fmicb.2019.00009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 01/07/2019] [Indexed: 12/30/2022] Open
Abstract
Xi class glutathione transferases (GSTs) are a recently identified group, within this large superfamily of enzymes, specifically endowed with glutathione-dependent reductase activity on glutathionyl-hydroquinone. Enzymes belonging to this group are widely distributed in bacteria, fungi, and plants but not in higher eukaryotes. Xi class GSTs are also frequently found in archaea and here we focus on the enzyme produced by the extreme haloalkaliphilic archaeon Natrialba magadii (NmGHR). We investigated its function and stability and determined its 3D structure in the apo form by X-ray crystallography. NmGHR displays the same fold of its mesophilic counterparts, is enriched in negatively charged residues, which are evenly distributed along the surface of the protein, and is characterized by a peculiar distribution of hydrophobic residues. A distinctive feature of haloalkaliphilic archaea is their preference for γ-glutamyl-cysteine over glutathione as a reducing thiol. Indeed we found that the N. magadii genome lacks a gene coding for glutathione synthase. Analysis of NmGHR structure suggests that the thiol binding site (G-site) of the enzyme is well suited for hosting γ-glutamyl-cysteine.
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Affiliation(s)
- Adele Di Matteo
- Institute of Molecular Biology and Pathology, CNR, Rome, Italy
| | - Luca Federici
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy.,CeSI-MeT, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Michele Masulli
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Erminia Carletti
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy.,CeSI-MeT, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Daniele Santorelli
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy.,CeSI-MeT, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Jennifer Cassidy
- Synthesis and Solid State Pharmaceutical Centre (SSPC), School of Chemistry, University College Dublin, Dublin, Ireland
| | - Francesca Paradisi
- Synthesis and Solid State Pharmaceutical Centre (SSPC), School of Chemistry, University College Dublin, Dublin, Ireland.,School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Carmine Di Ilio
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Nerino Allocati
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
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5
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Malik A, Khan JM, Alamery SF, Fouad D, Labrou NE, Daoud MS, Abdelkader MO, Ataya FS. Monomeric Camelus dromedarius GSTM1 at low pH is structurally more thermostable than its native dimeric form. PLoS One 2018; 13:e0205274. [PMID: 30303997 PMCID: PMC6179282 DOI: 10.1371/journal.pone.0205274] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 09/21/2018] [Indexed: 01/01/2023] Open
Abstract
Glutathione S‒transferases (GSTs) are multifunctional enzymes that play an important role in detoxification, cellular signalling, and the stress response. Camelus dromedarius is well-adapted to survive in extreme desert climate and it has GSTs, for which limited information is available. This study investigated the structure-function and thermodynamic properties of a mu-class camel GST (CdGSTM1) at different pH. Recombinant CdGSTM1 (25.7 kDa) was expressed in E. coli and purified to homogeneity. Dimeric CdGSTM1 dissociated into stable but inactive monomeric subunits at low pH. Conformational and thermodynamic changes during the thermal unfolding pathway of dimeric and monomeric CdGSTM1 were characterised via a thermal shift assay and dynamic multimode spectroscopy (DMS). The thermal shift assay based on intrinsic tryptophan fluorescence revealed that CdGSTM1 underwent a two-state unfolding pathway at pH 1.0-10.0. Its Tm value varied with varying pH. Another orthogonal technique based on far-UV CD also exhibited two-state unfolding in the dimeric and monomeric states. Generally, proteins tend to lose structural integrity and stability at low pH; however, monomeric CdGSTM1 at pH 2.0 was thermally more stable and unfolded with lower van't Hoff enthalpy. The present findings provide essential information regarding the structural, functional, and thermodynamic properties of CdGSTM1 at pH 1.0-10.0.
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Affiliation(s)
- Ajamaluddin Malik
- Department of Biochemistry, Protein Research Chair, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Javed M. Khan
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Salman F. Alamery
- Department of Biochemistry, Protein Research Chair, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Dalia Fouad
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Zoology and Entomology, Faculty of Science, Helwan University, Ein Helwan, Cairo, Egypt
| | - Nikolaos E. Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece
| | - Mohamed S. Daoud
- Department of Biochemistry, Protein Research Chair, College of Science, King Saud University, Riyadh, Saudi Arabia
- King Fahd Unit Laboratory, Department of Clinical and Chemical Pathology, Kasr Al-Ainy University Hospital, Cairo University, El-Manial, Cairo, Egypt
| | - Mohamed O. Abdelkader
- Department of Biochemistry, Protein Research Chair, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Farid S. Ataya
- Department of Biochemistry, Protein Research Chair, College of Science, King Saud University, Riyadh, Saudi Arabia
- Molecular Biology Department, Genetic Engineering Division, National Research Centre, Dokki, Giza, Egypt
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6
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Kalita J, Shukla R, Tripathi T. Structural basis of urea‐induced unfolding of
Fasciola gigantica
glutathione S‐transferase. J Cell Physiol 2018; 234:4491-4503. [DOI: 10.1002/jcp.27253] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/19/2018] [Indexed: 01/15/2023]
Affiliation(s)
- Jupitara Kalita
- Department of Biochemistry Molecular and Structural Biophysics Laboratory, North‐Eastern Hill University Umshing Shillong India
| | - Rohit Shukla
- Department of Biochemistry Molecular and Structural Biophysics Laboratory, North‐Eastern Hill University Umshing Shillong India
| | - Timir Tripathi
- Department of Biochemistry Molecular and Structural Biophysics Laboratory, North‐Eastern Hill University Umshing Shillong India
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7
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Kalita J, Shukla R, Shukla H, Gadhave K, Giri R, Tripathi T. Comprehensive analysis of the catalytic and structural properties of a mu-class glutathione s-transferase from Fasciola gigantica. Sci Rep 2017; 7:17547. [PMID: 29235505 PMCID: PMC5727538 DOI: 10.1038/s41598-017-17678-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 11/28/2017] [Indexed: 01/12/2023] Open
Abstract
Glutathione S‒transferases (GSTs) play an important role in the detoxification of xenobiotics. They catalyze the nucleophilic addition of glutathione (GSH) to nonpolar compounds, rendering the products water-soluble. In the present study, we investigated the catalytic and structural properties of a mu-class GST from Fasciola gigantica (FgGST1). The purified recombinant FgGST1 formed a homodimer composed of 25 kDa subunit. Kinetic analysis revealed that FgGST1 displays broad substrate specificity and shows high GSH conjugation activity toward 1-chloro-2,4-dinitrobenzene, 4-nitroquinoline-1-oxide, and trans-4-phenyl-3-butene-2-one and peroxidase activity towards trans-2-nonenal and hexa-2,4-dienal. The FgGST1 was highly sensitive to inhibition by cibacron blue. The cofactor (GSH) and inhibitor (cibacron blue) were docked, and binding sites were identified. The molecular dynamics studies and principal component analysis indicated the stability of the systems and the collective motions, respectively. Unfolding studies suggest that FgGST1 is a highly cooperative molecule because, during GdnHCl-induced denaturation, a simultaneous unfolding of the protein without stabilization of any partially folded intermediate is observed. The protein is stabilized with a conformational free energy of about 10 ± 0.3 kcal mol-1. Additionally, the presence of conserved Pro-53 and structural motifs such as N-capping box and hydrophobic staple, further aided in the stability and proper folding of FgGST1.
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Affiliation(s)
- Jupitara Kalita
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Rohit Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Harish Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Kundlik Gadhave
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, 175005, India
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, 175005, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India.
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8
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Pairas GN, Tsoungas PG. H-Bond: Τhe Chemistry-Biology H-Bridge. ChemistrySelect 2016; 1:4520-4532. [PMID: 32328512 PMCID: PMC7169486 DOI: 10.1002/slct.201600770] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 07/29/2016] [Indexed: 12/19/2022]
Abstract
H-bonding, as a non covalent stabilizing interaction of diverse nature, has a central role in the structure, function and dynamics of chemical and biological processes, pivotal to molecular recognition and eventually to drug design. Types of conventional and non conventional (H-H, dihydrogen, H- π, CH- π, anti- , proton coordination and H-S) H-bonding interactions are discussed as well as features emerging from their interplay, such as cooperativity (σ- and π-) effects and allostery. Its utility in many applications is described. Catalysis, proton and electron transfer processes in various materials or supramolecular architectures of preorganized hosts for guest binding, are front-line technology. The H-bond-related concept of proton transfer (PT) addresses energy issues or deciphering the mechanism of many natural and synthetic processes. PT is also of paramount importance in the functions of cells and is assisted by large complex proteins embedded in membranes. Both intermolecular and intramolecular PT in H-bonded systems has received attention, theoretically and experimentally, using prototype molecules. It is found in rearrangement reactions, protein functions, and enzyme reactions or across proton channels and pumps. Investigations on the competition between intra- and intermolecular H bonding are discussed. Of particular interest is the H-bond furcation, a common phenomenon in protein-ligand binding. Multiple H-bonding (H-bond furcation) is observed in supramolecular structures.
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Affiliation(s)
- George N. Pairas
- Department of PharmacyLaboratory of Medicinal ChemistryUniversity of PatrasGR-265 04PatrasGreece
| | - Petros G. Tsoungas
- Laboratory of BiochemistryHellenic Pasteur Institute127 Vas. Sofias Ave.GR-115 21AthensGreece
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Pandey T, Singh SK, Chhetri G, Tripathi T, Singh AK. Characterization of a Highly pH Stable Chi-Class Glutathione S-Transferase from Synechocystis PCC 6803. PLoS One 2015; 10:e0126811. [PMID: 25965384 PMCID: PMC4429112 DOI: 10.1371/journal.pone.0126811] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 04/08/2015] [Indexed: 01/01/2023] Open
Abstract
Glutathione S-transferases (GSTs) are multifunctional enzymes present in virtually all organisms. Besides having an essential role in cellular detoxification, they also perform various other functions, including responses in stress conditions and signaling. GSTs are highly studied in plants and animals; however, the knowledge regarding GSTs in cyanobacteria seems rudimentary. In this study, we report the characterization of a highly pH stable GST from the model cyanobacterium- Synechocystis PCC 6803. The gene sll0067 was expressed in Escherichia coli (E. coli), and the protein was purified to homogeneity. The expressed protein exists as a homo-dimer, which is composed of about 20 kDa subunit. The results of the steady-state enzyme kinetics displayed protein’s glutathione conjugation activity towards its class specific substrate- isothiocyanate, having the maximal activity with phenethyl isothiocyanate. Contrary to the poor catalytic activity and low specificity towards standard GST substrates such as 1-chloro-2,4-dinitrobenzene by bacterial GSTs, PmGST B1-1 from Proteus mirabilis, and E. coli GST, sll0067 has broad substrate degradation capability like most of the mammalian GST. Moreover, we have shown that cyanobacterial GST sll0067 is catalytically efficient compared to the best mammalian enzymes. The structural stability of GST was studied as a function of pH. The fluorescence and CD spectroscopy in combination with size exclusion chromatography showed a highly stable nature of the protein over a broad pH range from 2.0 to 11.0. To the best of our knowledge, this is the first GST with such a wide range of pH related structural stability. Furthermore, the presence of conserved Proline-53, structural motifs such as N-capping box and hydrophobic staple further aid in the stability and proper folding of cyanobacterial GST- sll0067.
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Affiliation(s)
- Tripti Pandey
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, India
| | - Sudhir Kumar Singh
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, India
| | - Gaurav Chhetri
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, India
- * E-mail: (TT); (AKS)
| | - Arvind Kumar Singh
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, India
- * E-mail: (TT); (AKS)
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10
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Zhou X, Gao L, Yang G, Liu D, Bai A, Li B, Deng Z, Feng Y. Design of hyperthermophilic lipase chimeras by key motif-directed recombination. Chembiochem 2014; 16:455-62. [PMID: 25530200 DOI: 10.1002/cbic.201402456] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Indexed: 11/12/2022]
Abstract
Recombination of diverse natural evolved domains within a superfamily offers greater opportunity for enzyme function leaps. How to recombine protein modules from distant parents with less disruption in cross-interfaces is a challenging issue. Here, we identified the existence of a key motif, the sequence VVSVN(D)YR, within a structural motif ψ loop in the α/β-hydrolase fold superfamily, by using a MEME server and the PROMOTIF program. To obtain thermostable lipase-like enzymes, two chimeras were engineered at the key motif regions through recombination of domains from a mesophilic lipase and a hyperthermophilic esterase/peptidase with amino acid identity less than 21 %. The chimeras retained the desirable substrate preference of their mesophilic parent and exhibited more than 100-fold increased thermostability at 50 °C. Through site-directed mutation, we further improved activity of the chimera by 4.6-fold. The recombination strategy presented here enables the creation of novel catalysts.
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Affiliation(s)
- Xiaoli Zhou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240 (P. R. China); Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun 130023 (P. R. China)
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11
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Longkumer T, Parthasarathy S, Vemuri SG, Siddavattam D. OxyR-dependent expression of a novel glutathione S-transferase (Abgst01) gene in Acinetobacter baumannii DS002 and its role in biotransformation of organophosphate insecticides. MICROBIOLOGY-SGM 2013; 160:102-112. [PMID: 24136898 DOI: 10.1099/mic.0.070664-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
While screening a genomic library of Acinetobacter baumannii DS002 isolated from organophosphate (OP)-polluted soils, nine ORFs were identified coding for glutathione S-transferase (GST)-like proteins. These GSTs (AbGST01-AbGST09) are phylogenetically related to a number of well-characterized GST classes found in taxonomically diverse groups of organisms. Interestingly, expression of Abgst01 (GenBank accession no. KF151191) was upregulated when the bacterium was grown in the presence of an OP insecticide, methyl parathion (MeP). The gene product, AbGST01, dealkylated MeP to desMeP. An OxyR-binding motif was identified directly upstream of Abgst01. An Abgst-lacZ gene fusion lacking the OxyR-binding site showed a drastic reduction in promoter activity. Very low β-galactosidase activity levels were observed when the Abgst-lacZ fusion was mobilized into an oxyR (GenBank accession no. KF151190) null mutant of A. baumannii DS002, confirming the important role of OxyR. The OxyR-binding sites are not found upstream of other Abgst (Abgst02-Abgst09) genes. However, they contained consensus sequence motifs that can serve as possible target sites for certain well-characterized transcription factors. In support of this observation, the Abgst genes responded differentially to different oxidative stress inducers. The Abgst genes identified in A. baumannii DS002 are found to be conserved highly among all known genome sequences of A. baumannii strains. The versatile ecological adaptability of A. baumannii strains is apparent if sequence conservation is seen together with their involvement in detoxification processes.
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Affiliation(s)
- Toshisangba Longkumer
- Department of Animal Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - Sunil Parthasarathy
- Department of Animal Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - Sujana Ghanta Vemuri
- Department of Animal Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - Dayananda Siddavattam
- Department of Animal Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
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12
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A glutathione transferase from Agrobacterium tumefaciens reveals a novel class of bacterial GST superfamily. PLoS One 2012; 7:e34263. [PMID: 22496785 PMCID: PMC3319563 DOI: 10.1371/journal.pone.0034263] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 02/24/2012] [Indexed: 01/07/2023] Open
Abstract
In the present work, we report a novel class of glutathione transferases (GSTs) originated from the pathogenic soil bacterium Agrobacterium tumefaciens C58, with structural and catalytic properties not observed previously in prokaryotic and eukaryotic GST isoenzymes. A GST-like sequence from A. tumefaciens C58 (Atu3701) with low similarity to other characterized GST family of enzymes was identified. Phylogenetic analysis showed that it belongs to a distinct GST class not previously described and restricted only in soil bacteria, called the Eta class (H). This enzyme (designated as AtuGSTH1-1) was cloned and expressed in E. coli and its structural and catalytic properties were investigated. Functional analysis showed that AtuGSTH1-1 exhibits significant transferase activity against the common substrates aryl halides, as well as very high peroxidase activity towards organic hydroperoxides. The crystal structure of AtuGSTH1-1 was determined at 1.4 Å resolution in complex with S-(p-nitrobenzyl)-glutathione (Nb-GSH). Although AtuGSTH1-1 adopts the canonical GST fold, sequence and structural characteristics distinct from previously characterized GSTs were identified. The absence of the classic catalytic essential residues (Tyr, Ser, Cys) distinguishes AtuGSTH1-1 from all other cytosolic GSTs of known structure and function. Site-directed mutagenesis showed that instead of the classic catalytic residues, an Arg residue (Arg34), an electron-sharing network, and a bridge of a network of water molecules may form the basis of the catalytic mechanism. Comparative sequence analysis, structural information, and site-directed mutagenesis in combination with kinetic analysis showed that Phe22, Ser25, and Arg187 are additional important residues for the enzyme's catalytic efficiency and specificity.
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13
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Allocati N, Federici L, Masulli M, Di Ilio C. Distribution of glutathione transferases in Gram-positive bacteria and Archaea. Biochimie 2011; 94:588-96. [PMID: 21945597 DOI: 10.1016/j.biochi.2011.09.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 09/08/2011] [Indexed: 11/29/2022]
Abstract
Glutathione transferases (GSTs) have been widely studied in Gram-negative bacteria and the structure and function of several representatives have been elucidated. Conversely, limited information is available about the occurrence, classification and functional features of GSTs both in Gram-positive bacteria and in Archaea. An analysis of 305 fully-sequenced Gram-positive genomes highlights the presence of 49 putative GST genes in the genera of both Firmicutes and Actinobacteria phyla. We also performed an analysis on 81 complete genomes of the Archaea domain. Eleven hits were found in the Halobacteriaceae family of the Euryarchaeota phylum and only one in the Crenarchaeota phylum. A comparison of the identified sequences with well-characterized GSTs belonging to both Gram-negative and eukaryotic GSTs sheds light on their putative function and the evolutionary relationships within the large GST superfamily. This analysis suggests that the identified sequences mainly cluster in the new Xi class, while Beta class GSTs, widely distributed in Gram-negative bacteria, are under-represented in Gram-positive bacteria and absent in Archaea.
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Affiliation(s)
- Nerino Allocati
- Dipartimento di Scienze Biomediche, Università G. d'Annunzio, Via dei Vestini 31, I-66013 Chieti, Italy
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Overlapping protective roles for glutathione transferase gene family members in chemical and oxidative stress response in Agrobacterium tumefaciens. Funct Integr Genomics 2011; 12:157-72. [PMID: 21909786 DOI: 10.1007/s10142-011-0248-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 08/06/2011] [Accepted: 08/16/2011] [Indexed: 10/17/2022]
Abstract
In the present work, we describe the characterisation of the glutathione transferase (GST) gene family from Agrobacterium tumefaciens C58. A genome survey revealed the presence of eight GST-like proteins in A. tumefaciens (AtuGSTs). Comparison by multiple sequence alignment generated a dendrogram revealing the phylogenetic relationships of AtuGSTs-like proteins. The beta and theta classes identified in other bacterial species are represented by five members in A. tumefaciens C58. In addition, there are three "orphan" sequences that do not fit into any previously recognised GST classes. The eight GST-like genes were cloned, expressed in Escherichia coli and their substrate specificity was determined towards 17 different substrates. The results showed that AtuGSTs catalyse a broad range of reactions, with different members of the family exhibiting quite varied substrate specificity. The 3D structures of AtuGSTs were predicted using molecular modelling. The use of comparative sequence and structural analysis of the AtuGST isoenzymes allowed us to identify local sequence and structural characteristics between different GST isoenzymes and classes. Gene expression profiling was conducted under normal culture conditions as well as under abiotic stress conditions (addition of xenobiotics, osmotic stress and cold and heat shock) to induce and monitor early stress-response mechanisms. The results reveal the constitutive expression of GSTs in A. tumefaciens and a modulation of GST activity after treatments, indicating that AtuGSTs presumably participate in a wide range of functions, many of which are important in counteracting stress conditions. These functions may be relevant to maintaining cellular homeostasis as well as in the direct detoxification of toxic compounds.
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Federici L, Masulli M, Gianni S, Di Ilio C, Allocati N. A conserved hydrogen-bond network stabilizes the structure of Beta class glutathione S-transferases. Biochem Biophys Res Commun 2009; 382:525-9. [DOI: 10.1016/j.bbrc.2009.03.052] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Accepted: 03/10/2009] [Indexed: 11/24/2022]
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Abstract
Bacterial glutathione transferases (GSTs) are part of a superfamily of enzymes that play a key role in cellular detoxification. GSTs are widely distributed in prokaryotes and are grouped into several classes. Bacterial GSTs are implicated in a variety of distinct processes such as the biodegradation of xenobiotics, protection against chemical and oxidative stresses and antimicrobial drug resistance. In addition to their role in detoxification, bacterial GSTs are also involved in a variety of distinct metabolic processes such as the biotransformation of dichloromethane, the degradation of lignin and atrazine, and the reductive dechlorination of pentachlorophenol. This review article summarizes the current status of knowledge regarding the functional and structural properties of bacterial GSTs.
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Affiliation(s)
- Nerino Allocati
- Dipartimento di Scienze Biomediche, Università G. d'Annunzio, Chieti, Italy.
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Characterization of the activity and folding of the glutathione transferase from Escherichia coli and the roles of residues Cys(10) and His(106). Biochem J 2009; 417:55-64. [PMID: 18778244 DOI: 10.1042/bj20071702] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
GSTs (glutathione transferases) are an important class of enzymes involved in cellular detoxification. GSTs are found in all classes of organisms and are implicated in resistance towards drugs, pesticides, herbicides and antibiotics. The activity, structure and folding, particularly of eukaryotic GSTs, have therefore been widely studied. The crystal structure of EGST (GST from Escherichia coli) was reported around 10 years ago and it suggested Cys(10) and His(106) as potential catalytic residues. However, the role of these residues in catalysis has not been further investigated, nor have the folding properties of the protein been described. In the present study we investigated the contributions of residues Cys(10) and His(106) to the activity and stability of EGST. We found that EGST shows a complex equilibrium unfolding profile, involving a population of at least two partially folded intermediates, one of which is dimeric. Mutation of residues Cys(10) and His(106) leads to stabilization of the protein and affects the apparent steady-state kinetic parameters for enzyme catalysis. The results suggest that the imidazole ring of His(106) plays an important role in the catalytic mechanism of the enzyme, whereas Cys(10) is involved in binding of the substrate, glutathione. Engineering of the Cys(10) site can be used to increase both the stability and GST activity of EGST. However, in addition to GST activity, we discovered that EGST also possesses thiol:disulfide oxidoreductase activity, for which the residue Cys(10) plays an essential role. Further, tryptophan quenching experiments indicate that a mixed disulfide is formed between the free thiol group of Cys(10) and the substrate, glutathione.
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Wiktelius E, Stenberg G. Novel class of glutathione transferases from cyanobacteria exhibit high catalytic activities towards naturally occurring isothiocyanates. Biochem J 2007; 406:115-23. [PMID: 17484723 PMCID: PMC1948994 DOI: 10.1042/bj20070328] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In the present paper, we report a novel class of GSTs (glutathione transferases), called the Chi class, originating from cyanobacteria and with properties not observed previously in prokaryotic enzymes. GSTs constitute a widespread multifunctional group of proteins, of which mammalian enzymes are the best characterized. Although GSTs have their origin in prokaryotes, few bacterial representatives have been characterized in detail, and the catalytic activities and substrate specificities observed have generally been very modest. The few well-studied bacterial GSTs have largely unknown physiological functions. Genome databases reveal that cyanobacteria have an extensive arsenal of glutathione-associated proteins. We have studied two cyanobacterial GSTs which are the first examples of bacterial enzymes that are as catalytically efficient as the best mammalian enzymes. GSTs from the thermophile Thermosynechococcus elongatus BP-1 and from Synechococcus elongatus PCC 6301 were found to catalyse the conjugation of naturally occurring plant-derived isothiocyanates to glutathione at high rates. The cyanobacterial GSTs studied are smaller than previously described members of this enzyme family, but display many of the typical structural features that are characteristics of GSTs. They are also active towards several classical substrates, but at the same moderate rates that have been observed for other GSTs derived from prokaryotes. The cloning, expression and characterization of two cyanobacterial GSTs are described. The possible significance of the observed catalytic properties is discussed in the context of physiological relevance and GST evolution.
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Affiliation(s)
- Eric Wiktelius
- Department of Biochemistry and Organic Chemistry, Biomedical Centre, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Gun Stenberg
- Department of Biochemistry and Organic Chemistry, Biomedical Centre, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
- To whom correspondence should be addressed (email )
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Abstract
The characteristics of N--H...O, O--H...O, and C--H...O hydrogen bonds and other weak intermolecular interactions are analyzed in a large and diverse group of 251 protein-ligand complexes using a new computer program that was developed in-house for this purpose. The interactions examined in the present study are those which occur in the active sites, defined here as a sphere of 10 A radius around the ligand. Notably, N--H...O and O--H...O bonds tend towards linearity. Multifurcated interactions are especially common, especially multifurcated acceptors, and the average degree of furcation is 2.6 hydrogen bonds per furcated acceptor. A significant aspect of this study is that we have been able to assess the reliability of hydrogen bond geometry as a function of crystallographic resolution. Thresholds of 2.3 and 2.0 A are established for strong and weak hydrogen bonds, below which hydrogen bond geometries may be safely considered for detailed analysis. Interactions involving water as donor or acceptor, and C--H...O bonds with Gly and Tyr as donors are ubiquitous in the active site. A similar trend was observed in an external test set of 233 protein-ligand complexes belonging to the kinase family. Weaker interactions like X--H...pi (X = C, N, O) and those involving halogen atoms as electrophiles or nucleophiles have also been studied. We conclude that the strong and weak hydrogen bonds are ubiquitous in protein-ligand recognition, and that with suitable computational tools very large numbers of strong and weak intermolecular interactions in the ligand-protein interface may be analyzed reliably. Results confirm earlier trends reported previously by us but the extended nature of the present data set mean that the observed trends are more reliable.
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Affiliation(s)
- Sunil K Panigrahi
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India
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Tocheva EI, Fortin PD, Eltis LD, Murphy MEP. Structures of Ternary Complexes of BphK, a Bacterial Glutathione S-Transferase That Reductively Dechlorinates Polychlorinated Biphenyl Metabolites. J Biol Chem 2006; 281:30933-40. [PMID: 16920719 DOI: 10.1074/jbc.m603125200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Prokaryotic glutathione S-transferases are as diverse as their eukaryotic counterparts but are much less well characterized. BphK from Burkholderia xenovorans LB400 consumes two GSH molecules to reductively dehalogenate chlorinated 2-hydroxy-6-oxo-6-phenyl-2,4-dienoates (HOPDAs), inhibitory polychlorinated biphenyl metabolites. Crystallographic structures of two ternary complexes of BphK were solved to a resolution of 2.1A. In the BphK-GSH-HOPDA complex, GSH and HOPDA molecules occupy the G- and H-subsites, respectively. The thiol nucleophile of the GSH molecule is positioned for SN2 attack at carbon 3 of the bound HOPDA. The respective sulfur atoms of conserved Cys-10 and the bound GSH are within 3.0A, consistent with product release and the formation of a mixed disulfide intermediate. In the BphK-(GSH)2 complex, a GSH molecule occupies each of the two subsites. The three sulfur atoms of the two GSH molecules and Cys-10 are aligned suitably for a disulfide exchange reaction that would regenerate the resting enzyme and yield disulfide-linked GSH molecules. A second conserved residue, His-106, is adjacent to the thiols of Cys-10 and the GSH bound to the G-subsite and thus may stabilize a transition state in the disulfide exchange reaction. Overall, the structures support and elaborate a proposed dehalogenation mechanism for BphK and provide insight into the plasticity of the H-subsite.
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Affiliation(s)
- Elitza I Tocheva
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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