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Hilario E, De Keyser S, Fan L. Structural and biochemical characterization of a glutathione transferase from the citrus canker pathogen Xanthomonas. Acta Crystallogr D Struct Biol 2020; 76:778-789. [PMID: 32744260 PMCID: PMC7397488 DOI: 10.1107/s2059798320009274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 07/07/2020] [Indexed: 11/10/2022] Open
Abstract
The genus Xanthomonas comprises several cosmopolitan plant-pathogenic bacteria that affect more than 400 plant species, most of which are of economic interest. Citrus canker is a bacterial disease that affects citrus species, reducing fruit yield and quality, and is caused by the bacterium Xanthomonas citri subsp. citri (Xac). The Xac3819 gene, which has previously been reported to be important for citrus canker infection, encodes an uncharacterized glutathione S-transferase (GST) of 207 amino-acid residues in length (XacGST). Bacterial GSTs are implicated in a variety of metabolic processes such as protection against chemical and oxidative stresses. XacGST shares high sequence identity (45%) with the GstB dehalogenase from Escherichia coli O6:H1 strain CFT073 (EcGstB). Here, XacGST is reported to be able to conjugate glutathione (GSH) with bromoacetate with a Km of 6.67 ± 0.77 mM, a kcat of 42.69 ± 0.32 s-1 and a kcat/Km of 6.40 ± 0.72 mM-1 s-1 under a saturated GSH concentration (3.6 mM). These values are comparable to those previously reported for EcGstB. In addition, crystal structures of XacGST were determined in the apo form (PDB entry 6nxv) and in a GSH-bound complex (PDB entry 6nv6). XacGST has a canonical GST-like fold with a conserved serine residue (Ser12) at the GSH-binding site near the N-terminus, indicating XacGST to be a serine-type GST that probably belongs to the theta-class GSTs. GSH binding stabilizes a loop of about 20 residues containing a helix that is disordered in the apo XacGST structure.
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Affiliation(s)
- Eduardo Hilario
- Department of Biochemistry, University of California-Riverside, Riverside, California, USA
| | - Sawyer De Keyser
- Department of Biochemistry, University of California-Riverside, Riverside, California, USA
| | - Li Fan
- Department of Biochemistry, University of California-Riverside, Riverside, California, USA
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Ang TF, Maiangwa J, Salleh AB, Normi YM, Leow TC. Dehalogenases: From Improved Performance to Potential Microbial Dehalogenation Applications. Molecules 2018; 23:E1100. [PMID: 29735886 PMCID: PMC6100074 DOI: 10.3390/molecules23051100] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/07/2018] [Accepted: 04/09/2018] [Indexed: 11/16/2022] Open
Abstract
The variety of halogenated substances and their derivatives widely used as pesticides, herbicides and other industrial products is of great concern due to the hazardous nature of these compounds owing to their toxicity, and persistent environmental pollution. Therefore, from the viewpoint of environmental technology, the need for environmentally relevant enzymes involved in biodegradation of these pollutants has received a great boost. One result of this great deal of attention has been the identification of environmentally relevant bacteria that produce hydrolytic dehalogenases—key enzymes which are considered cost-effective and eco-friendly in the removal and detoxification of these pollutants. These group of enzymes catalyzing the cleavage of the carbon-halogen bond of organohalogen compounds have potential applications in the chemical industry and bioremediation. The dehalogenases make use of fundamentally different strategies with a common mechanism to cleave carbon-halogen bonds whereby, an active-site carboxylate group attacks the substrate C atom bound to the halogen atom to form an ester intermediate and a halide ion with subsequent hydrolysis of the intermediate. Structurally, these dehalogenases have been characterized and shown to use substitution mechanisms that proceed via a covalent aspartyl intermediate. More so, the widest dehalogenation spectrum of electron acceptors tested with bacterial strains which could dehalogenate recalcitrant organohalides has further proven the versatility of bacterial dehalogenators to be considered when determining the fate of halogenated organics at contaminated sites. In this review, the general features of most widely studied bacterial dehalogenases, their structural properties, basis of the degradation of organohalides and their derivatives and how they have been improved for various applications is discussed.
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Affiliation(s)
- Thiau-Fu Ang
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Jonathan Maiangwa
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Abu Bakar Salleh
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Institute of Bioscience, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Yahaya M Normi
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Thean Chor Leow
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Institute of Bioscience, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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Sudi IY, Shamsir MS, Jamaluddin H, Wahab RA, Huyop F. Interactions of non-natural halogenated substrates with D-specific dehalogenase (DehD) mutants using in silico studies. BIOTECHNOL BIOTEC EQ 2014; 28:949-957. [PMID: 26019583 PMCID: PMC4433833 DOI: 10.1080/13102818.2014.960663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 07/17/2014] [Indexed: 10/26/2022] Open
Abstract
The D-2-haloacid dehalogenase of D-specific dehalogenase (DehD) from Rhizobium sp. RC1 catalyses the hydrolytic dehalogenation of D-haloalkanoic acids, inverting the substrate-product configuration and thereby forming the corresponding L-hydroxyalkanoic acids. Our investigations were focused on DehD mutants: R134A and Y135A. We examined the possible interactions between these mutants with haloalkanoic acids and characterized the key catalytic residues in the wild-type dehalogenase, to design dehalogenase enzyme(s) with improved potential for dehalogenation of a wider range of substrates. Three natural substrates of wild-type DehD, specifically, monochloroacetate, monobromoacetate and D,L-2,3-dichloropropionate, and eight other non-natural haloalkanoic acids substrates of DehD, namely, L-2-chloropropionate; L-2-bromopropionate; 2,2-dichloropropionate; dichloroacetate; dibromoacetate; trichloroacetate; tribromoacetate; and 3-chloropropionate, were docked into the active site of the DehD mutants R134A and Y135A, which produced altered catalytic functions. The mutants interacted strongly with substrates that wild-type DehD does not interact with or degrade. The interaction was particularly enhanced with 3-chloropropionate, in addition to monobromoacetate, monochloroacetate and D,L-2,3-dichloropropionate. In summary, DehD variants R134A and Y135A demonstrated increased propensity for binding haloalkanoic acid and were non-stereospecific towards halogenated substrates. The improved characteristics in these mutants suggest that their functionality could be further exploited and harnessed in bioremediations and biotechnological applications.
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Affiliation(s)
- Ismaila Yada Sudi
- Department of Biotechnology and Medical Engineering, Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia
| | - Mohd Shahir Shamsir
- Department of Biotechnology and Medical Engineering, Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia
| | - Haryati Jamaluddin
- Department of Biotechnology and Medical Engineering, Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia
| | - Fahrul Huyop
- Department of Biotechnology and Medical Engineering, Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia
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Floor RJ, Wijma HJ, Colpa DI, Ramos-Silva A, Jekel PA, Szymański W, Feringa BL, Marrink SJ, Janssen DB. Computational library design for increasing haloalkane dehalogenase stability. Chembiochem 2014; 15:1660-72. [PMID: 24976371 DOI: 10.1002/cbic.201402128] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Indexed: 11/05/2022]
Abstract
We explored the use of a computational design framework for the stabilization of the haloalkane dehalogenase LinB. Energy calculations, disulfide bond design, molecular dynamics simulations, and rational inspection of mutant structures predicted many stabilizing mutations. Screening of these in small mutant libraries led to the discovery of seventeen point mutations and one disulfide bond that enhanced thermostability. Mutations located in or contacting flexible regions of the protein had a larger stabilizing effect than mutations outside such regions. The combined introduction of twelve stabilizing mutations resulted in a LinB mutant with a 23 °C increase in apparent melting temperature (Tm,app , 72.5 °C) and an over 200-fold longer half-life at 60 °C. The most stable LinB variants also displayed increased compatibility with co-solvents, thus allowing substrate conversion and kinetic resolution at much higher concentrations than with the wild-type enzyme.
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Affiliation(s)
- Robert J Floor
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands)
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Huang X, Wang C, Celeste LR, Lovelace LL, Sun S, Dawson JH, Lebioda L. Complex of myoglobin with phenol bound in a proximal cavity. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1465-71. [PMID: 23192025 PMCID: PMC3509966 DOI: 10.1107/s1744309112045514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 11/03/2012] [Indexed: 11/10/2022]
Abstract
Sperm whale myoglobin (Mb) has weak dehaloperoxidase activity and catalyzes the peroxidative dehalogenation of 2,4,6-trichlorophenol (TCP) to 2,6-dichloroquinone. Crystals of Mb and of its more active G65T variant were used to study the binding of TCP, 4-iodophenol (4-IP) and phenol. The structures of crystals soaked overnight in a 10 mM solution of phenol revealed that a phenol molecule binds in the proximal cavity, forming a hydrogen bond to the hydroxyl of Tyr146 and hydrophobic contacts which include interactions with Cβ and Cγ of the proximal histidine His93. The phenol position corresponds to the strongest xenon binding site, Xe1. It appears that the ligand enters the proximal cavity through a gate formed by the flexible loops 79-86 and 93-103. TCP and 4-IP do not bind to Mb in this manner under similar conditions; however, it appears to be likely that dimethyl sulfoxide (DMSO), which was used at a concentration of 0.8 M to facilitate 4-IP dissolution, binds in the phenol/Xe1 binding site. In this structure, a water molecule coordinated to the heme iron was replaced by an oxygen molecule, reflecting the reduction of the heme. Crystals of Mb and G65T Mb soaked for 5-10 min did not show bound phenol. Kinetic studies of TCP dechlorination showed that phenol has a dual effect: it acts as a competitive inhibitor that is likely to interfere with TCP binding at the heme edge and as a weak activator, likely through binding in the proximal cavity. The lack of phenol bound at the heme edge in the crystal structures suggests that its inhibitory binding only takes place when the heme is activated by hydrogen peroxide.
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Affiliation(s)
- Xiao Huang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 20208, USA
| | - Chunxue Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 20208, USA
| | - Lesa R. Celeste
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 20208, USA
| | - Leslie L. Lovelace
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 20208, USA
| | - Shenfang Sun
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 20208, USA
| | - John H. Dawson
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 20208, USA
- School of Medicine, University of South Carolina, Columbia, SC 20208, USA
| | - Lukasz Lebioda
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 20208, USA
- South Carolina Colon Cancer Center, University of South Carolina, Columbia, SC 29210, USA
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Pegan SD, Serrano H, Whitman CP, Mesecar AD. Structural and mechanistic analysis of trans-3-chloroacrylic acid dehalogenase activity. Acta Crystallogr D Biol Crystallogr 2008; 64:1277-82. [PMID: 19018104 PMCID: PMC2631126 DOI: 10.1107/s0907444908034707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Accepted: 10/23/2008] [Indexed: 11/10/2022]
Abstract
Trans-3-chloroacrylic acid dehalogenase (CaaD) is a critical enzyme in the trans-1,3-dichloropropene (DCP) degradation pathway in Pseudomonas pavonaceae 170. This enzyme allows bacteria to use trans-DCP, a common component in commercially produced fumigants, as a carbon source. CaaD specifically catalyzes the fourth step of the pathway by cofactor-independent dehalogenation of a vinyl carbon-halogen bond. Previous studies have reported an X-ray structure of CaaD under acidic conditions with a covalent modification of the catalytic betaPro1 residue. Here, the 1.7 A resolution X-ray structure of CaaD under neutral (pH 6.5) conditions is reported without the presence of the covalent adduct. In this new structure, a substrate-like acetate molecule is bound within the active site in a position analogous to the putative substrate-binding site. Additionally, a catalytically important water molecule was identified, consistent with previously proposed reaction schemes. Finally, flexibility of the catalytically relevant side chain alphaGlu52 is observed in the structure, supporting its role in the catalytic mechanism.
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Affiliation(s)
- Scott D. Pegan
- Center of Pharmaceutical Biotechnology and the Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, Chicago, USA
| | - Hector Serrano
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas, Austin, USA
| | - Christian P. Whitman
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas, Austin, USA
| | - Andrew D. Mesecar
- Center of Pharmaceutical Biotechnology and the Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, Chicago, USA
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Omi R, Jitsumori K, Yamauchi T, Ichiyama S, Kurihara T, Esaki N, Kamiya N, Hirotsu K, Miyahara I. Expression, purification and preliminary X-ray characterization of DL-2-haloacid dehalogenase from Methylobacterium sp. CPA1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:586-9. [PMID: 17620717 PMCID: PMC2335131 DOI: 10.1107/s1744309107027273] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2007] [Accepted: 06/04/2007] [Indexed: 05/16/2023]
Abstract
DL-2-Haloacid dehalogenase from Methylobacterium sp. CPA1 (DL-DEX Mb) is a unique enzyme that catalyzes the dehalogenation reaction without the formation of an ester intermediate. A recombinant form of DL-DEX Mb has been expressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. The crystal belongs to the hexagonal space group P6(3), with unit-cell parameters a = b = 186.2, c = 114.4 A. The crystals are likely to contain between four and eight monomers in the asymmetric unit, with a V(M) value of 4.20-2.10 A3 Da(-1). A self-rotation function revealed peaks on the chi = 180 degrees section. X-ray data have been collected to 1.75 A resolution.
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Affiliation(s)
- Rie Omi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Department of Chemistry, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Keiji Jitsumori
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Takahiro Yamauchi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Susumu Ichiyama
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tatsuo Kurihara
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Nobuyoshi Esaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Nobuo Kamiya
- Department of Chemistry, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Ken Hirotsu
- Department of Chemistry, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Ikuko Miyahara
- Department of Chemistry, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
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