Dehalogenases: From Improved Performance to Potential Microbial Dehalogenation Applications
Abstract
:1. Introduction
1.1. Dehalogenases and Different Dehalogenation Processes
1.1.1. Reductive Dehalogenation
1.1.2. Hydrolytic Dehalogenation
1.1.3. The Haloacid Dehalogenase
1.1.4. The Haloalkane Dehalogenase
1.1.5. The Fluoroacetate Dehalogenase
1.1.6. The 4-Chlorobenzoyl CoA Dehalogenase
1.2. Microbial Dehalogenation and Their Significant Properties
1.3. Structural Studies on Dehalogenases and Reaction Mechanisms
1.4. Protein Engineering in Dehalogenases
1.5. Screening and Prospecting of Dehalogenase in Microbes
1.6. Metal Co-Factor-Dependent Dehalogenases
1.7. Creating an Artificial Metal Binding Site
1.8. Potential Applications of Dehalogenases
1.8.1. Application in the Construction of Expression Cassettes
1.8.2. Application in the Production of Useful Compounds
1.8.3. Applications in Bioremediation
1.8.4. Applications in Drinking Water Treatment
1.8.5. Applications in Detoxification
1.8.6. Applications in Decontamination
1.8.7. Applications in Biosensing
1.9. Other Persistent Organic Pollutant (POPS) of PCDD/Fs
2. Conclusions
Acknowledgments
Conflicts of Interest
References
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Sample Availability: Samples of the compounds are not available from the authors. |
Organism | Dehalogenase Designate | Habitats | Substrate of Halogenation | Corresponding Product | Property of Reaction Mechanism | References |
---|---|---|---|---|---|---|
Moraxella Sp. strain B | haloacetate dehalogenase H-1 and H-2 | soil | l-2-haloacid | d-2-hydroxy acids | stereospecific | [95] |
Pseudomonas Sp. YL, Pseudomonas putida No. l09, Pseudomonas Sp. CBS3 | l-2-haloacid dehalogenase, 2-haloacid dehalogenase | soil | l-2- chloropropionate, 2-monochloropropionate | lactate, glyoxylate, and pyruvate | stereospecific | [49,57,96] |
Pseudomonas cepacia MBA4 | l-2-haloalkanoic acid dehalogenase IVa | soil | monobromoacetic acid | N.S | stereospecific | [47] |
Xanthobacter autotrophicus GJ10 | haloacid dehalogenase (dhlB) | soil | 2-halogenated carboxylic acids | d-Lactate | stereospecific | [53,97] |
Pseudomonas. putida AJ1 (hadL) | l-2-haloakanoic acid halidohydrolase | soil | 2-monochloropropionic acid | lactate with the release of chloride | stereospecific | [98] |
Pseudomonas Sp. 113 | d,l-2-haloacid dehalogenase | d- and l-2-haloalkanoic acids, producing | l- and d-2-hydroxyalkanoic acids | non-stereospecific | [51] | |
Pseudomonas putida strain PP3 | α-haloacid dehalogenase DehI and DehII | soil | d- and l-2-haloalkanoic acids | l- and d-2-hydroxyalkanoic | stereospecific | [99] |
Microbacterium Sp. strain, ITRC1 | hydrolytic dehalogenase (linB) and dehydrogenase (linC) | soil | γ-pentachlorocyclohexen and a 2,5-dichloro-2,5-cyclohexadiene-1,4-diol | 2,5-dichlorophenol (2,5-DCP) | non-stereospecific | [100] |
Agrobacterium tumefaciens RS5 | hydrolytic haloalkanoic acid dehalogenase (DhlS5II) and cryptic l-isomer-specific dehalogenase (DhlS5I) | soil | 2,2-dichloropropionate (DCPA), chloroacetic acid (MCA), dichloroacetic acid (DCA), and 2-chloropropionic acid (CPA) | N.S | non-stereospecific and stereospecific | [101] |
Burkholderia cepacia MBA4 | dehalogenase IVa (hdlIVa) | soil | l-2-haloacid | d-2-hydroxyacids | stereospecific | [47,56] |
Pseudomonas pavonaceae | cis- and trans-3-chloroacrylic acid dehalogenase (CaaD and cis-CaaD) | soil | cis- and trans-3-chloroacrylate | malonate semialdehyde | specific hydrolysis | [102] |
Burkholderia Sp. WS | (S)-2-haloacid dehalogenase, 2-haloacrylate r | soil | (S)-2-haloalkanoic acids, 2-chloroacrylate | (S)-2-chloropropionate, (R)-lactate, (S)-2-chloropropionic | NADPH-dependent reduction | [103,104] |
Pseudomonas Sp. Strain CBS3 | 4-chlorobenzoate dehalogenase | soil | 4-chlorobenzoate | 4-hydroxybenzoate | non-stereospecific | [105] |
Pseudomonas Sp. strain YL | 2-haloacrylate hydratase l-2-haloacid dehalogenase (l-DEX) (d,l-DEX) | soil | l-2-chloropropionate –chloroacrylate (2-CAA) of l and d isomers of 2-CPA of l-2-haloalkanoic acid, monochloroacetate and monoiodoacetate, as 2-bromohexadecanoate | 2-chloro-2-hydroxypropionate, d- and l-lactates, d-2-hydroxyalkanoic acids | Stereo and non-stereospecific | [106] |
Methylobacterium Sp. CPA1 (dl-DEX Mb) | d,l-2-Haloacid dehalogenase | soil | d- and l-2-haloalkanoic acids, d- and L-2-chloropropionates | l- and d-2-hydroxyalkanoic acids | non-stereospecific | [50] |
Sulfolobus tokodaii | l-2-haloacid dehalogenase | soil | chloropropionic acid | stereospecific | [107] | |
Marine Rhodobacteraceae | l-haloacid dehalogenase | soil | monobromoacetic acid (100%) followed by monochloroacetic acid (MCAA) (71%), S-bromopropionic acid (71%), S-chloropropionic acid (MCPA) (10%) and dichloroacetic acid | N.S | stereospecific | [108] |
Burkholderia Sp. FA1 | fluroacetate dehalogenase | soil | fluoroacetate to glycolate | glycolate | non-stereospecific | [74] |
Rhodopseudomonas palustris CGA009 | reductive dehalogenase | soil | 3-chlorobenzoate | 3-chlorobenzoyl coenzyme A (3-chlorobenzoyl–CoA) to benzoyl-CoA and further to | non-stereospecific | [109] |
Rhodococcus Sp. m15-3 (DhaA) and Xanthobacter autotrophicus GJ10 (DhlA) | haloalkane dehalogenase | soil | 1,2-dichloroethane andtrihalopropanes to 2,3-dihalogenated propanols | 2-chloroethanol, chloroacetaldehyde, chloroacetate, and glycolate | non-stereospecific | [110,111] |
Alcanivorax dieselolei B-5 | haloalkane Dehalogenase (DadB) | arctic Ocean | haloalkanes | alkanols | non-stereospecific | [112,113,114] |
Pseudomonas Sp. strain 113 | d,l-2-haloacid Dehalogenase, | soil | d - and l-2-chloropropionates, trichloroacetate | l- and d-lactates, oxalate | non-stereospecific dehalogenation | [59] |
Arthrobacter Sp. strain TM-1 | 4-chlorobenzoyl-coenzyme A dehalogenase | soil | 4-chlorobenzoyl coenzyme A (4-CBA-CoA), 4-chlorobenzoyl-CoA | 4-hydroxybenzoyl coenzyme A (4-HBA-CoA), 4-hydroxybenzoyl-CoA | hydrolytic substitution | [115] |
Paracoccus Sp. DEH99 | 2-haloacid dehalogenase | Marine sponge H. perlevis | 2-CPA, 2-bromopropionic acid (2-BPA), and iodoacetic acid | chiral reagents | stereospecific dehalogenation | [116] |
Alcaligenes xylosoxidans Sp. denitrificans ABIV | d,l-2-haloalkanoic acid halidohydrolase (DhlIV) | Soil | mono- and dichloroacetic acid and mono- and dichloropropionic acid | glycolate and pyruvate | specific hydrolysis | [117] |
Rhizobium Sp. | haloalkanoate dehalogenases (DehL, (DehD, (DehE))) | soil | 2,2-dichloropropionic acid, 2-chloropropionic acid, monochloroacetic acid, dichloroacetic acid, 2-chlorobutyric acid and 2,3-dichloropropionic acid | d(−) and l(+) lactate, pyruvate | stereo/non-stereospecific | [118,119,120] |
Methylobacterium Sp. HJ1 | 2-haloalkanoic acid hydrolytic dehalogenase (DehE) | soil | 2,2-dichloropropionic acid and d,l-2-chloro-propionic acid | to produce pyruvate and lactate | non-stereospecific | [121] |
Arthrobacter Sp. strain S1 | ||||||
Dehalococcoides ethenogenes | TCE reductive dehalogenase (TCE-RDase) | tetrachloroethene or trichloroethene (TCE) | ethene | non-stereospecific | [122] | |
Dehalococcoides Sp. Strain BAV1 | reductive dehalogenase (RDase) | aquifer | chloroethene | ethene | non-stereospecific | [33,34,123,124] |
Sphingomonas chlorophenolica | tetrachlorohydroquinone dehalogenase | soil | pentacholophenol | tetrachlorohydroquinone (TCHQ), trichlorohydroquinone, and 2,6-dichlorohydroquinone | non-stereospecific | [125] |
Shewanella sediminis | reductive tetrachloroethene dehalogenase | soil | tetrachloroethene (PCE) | trichloroethene (TCE) | non-stereospecific | [126] |
Psychrobacter cryohalolentis K5 | haloalkane dehalogenase (DpcA) | Saline-water (Siberian permafrost | 1b and other halogenated subtrates | non-stereospecific | [117,120] | |
Sphingomonas paucimobilis UT26 | haloalkane dehalogenase LinB | soil | 1,3,4,6-tetrachloro-1,4-cyclo- hexadiene to 2,5-dichloro-2,5-cyclohexadiene-1,4-diol via 2,4,5-trichloro-2,5-cyclohexane-1-ol during γ-HCH dechlorination | chlorophenols | non-stereospecific | [66,121,124] |
Agrobacterium radiobacter strain AD1 | haloalcohol dehalogenase (HheC) | soil | 1,3-dichloro-2-propanol | eposide (chloride, halide and proton) | non-specific | [127] |
Organisms | Dehalogenase Complex | Gene | PDB Entry | Catalytically Active Residue | Halide-Stabilizing Residues | Refinement Resolution (Å) | Family | Reference |
---|---|---|---|---|---|---|---|---|
Pseudomonas Sp. YL | l-2-haloacid dehalogenase | l-DEX YL | 1JUD | Asp-10, Asn-177 and Lys-151 | Tyr-12, Asn-119, Lys-151, Asn-177 and Trp-179 | 2.5 | homodimeric | [23] |
Pseudomonas Sp. ADP | atrazine chlorohydrolase | AtzA | 4v1x, 4v1y | Asp-327, Glu-246, His-243 | N.S | 2.2, 2.8 | hexameric | [175] |
Xanthobacter autotrophicus | haloalkane dehalogenase | dhlA | 2DHC | Asp-124, His-289, Asp-260 | Trp-125, Trp-175 | 1.9 | α/β fold | [19] |
Rhodococcus Sp. | haloalkane dehalogenase | dhaA | 1BN6 | Asp-117, His-283, Glu-141 | Asn-52, Trp-118 | 1.5 | monomer | [65] |
Mycobacterium tuberculosis H37Rv | haloalkane dehalogenase | Rv2579 | 2QVB | Asp-109, His-273, Glu-133 | Asn-39, Trp-110 | 1.19 | monomer | [117] |
Bradyrhizobium japonicum | haloalkane dehalogenase | dhaA | 3A2M | Asp-103, His-280, Glu-127 | Asn-38, Trp-104 | 1.84 | homodimer | [120] |
Marine microbial consortium | haloalkane dehalogenase | dmmA | 3U1T | Asp-144, His-315, Glu-168 | Asn-78, Trp-145 | 2.2 | monomer | [21] |
Sphingobium Sp. MI1205 | haloalkane dehalogenase | linB | 4H77 | Asp-108, His-272, Glu-132 | Asn-38, Trp-109 | 1.6 | monomer | [121] |
Agrobacterium tumefaciens C58 | haloalkane dehalogenase | datA | 3WI7 | Asp-108, His-274, Glu-132 | Asn-43, Tyr-109 | 1.7 | monomer | [124] |
Bradyrhizobium elkani USDA94 | haloalkane dehalogenase | dbeA | 4K2A | Asp-103, His-271, Glu-127 | Asn-38, Trp-104 | 2.2 | homodimer | [125] |
Bradyhizobium japonicum USDA110 | haloalkane dehalogenase | dbjA | 3A2N | Asp-103, His-280, Glu-127 | Asn-38, Trp-104 | 1.89 | homodimer | [120] |
Plesiocystis pacifica SIR-1 | dppA | 2XT0 | Asp-123, His-178, Asp-249 | Trp-124, Trp-163 | [264] | |||
Strongylocentrotus purpuratus | dspA | NA | Asp-120, His-285, Glu-144 | Asn-53, Trp-121 | N.S | N.S | [265] | |
Alcanivorax dieselolei B-5 | dadB | NA | Asp-108, His-271, Glu-132 | Asn-37, Trp-109 | N.S | N.S | [112] | |
Pseudomonas Sp. YL | l-2-haloacid dehalogenase complexed with monochloroacetate, l-2-chlorobutyrate, l-2-chloro-3-methylbutyrate, or l-2-chloro-4-methylvalerate | l-DEX | 1ZRN, 1ZRM | Asp-10 | Arg-41 | 1.83, 2.0, 2.2, 2.2, | homodimer | [104] |
Burkholderia cepacia | haloacid dehalogenase, l-2-monochloropropanoate intermediate | DehIVa | 2NO4, 2NO5 | Asp11 (Asp108), Ser119 and Asp181 | Arg42 (Arg41, 39), Asn120 (Asn119, 115), Trp180 (Trp 179, Phe175) | 1.93, 2.7 | homodimer | [54] |
Rhodopseudomonas palustris | fluoroacetate dehalogenases | RPA1163 | 3R3U, 3R3V, 3R3W, 3R3X, 3R3Y, 3R3Z, 3R40, 3R41 | Asp110, His280, Asp134 | His155, Trp156 and Tyr219 | 1.6, 1.5, 1.6, 1.8, 1.15, 1.7, 1.05, 1.05, 1.05 | homodimeric | [266] |
Methylobacterium Sp. CPA1 | D,l-2-haloacid dehalogenase | 4N2X | N.S | N.S | 1.7 | hexamer | [179] | |
Pseudomonas putida strain PP3 | group I α-haloacid dehalogenase | Dehl | 3BJX | (Thr-62, Glu-66), and Asp189 | N.S | 2.3 | homodimer | [267] |
Sphingomonas paucimobilis UT26 | haloalkane dehalogenase | LinB | 1MJ5 | Asp-108, His-272, and Glu-132 | Asn-38 and Trp-109 | 0.95 | monomer | [12] |
Sphingomonas paucimobilis UT26 | haloalkane dehalogenase and complexes of linb with 1,2-propanediol/l-bromopropane-2-ol and 2-bromo-2-propene-l-ol | LinB | 1K6E, 1K63 | Asp-108, Glu-132, and His-272 | Primary (Asn-38 and Trp-109), Secondary (Trp-207, Pro-208, and Ile-211) | 1.85 | monomer | [177] |
Sphingomonas paucimobilis UT26 | haloalkane dehalogenase LinB/LinB with 1,3-propanediol | LinB | 1CV2, 1D07 | Asp-108, His-272, and Glu-132 | Asn-38 and Trp-109 | 1.58 Å, 2.0 Å | monomer | [66] |
Sphingomonas paucimobilis UT26 | 1,3,4,6-tetrachloro-1,4-cyclohexadiene hydrolase linB complexed with 1,2-dichloropropane | LinB | 1G42 | Asp-108, Glu-132, and His-272 | Asn-38 and Trp-109 | 1.8 | monomer | [189] |
Burkholderia Sp. Strain FA1 | fluoroacetate dehalogenase | FAcD | 1Y37 | Asp-104, His-271, Asp-128 | Trp-150 and His-149 | 1.5 | homodimer | [191] |
Pseudomonas Sp. Strain CBS-3 | 4-chlorobenzoyl-coenzyme A dehalogenase | CoA | 1NZY | Asp-145 and His-90, Gly-114/Ala-121 | Asp-145 | 1.8 | hexamer | [166] |
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Ang, T.-F.; Maiangwa, J.; Salleh, A.B.; Normi, Y.M.; Leow, T.C. Dehalogenases: From Improved Performance to Potential Microbial Dehalogenation Applications. Molecules 2018, 23, 1100. https://doi.org/10.3390/molecules23051100
Ang T-F, Maiangwa J, Salleh AB, Normi YM, Leow TC. Dehalogenases: From Improved Performance to Potential Microbial Dehalogenation Applications. Molecules. 2018; 23(5):1100. https://doi.org/10.3390/molecules23051100
Chicago/Turabian StyleAng, Thiau-Fu, Jonathan Maiangwa, Abu Bakar Salleh, Yahaya M. Normi, and Thean Chor Leow. 2018. "Dehalogenases: From Improved Performance to Potential Microbial Dehalogenation Applications" Molecules 23, no. 5: 1100. https://doi.org/10.3390/molecules23051100