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Literature summary extracted from
- Biochemical and biophysical characterisation of haloalkane dehalogenases DmrA and DmrB in Mycobacterium strain JS60 and their role in growth on haloalkanes (2015), Mol. Microbiol., 97, 439-453.
Application
| EC Number | Application | Comment | Organism |
|---|---|---|---|
| 3.8.1.5 | environmental protection | HLD-containing bacteria are interesting as a cleanup technology for toxic haloalkane wastes produced from industries such as plastics and pesticides manufacture | Mycolicibacterium rhodesiae |
| 3.8.1.5 | synthesis | the enzymes are of interest for biocatalysis, due to their ability to create enantiomerically pure alcohols | Mycolicibacterium rhodesiae |
Cloned(Commentary)
| EC Number | Cloned (Comment) | Organism |
|---|---|---|
| 3.8.1.5 | gene dmrA, sequence comparisons and phylogenetic analysis, overexpression of C-terminally His6-tagged enzyme in Escherichia coli strain BL21 (DE3) | Mycolicibacterium rhodesiae |
| 3.8.1.5 | gene dmrB, sequence comparisons and phylogenetic analysis, overexpression of C-terminally His6-tagged enzyme in Escherichia coli strain BL21 (DE3) | Mycolicibacterium rhodesiae |
Crystallization (Commentary)
| EC Number | Crystallization (Comment) | Organism |
|---|---|---|
| 3.8.1.5 | X-ray diffraction structure determination and analysis, hanging drop vapour diffusion method, mixing of equal volumes of 18 mg/ml protein solution and well solution containing 0.1 M Bis-Tris propane, pH 6.5, 0.2 M KSCN, 16% w/v PEG 3350, to 0.004 ml drops, equilibration against 1 ml reservori solution, microseeding, crystals of selenomethionyl-labeled DmrA diffract to 1.7 A resolution, PDB ID 4MJE | Mycolicibacterium rhodesiae |
| 3.8.1.5 | X-ray diffraction structure determination, hanging drop vapour diffusion method, mixing of equal volumes of protein solution and well solution, best diffracting crystals for DmrB are generated using a stock protein concentration of 5 mg/ml against 0.1 M MES, pH 6.5, 30% PEG 1500, crystals of DmrB diffract only to a resolution of 8 A | Mycolicibacterium rhodesiae |
KM Value [mM]
| EC Number | KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|---|
| 3.8.1.5 | additional information | - |
additional information | Michaelis-Menten kinetics | Mycolicibacterium rhodesiae | |
| 3.8.1.5 | 1.9 | - |
4-bromobutyronitrile | pH 8.0, 25°C, recombinant enzyme | Mycolicibacterium rhodesiae |  |
Molecular Weight [Da]
| EC Number | Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
|---|---|---|---|---|
| 3.8.1.5 | 35000 | - |
NMR spectroscopy and gel filtration | Mycolicibacterium rhodesiae |
| 3.8.1.5 | 35000 | - |
4 * 35000, multi-angle laser-light scattering analysis, NMR spectroscopy | Mycolicibacterium rhodesiae |
| 3.8.1.5 | 150000 | - |
NMR spectroscopy and gel filtration | Mycolicibacterium rhodesiae |
Natural Substrates/ Products (Substrates)
| EC Number | Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 3.8.1.5 | 1-haloalkane + H2O | Mycolicibacterium rhodesiae | - |
a primary alcohol + halide | - |
? | |
| 3.8.1.5 | 1-haloalkane + H2O | Mycolicibacterium rhodesiae JS60 | - |
a primary alcohol + halide | - |
? | |
Organism
| EC Number | Organism | UniProt | Comment | Textmining |
|---|---|---|---|---|
| 3.8.1.5 | Mycolicibacterium rhodesiae | G4I2J6 | derived from a vinylchloride contaminated site, using vinylchloride as the sole carbon and energy source for enrichment and isolation, gene dmrA | - |
| 3.8.1.5 | Mycolicibacterium rhodesiae | G4I5P8 | derived from a vinylchloride contaminated site, using vinylchloride as the sole carbon and energy source for enrichment and isolation, gene dmrB | - |
| 3.8.1.5 | Mycolicibacterium rhodesiae JS60 | G4I2J6 | derived from a vinylchloride contaminated site, using vinylchloride as the sole carbon and energy source for enrichment and isolation, gene dmrA | - |
| 3.8.1.5 | Mycolicibacterium rhodesiae JS60 | G4I5P8 | derived from a vinylchloride contaminated site, using vinylchloride as the sole carbon and energy source for enrichment and isolation, gene dmrB | - |
Purification (Commentary)
| EC Number | Purification (Comment) | Organism |
|---|---|---|
| 3.8.1.5 | recombinant C-terminally His6-tagged enzyme from Escherichia coli by nickel affinity chromatography and gel filtration | Mycolicibacterium rhodesiae |
| 3.8.1.5 | recombinant C-terminally His6-tagged enzyme from Escherichia coli by nickel affinity chromatography, anion exchange chromatography and gel filtration | Mycolicibacterium rhodesiae |
Source Tissue
| EC Number | Source Tissue | Comment | Organism | Textmining |
|---|---|---|---|---|
| 3.8.1.5 | additional information | proteomic analysis of strain JS60 | Mycolicibacterium rhodesiae | - |
Substrates and Products (Substrate)
| EC Number | Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 3.8.1.5 | 1,2-dibromoethane + H2O | - |
Mycolicibacterium rhodesiae | 2-bromoethanol + bromide | - |
? | |
| 3.8.1.5 | 1,2-dibromoethane + H2O | high activity | Mycolicibacterium rhodesiae | 2-bromoethanol + bromide | - |
? | |
| 3.8.1.5 | 1,2-dibromoethane + H2O | high activity | Mycolicibacterium rhodesiae JS60 | 2-bromoethanol + bromide | - |
? | |
| 3.8.1.5 | 1,2-dibromoethane + H2O | - |
Mycolicibacterium rhodesiae JS60 | 2-bromoethanol + bromide | - |
? | |
| 3.8.1.5 | 1,2-dichloroethane + H2O | low activity | Mycolicibacterium rhodesiae | 2-chloroethanol + chloride | - |
? | |
| 3.8.1.5 | 1,2-dichloroethane + H2O | low activity | Mycolicibacterium rhodesiae JS60 | 2-chloroethanol + chloride | - |
? | |
| 3.8.1.5 | 1,6-dibromohexane + H2O | - |
Mycolicibacterium rhodesiae | 6-bromohexanol + bromide | - |
? | |
| 3.8.1.5 | 1,6-dibromohexane + H2O | - |
Mycolicibacterium rhodesiae JS60 | 6-bromohexanol + bromide | - |
? | |
| 3.8.1.5 | 1-bromobutane + H2O | best substrate | Mycolicibacterium rhodesiae | 1-butanol + bromide | - |
? | |
| 3.8.1.5 | 1-bromobutane + H2O | best substrate | Mycolicibacterium rhodesiae JS60 | 1-butanol + bromide | - |
? | |
| 3.8.1.5 | 1-bromohexane + H2O | - |
Mycolicibacterium rhodesiae | 1-hexanol + bromide | - |
? | |
| 3.8.1.5 | 1-bromohexane + H2O | best substrate | Mycolicibacterium rhodesiae | 1-hexanol + bromide | - |
? | |
| 3.8.1.5 | 1-bromohexane + H2O | best substrate | Mycolicibacterium rhodesiae JS60 | 1-hexanol + bromide | - |
? | |
| 3.8.1.5 | 1-bromopentane + H2O | - |
Mycolicibacterium rhodesiae | 1-pentanol + bromide | - |
? | |
| 3.8.1.5 | 1-bromopentane + H2O | low activity | Mycolicibacterium rhodesiae | 1-pentanol + bromide | - |
? | |
| 3.8.1.5 | 1-bromopropane + H2O | - |
Mycolicibacterium rhodesiae | 1-propanol + bromide | - |
? | |
| 3.8.1.5 | 1-haloalkane + H2O | - |
Mycolicibacterium rhodesiae | a primary alcohol + halide | - |
? | |
| 3.8.1.5 | 1-haloalkane + H2O | - |
Mycolicibacterium rhodesiae JS60 | a primary alcohol + halide | - |
? | |
| 3.8.1.5 | 1-iodobutane + H2O | - |
Mycolicibacterium rhodesiae | 1-butanol + iodide | - |
? | |
| 3.8.1.5 | 1-iodopropane + H2O | - |
Mycolicibacterium rhodesiae | 1-propanol + iodide | - |
? | |
| 3.8.1.5 | 4-bromobutyronitrile + H2O | low activity | Mycolicibacterium rhodesiae | 4-hydroxybutyronitrile + bromide | - |
? | |
| 3.8.1.5 | 4-bromobutyronitrile + H2O | high activity | Mycolicibacterium rhodesiae | 4-hydroxybutyronitrile + bromide | - |
? | |
| 3.8.1.5 | bromocyclohexane + H2O | low activity | Mycolicibacterium rhodesiae | cyclohexanol + bromide | - |
? | |
| 3.8.1.5 | bromocyclohexane + H2O | low activity | Mycolicibacterium rhodesiae JS60 | cyclohexanol + bromide | - |
? | |
| 3.8.1.5 | additional information | no or poor activity with 1,1,2-trichloroethane and chloroform | Mycolicibacterium rhodesiae | ? | - |
? | |
| 3.8.1.5 | additional information | no or poor activity with chloroform | Mycolicibacterium rhodesiae | ? | - |
? | |
| 3.8.1.5 | additional information | no or poor activity with 1,1,2-trichloroethane and chloroform | Mycolicibacterium rhodesiae JS60 | ? | - |
? | |
| 3.8.1.5 | additional information | no or poor activity with chloroform | Mycolicibacterium rhodesiae JS60 | ? | - |
? | |
Subunits
| EC Number | Subunits | Comment | Organism |
|---|---|---|---|
| 3.8.1.5 | monomer | 1 * 35000, multi-angle laser-light scattering analysis, NMR spectroscopy | Mycolicibacterium rhodesiae |
| 3.8.1.5 | More | the protein contains 28% helical and 21% beta-strand content | Mycolicibacterium rhodesiae |
| 3.8.1.5 | More | the protein contains 31% helical and 19% beta-strand content | Mycolicibacterium rhodesiae |
| 3.8.1.5 | tetramer | 4 * 35000, multi-angle laser-light scattering analysis, NMR spectroscopy | Mycolicibacterium rhodesiae |
Synonyms
| EC Number | Synonyms | Comment | Organism |
|---|---|---|---|
| 3.8.1.5 | DmrA | - |
Mycolicibacterium rhodesiae |
| 3.8.1.5 | DmrB | - |
Mycolicibacterium rhodesiae |
| 3.8.1.5 | HLD | - |
Mycolicibacterium rhodesiae |
Temperature Optimum [°C]
| EC Number | Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|---|
| 3.8.1.5 | 25 | - |
assay at | Mycolicibacterium rhodesiae |
| 3.8.1.5 | 38 | - |
with 1-bromohexane | Mycolicibacterium rhodesiae |
Turnover Number [1/s]
| EC Number | Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|---|
| 3.8.1.5 | 3.1 | - |
4-bromobutyronitrile | pH 8.0, 25°C, recombinant enzyme | Mycolicibacterium rhodesiae | |
pH Optimum
| EC Number | pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|---|
| 3.8.1.5 | 8 | - |
assay at | Mycolicibacterium rhodesiae |
| 3.8.1.5 | 8 | - |
with 1-bromohexane | Mycolicibacterium rhodesiae |
Expression
| EC Number | Organism | Comment | Expression |
|---|---|---|---|
| 3.8.1.5 | Mycolicibacterium rhodesiae | haloalkane-mediated upregulation of dmrA is high by 23 to 33fold, the enzyme is also upregulated but to a lesser extent in response to starvation | up |
| 3.8.1.5 | Mycolicibacterium rhodesiae | haloalkane-mediated upregulation of dmrB is modest by 6 to 13fold, the enzyme is also upregulated but to a lesser extent in response to starvation | up |
General Information
| EC Number | General Information | Comment | Organism |
|---|---|---|---|
| 3.8.1.5 | evolution | the enzyme is a member of the alpha/beta hydrolase superfamily, which also includes epoxide hydrolases and carboxylesterases. Comparison of active site cavities and access tunnels of HLDs of type I and type II HLDs | Mycolicibacterium rhodesiae |
| 3.8.1.5 | evolution | the enzyme is a member of the alpha/beta hydrolase superfamily, which also includes epoxide hydrolases and carboxylesterases. Comparison of active site cavities and access tunnels of HLDs of type I and type II HLDs. The major structural difference between DmrA (HLD subfamily I) and the well-studied enzymes of HLD subfamily II is the different arrangement of helices in the cap domain | Mycolicibacterium rhodesiae |
| 3.8.1.5 | physiological function | haloalkane dehalogenases enable the first step in bacterial growth on haloalkanes as carbon and energy sources | Mycolicibacterium rhodesiae |
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