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Literature summary for 3.8.1.5 extracted from

  • Li, A.; Shao, Z.
    Biochemical characterization of a haloalkane dehalogenase DadB from Alcanivorax dieselolei B-5 (2014), PLoS ONE, 9, e89144.
    View publication on PubMedView publication on EuropePMC
Search for more literature for 3.8.1.5

Activating Compound

Activating Compound Comment Organism Structure
imidazole imidazole buffers promote the enzyme activity Alcanivorax dieselolei

Application

Application Comment Organism
environmental protection enzyme DadB and its host, Alcanivorax dieselolei strain B-5, are of potential use for biocatalysis and bioremediation applications Alcanivorax dieselolei
synthesis enzyme DadB and its host, Alcanivorax dieselolei strain B-5, are of potential use for biocatalysis and bioremediation applications Alcanivorax dieselolei

Cloned(Commentary)

Cloned (Comment) Organism
gene dadB, phylogenetic analysis Alcanivorax dieselolei

Inhibitors

Inhibitors Comment Organism Structure
3-(morpholin-4-yl)propane-1-sulfonic acid phosphate and MOPS buffers repress the enzyme activity Alcanivorax dieselolei
additional information no activity in glycine buffers Alcanivorax dieselolei
phosphate phosphate and MOPS buffers repress the enzyme activity Alcanivorax dieselolei

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
 additional information steady-state kinetics Alcanivorax dieselolei
0.82
-
 1,3-dibromopropane pH 8.6, 37°C, recombinant enzyme Alcanivorax dieselolei
4.88
-
 1-Chlorobutane pH 8.6, 37°C, recombinant enzyme Alcanivorax dieselolei
8.47
-
 4-bromobutyronitrile pH 8.6, 37°C, recombinant enzyme Alcanivorax dieselolei
8.7
-
 1,2-Dibromoethane pH 8.6, 37°C, recombinant enzyme Alcanivorax dieselolei
11.33
-
 3-chloro-2-methylprop-1-ene pH 8.6, 37°C, recombinant enzyme Alcanivorax dieselolei
15.06
-
 2,3-dichloroprop-1-ene pH 8.6, 37°C, recombinant enzyme Alcanivorax dieselolei

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1-haloalkane + H2O Alcanivorax dieselolei
-
 a primary alcohol + halide
-
 ?
additional information Alcanivorax dieselolei enzyme DadB possesses broad substrate range and has the highest overall activity among the identified haloalkanes dehalogenases. The enzyme prefers brominated substrates, chlorinated alkenes, and the C2-C3 substrates, including the persistent pollutants of 1,2-dichloroethane, 1,2-dichloropropane and 1,2,3-trichloropropane, but displays no detectable activity toward long-chain haloalkanes such as 1-chlorohexadecane and 1-chlorooctadecane ?
-
 ?
additional information Alcanivorax dieselolei B-5 enzyme DadB possesses broad substrate range and has the highest overall activity among the identified haloalkanes dehalogenases. The enzyme prefers brominated substrates, chlorinated alkenes, and the C2-C3 substrates, including the persistent pollutants of 1,2-dichloroethane, 1,2-dichloropropane and 1,2,3-trichloropropane, but displays no detectable activity toward long-chain haloalkanes such as 1-chlorohexadecane and 1-chlorooctadecane ?
-
 ?

Organism

Organism UniProt Comment Textmining
Alcanivorax dieselolei K0CAI2 gene dadB
-
Alcanivorax dieselolei B-5 K0CAI2 gene dadB
-

Specific Activity [micromol/min/mg]

Specific Activity Minimum [µmol/min/mg] Specific Activity Maximum [µmol/min/mg] Comment Organism
0.012
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1-chlorotetradecane Alcanivorax dieselolei
0.018
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1-chlorododecane Alcanivorax dieselolei
0.024
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1-chloro-2-methylpropane Alcanivorax dieselolei
0.06
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate dichloromethane Alcanivorax dieselolei
0.084
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1-chlorodecane Alcanivorax dieselolei
0.28
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate (bromomethyl)cyclohexane Alcanivorax dieselolei
0.31
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1,2-dichloropropane Alcanivorax dieselolei
0.34
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1,2,3-trichloropropane Alcanivorax dieselolei
0.702
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1,2-dichloroethane Alcanivorax dieselolei
0.76
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1-chlorohexane Alcanivorax dieselolei
0.862
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1-bromohexane Alcanivorax dieselolei
0.864
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1,5-dichloropentane Alcanivorax dieselolei
0.92
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1-iodohexane Alcanivorax dieselolei
1.11
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1-chlorobutane Alcanivorax dieselolei
1.48
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate bromocyclohexane Alcanivorax dieselolei
2.4
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1,3-diiodopropane Alcanivorax dieselolei
3.04
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1-iodobutane Alcanivorax dieselolei
3.54
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate chlorocyclopentane Alcanivorax dieselolei
3.63
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1-chloro-2-(2-chloroethoxy)ethane Alcanivorax dieselolei
3.88
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1-iodopropane Alcanivorax dieselolei
4.51
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1-bromobutane Alcanivorax dieselolei
5.33
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1,3-dichloropropane Alcanivorax dieselolei
7.48
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1,2-dibromopropane Alcanivorax dieselolei
8.14
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1,2-dibromo-3-chloropropane Alcanivorax dieselolei
8.3
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 2-bromo-1-chloropropane Alcanivorax dieselolei
9.92
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1-bromo-3-chloropropane Alcanivorax dieselolei
10.3
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1,3-dibromopropane Alcanivorax dieselolei
11.53
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1-bromo-2-chloroethane Alcanivorax dieselolei
12.66
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1-chlorooctane Alcanivorax dieselolei
13.54
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1,3-dichloropropene Alcanivorax dieselolei
14.05
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 2,3-dichloroprop-1-ene Alcanivorax dieselolei
14.16
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1,2-dibromoethane Alcanivorax dieselolei
14.44
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 4-bromobutyronitrile Alcanivorax dieselolei
15.13
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1,2,3-tribromopropane Alcanivorax dieselolei
24.05
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 3-chloro-2-methylprop-1-ene Alcanivorax dieselolei
26.48
-
 pH 8.6, 37°C, purified recombinant enzyme, substrate 1,2,3-trichloropropene Alcanivorax dieselolei

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
(bromomethyl)cyclohexane + H2O
-
 Alcanivorax dieselolei cyclohexylmethanol + bromide
-
 ?
1,2,3-tribromopropane + H2O
-
 Alcanivorax dieselolei 2,3-dibromopropanol + bromide
-
 ?
1,2,3-trichloropropane + H2O
-
 Alcanivorax dieselolei 2,3-dichloropropanol + chloride
-
 ?
1,2,3-trichloropropene + H2O
-
 Alcanivorax dieselolei 2,3-dichloropropenol + chloride
-
 ?
1,2-dibromo-3-chloropropane + H2O
-
 Alcanivorax dieselolei 2-bromo-3-chloropropanol + bromide
-
 ?
1,2-dibromoethane + H2O
-
 Alcanivorax dieselolei 2-bromoethanol + bromide
-
 ?
1,2-dibromoethane + H2O
-
 Alcanivorax dieselolei B-5 2-bromoethanol + bromide
-
 ?
1,2-dibromopropane + H2O
-
 Alcanivorax dieselolei 2-bromopropanol + bromide
-
 ?
1,2-dichloroethane + H2O
-
 Alcanivorax dieselolei 2-chloroethanol + chloride
-
 ?
1,2-dichloroethane + H2O
-
 Alcanivorax dieselolei B-5 2-chloroethanol + chloride
-
 ?
1,2-dichloropropane + H2O
-
 Alcanivorax dieselolei 2-chloropropanol + chloride
-
 ?
1,3-dibromopropane + H2O
-
 Alcanivorax dieselolei 3-bromopropanol + bromide
-
 ?
1,3-dichloropropane + H2O
-
 Alcanivorax dieselolei 3-chloropropanol + chloride
-
 ?
1,3-dichloropropene + H2O
-
 Alcanivorax dieselolei 3-chloropropenol + chloride
-
 ?
1,3-diiodopropane + H2O
-
 Alcanivorax dieselolei 3-iodopropanol + iodide
-
 ?
1,5-dichloropentane + H2O
-
 Alcanivorax dieselolei 5-chloropentanol + chloride
-
 ?
1-bromo-2-chloroethane + H2O
-
 Alcanivorax dieselolei 2-chloroethanol + bromide
-
 ?
1-bromo-3-chloropropane + H2O
-
 Alcanivorax dieselolei 3-chloropropanol + bromide
-
 ?
1-bromobutane + H2O
-
 Alcanivorax dieselolei 1-butanol + bromide
-
 ?
1-bromohexane + H2O
-
 Alcanivorax dieselolei 1-hexanol + bromide
-
 ?
1-chloro-2-(2-chloroethoxy)ethane + H2O
-
 Alcanivorax dieselolei 2-(2-chloroethoxy)ethanol + chloride
-
 ?
1-chloro-2-methylpropane + H2O
-
 Alcanivorax dieselolei 2-methylpropanol + chloride
-
 ?
1-chlorobutane + H2O
-
 Alcanivorax dieselolei 1-butanol + chloride
-
 ?
1-chlorodecane + H2O
-
 Alcanivorax dieselolei decanol + chloride
-
 ?
1-chlorododecane + H2O
-
 Alcanivorax dieselolei dodecanol + chloride
-
 ?
1-chlorohexane + H2O
-
 Alcanivorax dieselolei 1-hexanol + chloride
-
 ?
1-chlorooctane + H2O
-
 Alcanivorax dieselolei octanol + chloride
-
 ?
1-chlorotetradecane + H2O
-
 Alcanivorax dieselolei tetradecanol + chloride
-
 ?
1-haloalkane + H2O
-
 Alcanivorax dieselolei a primary alcohol + halide
-
 ?
1-iodobutane + H2O
-
 Alcanivorax dieselolei butanol + iodide
-
 ?
1-iodohexane + H2O
-
 Alcanivorax dieselolei hexanol + iodide
-
 ?
1-iodopropane + H2O
-
 Alcanivorax dieselolei propanol + iodide
-
 ?
1-iodopropane + H2O
-
 Alcanivorax dieselolei B-5 propanol + iodide
-
 ?
2,3-dichloroprop-1-ene + H2O
-
 Alcanivorax dieselolei ?
-
 ?
3-chloro-2-methylprop-1-ene + H2O
-
 Alcanivorax dieselolei ?
-
 ?
4-bromobutyronitrile + H2O
-
 Alcanivorax dieselolei 4-hydroxybutyronitrile + bromide
-
 ?
bromocyclohexane + H2O
-
 Alcanivorax dieselolei cyclohexanol + bromide
-
 ?
chlorocyclopentane + H2O
-
 Alcanivorax dieselolei cyclopentanol + chloride
-
 ?
dichloromethane + H2O
-
 Alcanivorax dieselolei ?
-
 ?
additional information enzyme DadB possesses broad substrate range and has the highest overall activity among the identified haloalkanes dehalogenases. The enzyme prefers brominated substrates, chlorinated alkenes, and the C2-C3 substrates, including the persistent pollutants of 1,2-dichloroethane, 1,2-dichloropropane and 1,2,3-trichloropropane, but displays no detectable activity toward long-chain haloalkanes such as 1-chlorohexadecane and 1-chlorooctadecane Alcanivorax dieselolei ?
-
 ?
additional information the enzyme DadB prefers brominated substrates over than their chlorinated and iodinated counterparts, its activities against brominated C1-C4 substrates are generally 20 times higher than the corresponding chlorinated substrates. In the case of halogenated butane, the activities are 1-bromobutane > 1-iodobutane > 1-chlorobutane. For 1,3-dihalogenated propane, the activities are 1,3-dibromopropane > 1-chloro-3-bromopropane > 1,3-dichloropropane > 1,3-diiodopropane. The activity of enzyme DadB against chlorinated alkenes, such as 2,3-dichloroprop-1-ene, 3-chloro-2-methylprop-1-ene, 1,3-dichloropropene, and 1,2,3-trichloropropene, is higher than the corresponding chlorinated alkanes. Substrate specificity, overview. No activity with 2-iodobutane, chlorocyclohexane, 1-chlorohexadecane, 1-bromohexadecane, 1-chlorooctadecane, trichloromethane, 1-chloro-3-nitrobenzene, 4-bromodiphenyl ether, decabromodiphenyl, and trichloroacetic acid Alcanivorax dieselolei ?
-
 ?
additional information enzyme DadB possesses broad substrate range and has the highest overall activity among the identified haloalkanes dehalogenases. The enzyme prefers brominated substrates, chlorinated alkenes, and the C2-C3 substrates, including the persistent pollutants of 1,2-dichloroethane, 1,2-dichloropropane and 1,2,3-trichloropropane, but displays no detectable activity toward long-chain haloalkanes such as 1-chlorohexadecane and 1-chlorooctadecane Alcanivorax dieselolei B-5 ?
-
 ?
additional information the enzyme DadB prefers brominated substrates over than their chlorinated and iodinated counterparts, its activities against brominated C1-C4 substrates are generally 20 times higher than the corresponding chlorinated substrates. In the case of halogenated butane, the activities are 1-bromobutane > 1-iodobutane > 1-chlorobutane. For 1,3-dihalogenated propane, the activities are 1,3-dibromopropane > 1-chloro-3-bromopropane > 1,3-dichloropropane > 1,3-diiodopropane. The activity of enzyme DadB against chlorinated alkenes, such as 2,3-dichloroprop-1-ene, 3-chloro-2-methylprop-1-ene, 1,3-dichloropropene, and 1,2,3-trichloropropene, is higher than the corresponding chlorinated alkanes. Substrate specificity, overview. No activity with 2-iodobutane, chlorocyclohexane, 1-chlorohexadecane, 1-bromohexadecane, 1-chlorooctadecane, trichloromethane, 1-chloro-3-nitrobenzene, 4-bromodiphenyl ether, decabromodiphenyl, and trichloroacetic acid Alcanivorax dieselolei B-5 ?
-
 ?

Subunits

Subunits Comment Organism
More DadB aggregates fast in the buffers with pH below pH 7.0, while keeps stable in monomer form when pH is above pH 7.5 Alcanivorax dieselolei

Synonyms

Synonyms Comment Organism
DadB
-
 Alcanivorax dieselolei
HLD
-
 Alcanivorax dieselolei

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
50
-
-
 Alcanivorax dieselolei

Temperature Range [°C]

Temperature Minimum [°C] Temperature Maximum [°C] Comment Organism
20 50 the enzyme activity increases gradually from 20°C to 50°C and decreases above 50°C, with the temperature optimum being 50°C, inactive at 60°C Alcanivorax dieselolei

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
1.17
-
 1-Chlorobutane pH 8.6, 37°C, recombinant enzyme Alcanivorax dieselolei
13.39
-
 1,3-dibromopropane pH 8.6, 37°C, recombinant enzyme Alcanivorax dieselolei
17.95
-
 1,2-Dibromoethane pH 8.6, 37°C, recombinant enzyme Alcanivorax dieselolei
20.06
-
 2,3-dichloroprop-1-ene pH 8.6, 37°C, recombinant enzyme Alcanivorax dieselolei
30.8
-
 4-bromobutyronitrile pH 8.6, 37°C, recombinant enzyme Alcanivorax dieselolei
34.26
-
 3-chloro-2-methylprop-1-ene pH 8.6, 37°C, recombinant enzyme Alcanivorax dieselolei

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
5.5 6 peak 1, first optimum Alcanivorax dieselolei
8 9 peak 2, second optimum Alcanivorax dieselolei

pH Range

pH Minimum pH Maximum Comment Organism
5 10 activity range Alcanivorax dieselolei

General Information

General Information Comment Organism
evolution enzyme DadB likely belongs to the HLD-II subfamily, closely related with LinB and DmbA, while DadA appears to be relatively independent from the HLD-II subfamily. This pentad includes the nucleophile residue D108, the basic residue H271, the acid catalytic residue E132, and the halide-binding residues N37 and W109. DadB possesses a large main tunnel opening, but it prefers small substrates Alcanivorax dieselolei
additional information DadB has an open active cavity with a large access tunnel, which is supposed important for larger molecules as opposed to C2-C3 substrates, homology modeling, residue I247 plays an important role in substrate selection. Homology modeling and structural analysis, overview. Enzyme DadB is composed of a core domain and a cap domain, identical catalytic pentad of HLD-II subfamily Alcanivorax dieselolei

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
0.24
-
 1-Chlorobutane pH 8.6, 37°C, recombinant enzyme Alcanivorax dieselolei
1.33
-
 2,3-dichloroprop-1-ene pH 8.6, 37°C, recombinant enzyme Alcanivorax dieselolei
2.06
-
 1,2-Dibromoethane pH 8.6, 37°C, recombinant enzyme Alcanivorax dieselolei
3.02
-
 3-chloro-2-methylprop-1-ene pH 8.6, 37°C, recombinant enzyme Alcanivorax dieselolei
3.64
-
 4-bromobutyronitrile pH 8.6, 37°C, recombinant enzyme Alcanivorax dieselolei
16.43
-
 1,3-dibromopropane pH 8.6, 37°C, recombinant enzyme Alcanivorax dieselolei