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Information on EC 3.8.1.5 - haloalkane dehalogenase and Organism(s) Rhodococcus rhodochrous and UniProt Accession P0A3G2

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EC Tree
     3 Hydrolases
         3.8 Acting on halide bonds
             3.8.1 In carbon-halide compounds
                3.8.1.5 haloalkane dehalogenase
IUBMB Comments
Acts on a wide range of 1-haloalkanes, haloalcohols, haloalkenes and some haloaromatic compounds.
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This record set is specific for:
Rhodococcus rhodochrous
UNIPROT: P0A3G2
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Word Map
The taxonomic range for the selected organisms is: Rhodococcus rhodochrous
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Synonyms
haloalkane dehalogenase, haloalkane dehalogenase linb, dhaa31, hld-i, rv2579, ehld-c, ylehd, 1-chlorohexane halidohydrolase, linbut, ehld-b, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
1-chlorohexane halidohydrolase
-
-
-
-
1-haloalkane dehalogenase
-
-
-
-
metallo-haloalkane dehalogenase
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
1-haloalkane + H2O = a primary alcohol + halide
show the reaction diagram
acts on a wide range of 1-haloalkanes, haloalcohols, haloalkenes and some haloaromatic compounds
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of C-halide
-
-
-
-
C-halide hydrolysis
-
-
SYSTEMATIC NAME
IUBMB Comments
1-haloalkane halidohydrolase
Acts on a wide range of 1-haloalkanes, haloalcohols, haloalkenes and some haloaromatic compounds.
CAS REGISTRY NUMBER
COMMENTARY hide
95990-29-7
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
1,2,3-tribromopropane + H2O
2,3-dibromo-1-propanol + bromide
show the reaction diagram
-
-
-
-
?
1,2,3-tribromopropane + H2O
?
show the reaction diagram
-
-
-
-
?
1,2,3-trichloropropane + H2O
(RS)-2,3-dichloropropan-1-ol + chloride
show the reaction diagram
1,2,3-trichloropropane + H2O
2,3-dichloro-1-propanol + chloride
show the reaction diagram
-
low activity
-
-
?
1,2,3-trichloropropane + H2O
2,3-dichloropropan-1-ol + chloride
show the reaction diagram
1,2,3-trichloropropane + H2O
2,3-dichlorpropane-1-ol + chloride
show the reaction diagram
-
-
-
ir
1,2,3-trichloropropane + H2O
?
show the reaction diagram
1,2-dibromoethane + H2O
2-bromo-1-ethanol + bromide
show the reaction diagram
-
-
-
-
?
1,2-dibromoethane + H2O
2-bromoethanol + bromide
show the reaction diagram
-
-
-
?
1,2-dibromopropane + H2O
2-bromo-1-propanol + bromide
show the reaction diagram
-
-
-
-
?
1,2-dichloropropane + H2O
2-chloro-1-propanol + chloride
show the reaction diagram
-
-
-
-
?
1,3-dibromopropane + H2O
3-bromo-1-propanol + bromide
show the reaction diagram
-
best substrate, the release of product 3-bromo-1-propanol is the rate limiting step
-
-
?
1,3-dichloropropane + H2O
3-chloro-1-propanol + chloride
show the reaction diagram
-
-
-
-
?
1-bromopropane + H2O
propanol + bromide
show the reaction diagram
-
-
-
-
?
1-chlorobutane + H2O
1-butanol + chloride
show the reaction diagram
-
-
-
-
?
1-chloropropane + H2O
propanol + chloride
show the reaction diagram
-
-
-
-
?
1-iodobutane + H2O
1-butanol + iodide
show the reaction diagram
-
-
-
-
?
2-bromoethanol + H2O
ethanol + bromide
show the reaction diagram
-
low activity
-
-
?
3-bromo-1-propanol + H2O
ethanol + bromide
show the reaction diagram
-
-
-
-
?
bis(2-chloroethyl) ether + H2O
?
show the reaction diagram
-
-
-
?
haloalkane + H2O
alcohol + halide
show the reaction diagram
-
comparison of substrate specificities and classification
-
-
?
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
1,2,3-trichloropropane + H2O
(RS)-2,3-dichloropropan-1-ol + chloride
show the reaction diagram
-
-
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.3
1,2,3-tribromopropane
-
pH 9.4, 30°C
2.2
1,2,3-trichloropropane
-
pH 9.4, 30°C
4
1,2-Dibromoethane
-
pH 9.4, 30°C
1
1,2-dibromopropane
-
pH 9.4, 30°C
0.005
1,3-dibromopropane
-
pH 9.4, 30°C
0.63
1,3-Dichloropropane
-
pH 9.4, 30°C
0.6
1-Bromopropane
-
pH 9.4, 30°C
1
1-Chloropropane
-
pH 9.4, 30°C
11
2-bromoethanol
-
above, pH 9.4, 30°C
3.3
3-bromo-1-propanol
-
pH 9.4, 30°C
2.7 - 6.9
bis(2-chloroethyl) ether
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3.6
1,2,3-tribromopropane
-
pH 9.4, 30°C
0.08
1,2,3-trichloropropane
-
pH 9.4, 30°C
14.3
1,2-Dibromoethane
-
pH 9.4, 30°C
2.3
1,2-dibromopropane
-
pH 9.4, 30°C
2.7
1,3-dibromopropane
-
pH 9.4, 30°C
1.3
1,3-Dichloropropane
-
pH 9.4, 30°C
2.7
1-Bromopropane
-
pH 9.4, 30°C
0.48
1-Chloropropane
-
pH 9.4, 30°C
3
2-bromoethanol
-
above, pH 9.4, 30°C
3
3-bromo-1-propanol
-
pH 9.4, 30°C
0.05 - 0.11
bis(2-chloroethyl) ether
additional information
additional information
-
rates of reaction steps
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.007 - 0.04
bis(2-chloroethyl) ether
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
-
DhaA31 is a mutant of DhaA with enhanced catalytic activity for 1,2,3-trichloropropane
physiological function
additional information
the enzyme has a core domain bearing the catalytic triad of Asp-His-Asp/Glu and a variable, mostly helical cap domain, which provides essential residues to stabilize the transition state, bind substrates and products and determine the selectivity. The essential residues D106 (nucleophile) and H272 (base) are involved in the catalytic mechanism of DhaA
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
DHAA_RHORH
293
0
33246
Swiss-Prot
-
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 35000, SDS-PAGE
additional information
-
the enzyme is composed of a main domain and a cap domain, with a catalytic pentad located between these domains
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
comparison of crystal structures of haloalkane dehalogenases by homology models
-
crystal structure determination and analysis, PDB ID 1CQW
mutant enzymes C176Y, I135F, and I135F/C176Y are crystallized by sitting drop vapour diffusion method, using either 80 mM bicine pH 9.0, 8% (v/v) PEG 8000, and 80 mM MgCl2 or 25% (v/v) PEG 4000, 8% 2-propanol, and 100 mM sodium acetate
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D106A
site-directed mutagenesis, inactive mutant
D106A/H272A
site-directed mutagenesis, inactive mutant
F168W/A172L/Y176G
-
site-directed mutagenesis, the mutant shows increased enantioselectivity with substrate TCP compared to the wild-type enzyme, 1,2,3-trichloropropane is docked in the active site in a configuration that leads to (R)-2,3-dichloropropan-1-ol formation
H271A
site-directed mutagenesis, inactive mutant
I135F/C176Y/V245F/L246I/Y273F
additional information
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
3
immobilized enzyme shows 25.9% remaining activity at pH 3.0
756951
3 - 9
multi-PEGylated enzyme with the thiosuccinimido butylamine linker and mono-PEGylated enzyme with the thiosuccinimido butylamine linker show the remaining activities comparable to wild-type enzyme
757271
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
23
immobilized enzyme shows 51.8% at room temperature for 30 days
additional information
PEGylation with the thiosuccinimido butylamine linker significantly increases the thermal stability of the enzyme
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
enzyme PEGylated with the thiosuccinimido butylamine linker shows the maximum resistance to high ionic strength (1 M NaCl)
immobilized enzyme exhibits a high stability in the extreme environmental conditions. The enzyme (DhaA) suffers from poor environmental stability and difficult recovery, which significantly increase the cost of DhaA. An effective enzyme immobilization strategy is developed to overcome the disadvantages of DhaA. DhaA is physically absorbed with amine-functionalized meso-cellular foam. The MCF-absorbed enzyme is intermolecularly crosslinked with 8-arm PEG N-hydroxysuccinimide ester and then PEGylated by maleimide-thiol chemistry
PEGylation with the thiosuccinimido butylamine linker significantly increases the stability of the enzyme
ORGANIC SOLVENT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimethyl sulfoxide
immobilized enzyme shows 99.8% remaining activity in 40% (v/v) dimethylsulfoxide for 5 h
Ethylene glycol
-
the enzyme retains activity
tetrahydrofuran
-
high inactivation rate
urea
immobilized enzyme shows 87.3% remaining activity in 3 M urea solution for 1 h
additional information
-
analysis of organic solvent stability of the enzyme, effects of co-solvents in enzyme assays, overview. Ethyene glycol and 1,4-dioxane have a positive effect on enantioselectivity of the enzyme
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
HiTrap Ni-chelating affinity resin chromatography and Superdex 75 gel filtration
Ni-NTA column chromatography
-
recombinant enzyme from Escherichia coli
-
recombinant His-tagged wild-type and mutant enzymes by nickel affinity chromatography
-
recombinant N-terminally His-tagged enzyme from Escherichia coli TOP10 by nickel affinity chromatography
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21 cells
expression in Escherichia coli
-
expression in Escherichia coli BL21(DE3)
gene dhaA, expression of a saturation mutagenesis library in Escherichia coli strain BL21(DE3)
gene dhaA, phylogenetic analysis
-
multiple alignment of protein sequences of cloned haloalkane dehalogenases
-
mutant enzyme H272F is expressed in Escherichia coli BL21 cells
-
phylogenetic analysis and tree
recombinant expression as N-terminally His-tagged enzyme in Escherichia coli TOP10
-
recombinant expression of His-tagged wild-type and mutant enzymes
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
agriculture
-
biocatalyzation and bioremediation of haloalkanes
biotechnology
-
enzyme, covalently immobilized on a polyethylenimine impregnated gamma-alumina support with an optimal loading of 70-75 mg/g and a maximal loading of 156 mg/g, retains more than 40% of its maximal activity, unaltered pH dependency compared to the native enzyme, thermostability and resistance towards inactivation by organic solvents of the immobilized enzyme are improved by an order of magnitude
environmental protection
synthesis
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Damborsky, J.; Koca, J.
Analysis of the reaction mechnism and substrate specificity of haloalkane dehalogenases by sequential and structural comparisons
Protein Eng.
12
989-998
1999
Rhodococcus rhodochrous, Rhodococcus rhodochrous NCIMB 13064, Sphingomonas paucimobilis, Sphingomonas paucimobilis UT26, Xanthobacter autotrophicus (P22643), Xanthobacter autotrophicus GJ10 (P22643), Xanthobacter autotrophicus GJ10
Manually annotated by BRENDA team
Bosma, T.; Pikkemaat, M.G.; Kingma, J.; Dijk, J.; Janssen, D.B.
Steady-state and pre-steady-state kinetic analysis of halopropane conversion by a Rhodococcus haloalkane dehalogenase
Biochemistry
42
8047-8053
2003
Rhodococcus rhodochrous, Rhodococcus rhodochrous NCIMB 13064
Manually annotated by BRENDA team
Dravis, B.C.; Swanson, P.E.; Russell, A.J.
Haloalkane hydrolysis with an immobilized haloalkane dehalogenase
Biotechnol. Bioeng.
75
416-423
2001
Rhodococcus rhodochrous
Manually annotated by BRENDA team
Stsiapanava, A.; Koudelakova, T.; Lapkouski, M.; Pavlova, M.; Damborsky, J.; Smatanova, I.K.
Crystals of DhaA mutants from Rhodococcus rhodochrous NCIMB 13064 diffracted to ultrahigh resolution: crystallization and preliminary diffraction analysis
Acta Crystallogr. Sect. F
64
137-140
2008
Rhodococcus rhodochrous (P0A3G2), Rhodococcus rhodochrous NCIMB 13064 (P0A3G2), Rhodococcus rhodochrous NCIMB 13064
Manually annotated by BRENDA team
Jesenska, A.; Sykora, J.; Olzynska, A.; Brezovsky, J.; Zdrahal, Z.; Damborsky, J.; Hof, M.
Nanosecond time-dependent Stokes shift at the tunnel mouth of haloalkane dehalogenases
J. Am. Chem. Soc.
131
494-501
2009
Rhodococcus rhodochrous, Bradyrhizobium japonicum (P59337), Bradyrhizobium japonicum USDA 110 (P59337), Rhodococcus rhodochrous NCIMB13064
Manually annotated by BRENDA team
Koudelakova, T.; Chovancova, E.; Brezovsky, J.; Monincova, M.; Fortova, A.; Jarkovsky, J.; Damborsky, J.
Substrate specificity of haloalkane dehalogenases
Biochem. J.
435
345-354
2011
Agrobacterium tumefaciens, Agrobacterium tumefaciens C58 / ATCC 33970, Bradyrhizobium elkanii, Bradyrhizobium elkanii USDA94, Bradyrhizobium japonicum, Bradyrhizobium japonicum USDA 110, Mycobacterium tuberculosis variant bovis, Mycobacterium tuberculosis variant bovis 5033/66, Rhodococcus rhodochrous, Rhodococcus rhodochrous NCIMB 13064, Rhodopirellula baltica, Rhodopirellula baltica SH1, Sphingobium indicum, Sphingobium indicum UT26, Xanthobacter autotrophicus, Xanthobacter autotrophicus GJ10
Manually annotated by BRENDA team
van Leeuwen, J.G.; Wijma, H.J.; Floor, R.J.; van der Laan, J.M.; Janssen, D.B.
Directed evolution strategies for enantiocomplementary haloalkane dehalogenases: from chemical waste to enantiopure building blocks
ChemBioChem
13
137-148
2012
Rhodococcus rhodochrous
Manually annotated by BRENDA team
Westerbeek, A.; van Leeuwen, J.; Szymanski, W.; Feringa, B.; Janssen, D.
Haloalkane dehalogenase catalysed desymmetrisation and tandem kinetic resolution for the preparation of chiral haloalcohols
Tetrahedron
68
7645-7650
2012
Bradyrhizobium japonicum, Bradyrhizobium japonicum USDA 110, Mesorhizobium loti, Mesorhizobium loti MAFF303099, Rhodococcus rhodochrous, Rhodococcus rhodochrous NCIMB13064, Sphingomonas paucimobilis, Sphingomonas paucimobilis UT26, Xanthobacter autotrophicus, Xanthobacter autotrophicus GJ10
-
Manually annotated by BRENDA team
Fibinger, M.P.; Davids, T.; Boettcher, D.; Bornscheuer, U.T.
A selection assay for haloalkane dehalogenase activity based on toxic substrates
Appl. Microbiol. Biotechnol.
99
8955-8962
2015
Rhodococcus rhodochrous (P0A3G2), Xanthobacter autotrophicus (P22643)
Manually annotated by BRENDA team
Nagata, Y.; Ohtsubo, Y.; Tsuda, M.
Properties and biotechnological applications of natural and engineered haloalkane dehalogenases
Appl. Microbiol. Biotechnol.
99
9865-9881
2015
Agrobacterium tumefaciens (E2RV69), Agrobacterium tumefaciens C58 / ATCC 33970 (E2RV69), Alcanivorax dieselolei, Alcanivorax dieselolei B-5, Arthrobacter sp., Bradyrhizobium elkanii (E2RV62), Bradyrhizobium elkanii USDA94 (E2RV62), Bradyrhizobium japonicum (P59337), Bradyrhizobium japonicum USDA 110 (P59337), Corynebacterium sp., Marinobacter sp. (A3JB27), Mesorhizobium loti (Q98C03), Mesorhizobium loti MAFF303099 (Q98C03), Mycobacterium avium (Q93K00), Mycobacterium avium N85 (Q93K00), Mycobacterium sp. (Q9ZER0), Mycobacterium sp. GP1 (Q9ZER0), Mycobacterium tuberculosis (P9WMR9), Mycobacterium tuberculosis H37Rv (P9WMR9), Mycobacterium tuberculosis variant bovis (A4Q9R7), Mycobacterium tuberculosis variant bovis (Q6EUU8), Mycobacterium tuberculosis variant bovis (Q9XB14), Mycobacterium tuberculosis variant bovis 5033/66 (A4Q9R7), Mycobacterium tuberculosis variant bovis 5033/66 (Q6EUU8), Mycobacterium tuberculosis variant bovis 5033/66 (Q9XB14), Plesiocystis pacifica (A6G7B1), Psychrobacter cryohalolentis (Q1QBB9), Psychrobacter cryohalolentis K5 (Q1QBB9), Rhodobacteraceae bacterium UDC319 (A0A023I2Y1), Rhodococcus rhodochrous (P0A3G2), Rhodococcus rhodochrous NCIMB 13064 (P0A3G2), Rhodococcus sp., Rhodopirellula baltica (G3XCP3), Rhodopirellula baltica SH1 (G3XCP3), Sphingobium indicum, Sphingobium indicum (P51698), Sphingobium indicum B90A, Sphingobium indicum UT26 (P51698), Sphingobium sp. (A4PEU6), Sphingobium sp. MI1205 (A4PEU6), Sphingomonas sp., Sphingomonas sp. BHC-A, Strongylocentrotus purpuratus, Xanthobacter autotrophicus (P22643), Xanthobacter autotrophicus GJ10 (P22643)
Manually annotated by BRENDA team
Koudelakova, T.; Bidmanova, S.; Dvorak, P.; Pavelka, A.; Chaloupkova, R.; Prokop, Z.; Damborsky, J.
Haloalkane dehalogenases: biotechnological applications
Biotechnol. J.
8
32-45
2013
Bradyrhizobium japonicum, Bradyrhizobium japonicum USDA 110, Rhodococcus rhodochrous, Sphingomonas paucimobilis
Manually annotated by BRENDA team
Ang, T.F.; Salleh, A.B.; Normi, Y.M.; Leow, T.C.
In silico design of potentially functional artificial metallo-haloalkane dehalogenase containing catalytic zinc
3 Biotech
8
314
2018
Rhodococcus rhodochrous (P0A3G2)
Manually annotated by BRENDA team
Wang, F.; Song, T.; Jiang, H.; Pei, C.; Huang, Q.; Xi, H.
Bacillus subtilis spore surface display of haloalkane dehalogenase DhaA
Curr. Microbiol.
76
1161-1167
2019
Rhodococcus rhodochrous (P0A3G2), Rhodococcus rhodochrous NCIMB 13064 (P0A3G2), Rhodococcus rhodochrous NCIMB 13064
Manually annotated by BRENDA team
Zheng, H.; Yu, W.L.; Guo, X.; Zhao, Y.Z.; Cui, Y.; Hu, T.; Zhong, J.Y.
An effective immobilized haloalkane dehalogenase DhaA from Rhodococcus rhodochrous by adsorption, crosslink and PEGylation on meso-cellular foam
Int. J. Biol. Macromol.
125
1016-1023
2019
Rhodococcus rhodochrous (P0A3G2), Rhodococcus rhodochrous
Manually annotated by BRENDA team
Zhao, Y.Z.; Yu, W.L.; Zheng, H.; Guo, X.; Guo, N.; Hu, T.; Zhong, J.Y.
PEGylation with the thiosuccinimido butylamine linker significantly increases the stability of haloalkane dehalogenase DhaA
J. Biotechnol.
254
25-33
2017
Rhodococcus rhodochrous (P0A3G2)
Manually annotated by BRENDA team
Marques, S.M.; Dunajova, Z.; Prokop, Z.; Chaloupkova, R.; Brezovsky, J.; Damborsky, J.
Catalytic cycle of haloalkane dehalogenases toward unnatural substrates explored by computational modeling
J. Chem. Inf. Model.
57
1970-1989
2017
Rhodococcus rhodochrous (P0A3G2)
Manually annotated by BRENDA team