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Enzyme Nomenclature
Information on EC 3.8.1.10 - 2-haloacid dehalogenase (configuration-inverting)
for references in articles please use BRENDA:EC3.8.1.10
Word Map on EC 3.8.1.10
- 3.8.1.10
-
dehalogenation
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l-2-haloalkanoic
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bioremediation
-
2-haloacids
- l-2-chloropropionate
-
alpha-carbon
- monochloroacetate
-
dechlorinate
- autotrophicus
- xanthobacter
-
haloalkanoates
- fluoroacetate
- synthesis
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The enzyme appears in viruses and cellular organisms
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EC NUMBER 
COMMENTARY 
3.8.1.10
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RECOMMENDED NAME
GeneOntology No.
2-haloacid dehalogenase (configuration-inverting)
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
(R)-2-haloacid + H2O = (S)-2-hydroxyacid + halide
Dehalogenates both (S)- and (R)-2-haloalkanoic acids to the corresponding (R)- and (S)-hydroxyalkanoic acids, respectively, with inversion of configuration at C-2. The enzyme from Pseudomonas sp. 113 acts on 2-haloalkanoic acids whose carbon chain lengths are five or less. See also EC 3.8.1.2 (S)-2-haloacid dehalogenase, EC 3.8.1.9 (R)-2-haloacid dehalogenase and EC 3.8.1.11 2-haloacid dehalogenase (configuration-retaining)
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(R)-2-haloacid + H2O = (S)-2-hydroxyacid + halide
group I enzymes, including DL-2-haloacid dehalogenase and D-2-haloacid dehalogenase, catalyze the reaction without forming an ester intermediate. Instead, a solvent water molecule directly attacks the alpha-carbon atom of the substrate to release the halide ion. DL-2-haloacid dehalogenase acts on both enantiomers of the substrate
(S)-2-haloacid + H2O = (R)-2-hydroxyacid + halide
Dehalogenates both (S)- and (R)-2-haloalkanoic acids to the corresponding (R)- and (S)-hydroxyalkanoic acids, respectively, with inversion of configuration at C-2. The enzyme from Pseudomonas sp. 113 acts on 2-haloalkanoic acids whose carbon chain lengths are five or less. See also EC 3.8.1.2 (S)-2-haloacid dehalogenase, EC 3.8.1.9 (R)-2-haloacid dehalogenase and EC 3.8.1.11 2-haloacid dehalogenase (configuration-retaining)
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(S)-2-haloacid + H2O = (R)-2-hydroxyacid + halide
group I enzymes, including DL-2-haloacid dehalogenase and D-2-haloacid dehalogenase, catalyze the reaction without forming an ester intermediate. Instead, a solvent water molecule directly attacks the alpha-carbon atom of the substrate to release the halide ion. DL-2-haloacid dehalogenase acts on both enantiomers of the substrate
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dehalogenation
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SYSTEMATIC NAME
IUBMB Comments
(S)-2-haloacid dehalogenase (configuration-inverting)
Dehalogenates both (S)- and (R)-2-haloalkanoic acids to the corresponding (R)- and (S)-hydroxyalkanoic acids, respectively, with inversion of configuration at C-2. The enzyme from Pseudomonas sp. 113 acts on 2-haloalkanoic acids whose carbon chain lengths are five or less. [See also EC 3.8.1.2 (S)-2-haloacid dehalogenase, EC 3.8.1.9 (R)-2-haloacid dehalogenase and EC 3.8.1.11 2-haloacid dehalogenase (configuration-retaining)]
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CAS REGISTRY NUMBER
COMMENTARY
89511-96-6
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
additional information
evolution
Based on their substrate specificities and the configurations of their products, 2-HADs are classified into three types. DL-2-HADs catalyse the dehalogenation of both D- and L-2-haloalkanoic acids, inverting the stereochemistry at the Calpha-atom position and producing the corresponding L- and D-products, respectively. D- and L-2-HADs act specifically on only one enantiomer and cause inversion of Calpha-atom stereochemistry in the hydroxyalkanoic acid product. Enzymatic activity analysis of Pseudomonas syringae 2-HAD reveals its capacity to catalyse the dehalogenation of both L- and D-substrates, but the structure of ps-2-HAD is completely different from that of DehI, which is the only DL-2-HAD enzyme that is structurally characterized, bps-2-HAD shows similar overall folding to L-HADs. Thus ps-2-HAD has a distinct active site and a unique catalytic behaviour compared with other HADs
evolution
the reaction proceeds in two steps, in the first step, a catalytic aspartate residue nucleophilically attacks the alpha-carbon atom of the substrate to release the halide ion, resulting in the formation of an ester intermediate in which the aspartate residue is covalently bound to the alpha-carbon atom of the substrate. In the second step, the ester intermediate is hydrolyzed by a solvent water molecule. This mechanism is not restricted to this group of enzymes, e.g., fluoroacetate dehalogenase catalyzes the reaction in the same manner, although this enzyme is not evolutionarily related to the group II enzymes. Group I enzymes, including DL-2-haloacid dehalogenase and D-2-haloacid dehalogenase, catalyze the reaction without forming an ester intermediate. Instead, a solvent water molecule directly attacks the alpha-carbon atom of the substrate to release the halide ion. DL-2-haloacid dehalogenase is an extraordinary enzyme that acts on both enantiomers of the substrate
additional information
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either the magnesium-binding cavity at least partially overlaps with the active site of ps-2-HAD or the coordinated residues or water molecules are involved directly in the catalytic reaction
additional information
either the magnesium-binding cavity at least partially overlaps with the active site of ps-2-HAD or the coordinated residues or water molecules are involved directly in the catalytic reaction
additional information
modeling of binding pocket and the active site and QM/QM calculations, docking study using (R)- and (S)-2-chloropropionates, overview. The binding site cavity is shielded from the solvent region, and is composed of eight hydrophobic residues (Trp37, Ala39, Phe40, Gly41, Ala192, Phe273, Ile274, and Ile277), and five hydrophilic residues (Asn117, Tyr120, Ser193, Asp194, and Tyr270)
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
(R)-2-chloropropionate + H2O
(S)-2-hydroxypropionate + chloride
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-
-
?
(S)-2-chloropropionate + H2O
(R)-2-hydroxypropionate + chloride
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-
-
?
2-bromo-2-methylpropionate + H2O
2-hydroxy-2-methylpropionate + bromide
slow substrate for the wild-type enzyme, but inhibitory for enzyme mutant D194N
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-
?
tribromoacetic acid + H2O
carbon monoxide + carbon dioxide + HBr
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-
-
?
(R)-2-chloropropionic acid + H2O
(S)-2-hydroxypropionic acid + chloride
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-
-
-
?
(R)-2-chloropropionic acid + H2O
(S)-2-hydroxypropionic acid + chloride
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-
-
-
?
(R)-2-chloropropionic acid + H2O
(S)-2-hydroxypropionic acid + chloride
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-
-
-
?
(R)-2-haloacid + H2O
(S)-2-hydroxyacid + halide
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-
-
-
?
(R)-2-haloacid + H2O
(S)-2-hydroxyacid + halide
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-
-
-
?
(R)-2-haloacid + H2O
(S)-2-hydroxyacid + halide
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-
-
-
?
(R)-2-haloacid + H2O
(S)-2-hydroxyacid + halide
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enzyme of 2-chloroacrylate grown cells
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?
(R)-2-haloacid + H2O
(S)-2-hydroxyacid + halide
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-
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-
?
(R)-2-haloacid + H2O
(S)-2-hydroxyacid + halide
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enzyme of 2-chloroacrylate grown cells
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-
?
(S)-2-chloropropionic acid + H2O
(R)-2-hydroxypropionic acid + chloride
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-
-
-
?
(S)-2-chloropropionic acid + H2O
(R)-2-hydroxypropionic acid + chloride
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-
-
-
?
(S)-2-chloropropionic acid + H2O
(R)-2-hydroxypropionic acid + chloride
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-
-
-
?
(S)-2-haloacid + H2O
(R)-2-hydroxyacid + halide
-
-
-
-
?
(S)-2-haloacid + H2O
(R)-2-hydroxyacid + halide
-
-
-
-
?
(S)-2-haloacid + H2O
(R)-2-hydroxyacid + halide
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-
-
-
?
(S)-2-haloacid + H2O
(R)-2-hydroxyacid + halide
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enzyme of 2-chloroacrylate grown cells
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?
(S)-2-haloacid + H2O
(R)-2-hydroxyacid + halide
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?
(S)-2-haloacid + H2O
(R)-2-hydroxyacid + halide
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enzyme of 2-chloroacrylate grown cells
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-
?
D-2-chloropropionate + H2O
L-lactate + HCl
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a step preceding the dehalogenation is partly rate-limiting when D-2-chloropropionate is used as the substrate
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-
?
D-2-chloropropionate + H2O
L-lactate + HCl
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a step preceding the dehalogenation is partly rate-limiting when D-2-chloropropionate is used as the substrate
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?
D-2-monochloropropionate + H2O
L-lactate + HCl
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D-2-monochloropropionate + H2O
L-lactate + HCl
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?
L-2-monochloropropionate + H2O
D-lactate + HCl
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?
additional information
?
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DL-2-haloacid dehalogenase, DL-DEX, converts both enantiomers of the substrate
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additional information
?
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not: chloroacetamide, chloroacetaldehyde, 3-chloropropionate, best substrate: 2-halopropionate, followed by monohaloacetate, 2-halobutyrate, and 2-halovalerate in that order
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additional information
?
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the enzyme has a single common active site for both reactions on L- and D-enantiomers, the reaction mechanismm does not proceed via an ester intermediate and not via a nucleophilic aspartate attacking the C-atom of the substrate to displace the halo-atom on contrast to the (S)-2-haloacid dehalogenase, EC 3.8.1.2. In the (S,R)-2-haloacid dehalogenase, a water molecule directly atacks the substrate for halide displacement, structure-function relationship, overview
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additional information
?
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the enzyme has a single common active site for both reactions on L- and D-enantiomers, the reaction mechanismm does not proceed via an ester intermediate and not via a nucleophilic aspartate attacking the C-atom of the substrate to displace the halo-atom on contrast to the (S)-2-haloacid dehalogenase, EC 3.8.1.2. In the (S,R)-2-haloacid dehalogenase, a water molecule directly atacks the substrate for halide displacement, structure-function relationship, overview
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additional information
?
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not: chloroacetamide, chloroacetaldehyde, 3-chloropropionate, best substrate: 2-halopropionate, followed by monohaloacetate, 2-halobutyrate, and 2-halovalerate in that order
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additional information
?
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the enzyme has a single common active site for both reactions on L- and D-enantiomers, the reaction mechanismm does not proceed via an ester intermediate and not via a nucleophilic aspartate attacking the C-atom of the substrate to displace the halo-atom on contrast to the (S)-2-haloacid dehalogenase, EC 3.8.1.2. In the (S,R)-2-haloacid dehalogenase, a water molecule directly atacks the substrate for halide displacement, structure-function relationship, overview
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additional information
?
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2-haloacid dehalogenases catalyse the hydrolytic dehalogenation of 2-haloalkanoic acids, cleaving the carbon-halide bond at the Calpha-atom position and releasing a halogen atom
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additional information
?
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2-haloacid dehalogenases catalyse the hydrolytic dehalogenation of 2-haloalkanoic acids, cleaving the carbon-halide bond at the Calpha-atom position and releasing a halogen atom
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additional information
?
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enzyme ps-2-HAD reveals its capacity to catalyse the dehalogenation of both L- and D-substrates
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additional information
?
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enzyme ps-2-HAD reveals its capacity to catalyse the dehalogenation of both L- and D-substrates
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
(R)-2-chloropropionic acid + H2O
(S)-2-hydroxypropionic acid + chloride
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-
-
-
?
(R)-2-chloropropionic acid + H2O
(S)-2-hydroxypropionic acid + chloride
-
-
-
-
?
(R)-2-chloropropionic acid + H2O
(S)-2-hydroxypropionic acid + chloride
-
-
-
-
?
(R)-2-haloacid + H2O
(S)-2-hydroxyacid + halide
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-
-
-
?
(S)-2-chloropropionic acid + H2O
(R)-2-hydroxypropionic acid + chloride
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-
-
-
?
(S)-2-chloropropionic acid + H2O
(R)-2-hydroxypropionic acid + chloride
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-
-
-
?
(S)-2-chloropropionic acid + H2O
(R)-2-hydroxypropionic acid + chloride
-
-
-
-
?
(S)-2-haloacid + H2O
(R)-2-hydroxyacid + halide
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?
additional information
?
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A6BM74
DL-2-haloacid dehalogenase, DL-DEX, converts both enantiomers of the substrate
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-
additional information
?
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2-haloacid dehalogenases catalyse the hydrolytic dehalogenation of 2-haloalkanoic acids, cleaving the carbon-halide bond at the Calpha-atom position and releasing a halogen atom
-
-
-
additional information
?
-
Q88B12
2-haloacid dehalogenases catalyse the hydrolytic dehalogenation of 2-haloalkanoic acids, cleaving the carbon-halide bond at the Calpha-atom position and releasing a halogen atom
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-
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2-bromo-2-methylpropionate
an inhibitor of the D194N mutant enzyme and slow substrate of the wild-type enzyme
additional information
-
not: 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide, Woodward reagent K
-
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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PDB
SCOP
CATH
UNIPROT
ORGANISM
Methylobacterium sp. CPA1;
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
68000
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
monomer
additional information
dimer
-
2 * 28000, SDS-PAGE; 2 * 34242, calculated from amino acid sequence; 2 * 35000, SDS-PAGE
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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
purified recombinant native and selenomethionine-labeled wild-type enzyme and recombinant D194N enzyme mutant complexed with inhibitor 2-bromo-2-methylpropionate, 15 mg/mL protein in 10 mM Hepes-NaOH, pH 7.5, is mixed with 3 M sodium formate, 5% glycerol v/v, as the reservoir solution, X-ray diffraction structure determination and analysis at 1.7-2.7 A resolution
purified enzyme, sitting drop vapour diffusion method, mixing of equal volumes of 9 mg/ml protein in 50 mM Tris, pH 8.0, and 25 mM NaCl, and of reservoir solution consisting of 0.2 M MgCl2 hexahydrate, 20-26% PEG 4000, 0.1 M Tris, pH 8.5, and equilibration against 0.1 ml of reservoir solution, 4°C, overnight, soaking of crystals in KI, X-ray diffraction structure determination and analysis at 1.98-2.0 A resolution, single-wavelength anomalous dispersion method, modeling
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
50
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15 min 50% loss of activity for D-2-chloropropionic acid and 40% loss of activity for L-2-chloropropionic acid
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, 25 mM potassium phosphate buffer containing 50% glycerol, pH 7.5, 1 year
-
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
expression in Escherichia coli, no significant sequence similarity between enzyme and L-2-haloacid dehalogenase is found, however, enzyme has significant sequence similarity with D-2-haloacid dehalogenase fom Pseudomonas putide AJ1
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D180A
-
the mutation destabilizes the rotation of the nucleophile D10, fixes catalytic water around D10, and prevents K151 from approaching D10
K151A
-
the mutant is almost inactive, the mutation destabilizes substrate orientation and affects the balance of the charge around the active site
D180A
-
the mutation destabilizes the rotation of the nucleophile D10, fixes catalytic water around D10, and prevents K151 from approaching D10
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K151A
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the mutant is almost inactive, the mutation destabilizes substrate orientation and affects the balance of the charge around the active site
-
D10A
site-directed mutagenesis, the D10A mutant shows over 50% reduced enzyme activity compared to the wild-type enzyme
D11A
site-directed mutagenesis, the D11A mutant shows highly reduced enzyme activity compared to the wild-type enzyme
D180A
site-directed mutagenesis, the D180A mutant shows over 50% reduced enzyme activity compared to the wild-type enzyme
D184A
site-directed mutagenesis, the mutant cannot be expressed recombinantly
D185A
site-directed mutagenesis, the mutant cannot be expressed recombinantly
D8A
site-directed mutagenesis, the D8A mutant retains about half the enzyme activity of the wild-type
K155A
site-directed mutagenesis, the mutant cannot be expressed recombinantly
T127A
site-directed mutagenesis, the mutant cannot be expressed recombinantly
additional information
additional information
-
each of the 26 residues with charged and polar side chains, which are conserved between enzyme and D-2-haloacid dehalogenase, is mutated, Thr65, Glu69 and Asp194 are found to be essential
additional information
-
each of the 26 residues with charged and polar side chains, which are conserved between enzyme and D-2-haloacid dehalogenase, is mutated, Thr65, Glu69 and Asp194 are found to be essential
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
synthesis
the enzyme is of interest for their potential use in bioremediation and in the synthesis of industrial chemicals
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LINKS TO OTHER DATABASES (specific for EC-Number 3.8.1.10)
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