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Information on EC 3.8.1.9 - (R)-2-haloacid dehalogenase
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EC Tree
3.8.1.9 (R)-2-haloacid dehalogenaseIUBMB Comments
Acts on acids of short chain lengths, C2 to C4, with inversion of configuration at C-2. [See also EC 3.8.1.2 (S)-2-haloacid dehalogenase, EC 3.8.1.10 2-haloacid dehalogenase (configuration-inverting) and EC 3.8.1.11 2-haloacid dehalogenase (configuration-retaining)]
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Word Map
- 3.8.1.9
-
dehalogenation
- putida
- dexamethasone
-
rhizobium
-
2-haloalkanoic
-
l-enantiomer
- 2-chloropropionate
-
enantiomers
-
2-haloacids
-
dl-2-haloacid
- monobromoacetate
- monochloroacetate
- dendrimer
-
tear
- halide
-
inflamed
-
subconjunctival
-
biodistribution
-
halogenated
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Synonyms
d-dex, d-2-haloacid dehalogenase, deh138, d-specific dehalogenase, hadd aj1, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
2-haloalkanoic acid dehalogenase
-
-
-
-
2-haloalkanoid acid halidohydrolase
-
-
-
-
D-2-haloacid dehalogenase
D-DEX
HadD AJ1
D-2-haloacid dehalogenase
-
-
-
-
D-DEX
-
-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
(R)-2-haloacid + H2O = (S)-2-hydroxyacid + halide
Acts on acids of short chain lengths, C2 to C4, with inversion of configuration at C-2, see also EC 3.8.1.2 (S)-2-haloacid dehalogenase, EC 3.8.1.10 2-haloacid dehalogenase (configuration-inverting) and EC 3.8.1.11 2-haloacid dehalogenase (configuration-retaining)
-
-
-
(R)-2-haloacid + H2O = (S)-2-hydroxyacid + halide
proposed reaction mechanism, conserved residue Arg134 plays a key role in the dehalogenation process. Residues Arg107, Arg134 and Tyr135 interact with the substrates and are the catalytic residues of DehD that are involved in the dehalogenation of D-2-chloropropionate and D-2-bromopropionate, while Glu20 activates the water molecule that attacks the carbon halogen bond on the alpha-carbon, thereby releasing chloride ion
(R)-2-haloacid + H2O = (S)-2-hydroxyacid + halide
the reaction mechanism of dehalogenation is catalysed by hydrolytic SN2-substitution reaction
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SYSTEMATIC NAME
IUBMB Comments
(R)-2-haloacid halidohydrolase
Acts on acids of short chain lengths, C2 to C4, with inversion of configuration at C-2. [See also EC 3.8.1.2 (S)-2-haloacid dehalogenase, EC 3.8.1.10 2-haloacid dehalogenase (configuration-inverting) and EC 3.8.1.11 2-haloacid dehalogenase (configuration-retaining)]
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CAS REGISTRY NUMBER
COMMENTARY
119345-29-8
-
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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-chloropropionic acid + H2O
(S)-2-hydroxypropionic acid + chloride
-
-
-
-
?
(R)-2-chloropropionic acid + H2O
(S)-2-hydroxypropionic acid + chloride
-
enantioselective
-
-
?
D-2-bromopropionate + H2O
L-2-hydroxypropionate + bromide
mutant enzyme L288I exhibits catalytic activity, no activity with wild-type enzyme
-
-
?
D-2-chloropropionate + H2O
L-2-hydroxypropionate + chloride
-
-
-
?
D-2-chloropropionate + H2O
L-2-hydroxypropionate + chloride
mutant enzyme L288I exhibits catalytic activity, no activity with wild-type enzyme
-
-
?
D-2-chloropropionate + H2O
L-2-hydroxypropionate + chloride
-
-
-
?
L-2-bromopropionate + H2O
?
mutant enzyme L288I exhibits catalytic activity, no activity with wild-type enzyme
-
-
?
L-2-chloropropionate + H2O
?
mutant enzyme L288I exhibits catalytic activity, no activity with wild-type enzyme
-
-
?
additional information
?
-
the D-2-haloacid dehalogenase of D-specific dehalogenase (DehD) from Rhizobium sp. RC1 catalyses the hydrolytic dehalogenation of D-haloalkanoic acids, inverting the substrate-product configuration and thereby forming the corresponding L-hydroxyalkanoic acids. Molecular docking of substrates into the active site of the DehD mutants R134A and Y135A, which produce altered catalytic functions. The mutants interact strongly with substrates that wild-type DehD does not interact with or degrade. The interaction is particularly enhanced with 3-chloropropionate, in addition to monobromoacetate, monochloroacetate and D,L-2,3-dichloropropionate. The mutants exhibit a strong interaction with 3-chloropropionate at Arg134
-
-
?
additional information
?
-
-
the D-2-haloacid dehalogenase of D-specific dehalogenase (DehD) from Rhizobium sp. RC1 catalyses the hydrolytic dehalogenation of D-haloalkanoic acids, inverting the substrate-product configuration and thereby forming the corresponding L-hydroxyalkanoic acids. Molecular docking of substrates into the active site of the DehD mutants R134A and Y135A, which produce altered catalytic functions. The mutants interact strongly with substrates that wild-type DehD does not interact with or degrade. The interaction is particularly enhanced with 3-chloropropionate, in addition to monobromoacetate, monochloroacetate and D,L-2,3-dichloropropionate. The mutants exhibit a strong interaction with 3-chloropropionate at Arg134
-
-
?
additional information
?
-
molecular docking of D-2-chloropropionate, D-2-bromopropionate, monochloroacetate, monobromoacetate, 2,2-dichloropropionate, DL-2,3-dichloropropionate, and 3-chloropropionate into the DehD active site, residues Arg107, Arg134 and Tyr135 interact with D-2-chloropropionate, and Glu20 activates the water molecule for hydrolytic dehalogenation
-
-
?
additional information
?
-
-
molecular docking of D-2-chloropropionate, D-2-bromopropionate, monochloroacetate, monobromoacetate, 2,2-dichloropropionate, DL-2,3-dichloropropionate, and 3-chloropropionate into the DehD active site, residues Arg107, Arg134 and Tyr135 interact with D-2-chloropropionate, and Glu20 activates the water molecule for hydrolytic dehalogenation
-
-
?
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NATURAL SUBSTRATE
NATURAL 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-chloropropionic acid + H2O
(S)-2-hydroxypropionic acid + chloride
-
-
-
-
?
additional information
?
-
the D-2-haloacid dehalogenase of D-specific dehalogenase (DehD) from Rhizobium sp. RC1 catalyses the hydrolytic dehalogenation of D-haloalkanoic acids, inverting the substrate-product configuration and thereby forming the corresponding L-hydroxyalkanoic acids. Molecular docking of substrates into the active site of the DehD mutants R134A and Y135A, which produce altered catalytic functions. The mutants interact strongly with substrates that wild-type DehD does not interact with or degrade. The interaction is particularly enhanced with 3-chloropropionate, in addition to monobromoacetate, monochloroacetate and D,L-2,3-dichloropropionate. The mutants exhibit a strong interaction with 3-chloropropionate at Arg134
-
-
?
additional information
?
-
-
the D-2-haloacid dehalogenase of D-specific dehalogenase (DehD) from Rhizobium sp. RC1 catalyses the hydrolytic dehalogenation of D-haloalkanoic acids, inverting the substrate-product configuration and thereby forming the corresponding L-hydroxyalkanoic acids. Molecular docking of substrates into the active site of the DehD mutants R134A and Y135A, which produce altered catalytic functions. The mutants interact strongly with substrates that wild-type DehD does not interact with or degrade. The interaction is particularly enhanced with 3-chloropropionate, in addition to monobromoacetate, monochloroacetate and D,L-2,3-dichloropropionate. The mutants exhibit a strong interaction with 3-chloropropionate at Arg134
-
-
?
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Corneal Neovascularization
Subconjunctival injectable dendrimer-dexamethasone gel for the treatment of corneal inflammation.
Dry Eye Syndromes
Subconjunctival injectable dendrimer-dexamethasone gel for the treatment of corneal inflammation.
Exanthema
Mandatory dexamethasone strictly monitored by pharmacists reduces the severity of pemetrexed-induced skin rash.
Keratitis
Subconjunctival injectable dendrimer-dexamethasone gel for the treatment of corneal inflammation.
Proteinuria
Glucocorticoid diminishes vascular endothelial growth factor and exacerbates proteinuria in rats with mesangial proliferative glomerulonephritis.
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
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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pH RANGE
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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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
from the intertidal coast of the Chinese Yellow Sea near Dalian City
-
-
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
additional information
-
the growth of DEH 138 strain culture is not affected by salinity of 0-15%. Growth on 1,2-dichloroethane, 3-chloro-1,2-propanediol, 2,2-dichloropropionic acid, and 2,4,6-trichlorophenol medium
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
three-dimensional enzyme structure modeling and analysis, molecular dynamics simulations, comparison with Pseudomonas putida enzyme structures from strain AJ1 and PP3, overview. Residues Arg107, Arg134 and Tyr135 interact with D-2-chloropropionate, and Glu20 activated the water molecule for hydrolytic dehalogenation
additional information
-
three-dimensional enzyme structure modeling and analysis, molecular dynamics simulations, comparison with Pseudomonas putida enzyme structures from strain AJ1 and PP3, overview. Residues Arg107, Arg134 and Tyr135 interact with D-2-chloropropionate, and Glu20 activated the water molecule for hydrolytic dehalogenation
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). A0A1J5Q2B7_9ZZZZ
125
0
13697
TrEMBL
other Location (Reliability: 2)
A0A1J5QQ71_9ZZZZ
125
0
13714
TrEMBL
other Location (Reliability: 2)
A0A2S6RCV9_9PROT
300
0
32626
TrEMBL
-
B2J4L7_NOSP7
Nostoc punctiforme (strain ATCC 29133 / PCC 73102)
656
1
73953
TrEMBL
-
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
29000
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
homotetramer
tetramer
additional information
additional information
three-dimensional enzyme structure modeling and analysis. The secondary structure is predominantly alpha-helical. The N-terminus consists of 24 residues, primarily in the loop region, whereas the C-terminus had only one residue in the loop region. The D-2-specific dehalogenase (DehD) is predominantly made of alpha-helices and coil-coils with highly curved bends and is without strands, secondary structural elements, overview
additional information
-
three-dimensional enzyme structure modeling and analysis. The secondary structure is predominantly alpha-helical. The N-terminus consists of 24 residues, primarily in the loop region, whereas the C-terminus had only one residue in the loop region. The D-2-specific dehalogenase (DehD) is predominantly made of alpha-helices and coil-coils with highly curved bends and is without strands, secondary structural elements, overview
additional information
three-dimensional structure of DehD wild-type and Y135A mutant
additional information
-
three-dimensional structure of DehD wild-type and Y135A mutant
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystals are obtained by hanging-drop vapour diffusion method. The enzyme is crystallized in the presence of the substrate D-2-chloropropionate at pH 5.5-6.4 and 4°C. 2.64 A resolution
crystals are obtained by the hanging-drop vapor-diffusion method. Crystals of the D205N mutant with D-2-chloropropionate are prepared by co-crystallization using the sitting drop method
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D205E
activity with D-2-chloropropionate is 10.1% compared to activity of the wild-type enzyme. The kcat value of wild-type enzyme is 13fold higher compared to mutant enzyme
D205N
F281A
activity with D-2-chloropropionate is 54.7% compared to activity of the wild-type enzyme
G50A
activity with D-2-chloropropionate is 5.1% compared to activity of the wild-type enzyme
I52G
activity with D-2-chloropropionate is 1.5% compared to activity of the wild-type enzyme
L285I
activity with D-2-chloropropionate is 24.4% compared to activity of the wild-type enzyme
L288A
the mutant enzyme is active toward L-enantiomers. The catalytic efficiency is less than 30% of mutant enzyme L288I
L288I
L288V
kcat/Km of the L288V mutant displays over 80% of that of the L288I mutant
M284C
activity with D-2-chloropropionate is 7.0% compared to activity of the wild-type enzyme
M284F
mutant enzyme shows no enantioselective changes in contrast to the wild-type enzyme
N131D
activity with D-2-chloropropionate is 4.4% compared to activity of the wild-type enzyme
N203A
N203S
activity with D-2-chloropropionate is 0.4% compared to activity of the wild-type enzyme
S204A
activity with D-2-chloropropionate is 4.9% compared to activity of the wild-type enzyme
S204T
activity with D-2-chloropropionate is 41.8% compared to activity of the wild-type enzyme
V51F
activity with D-2-chloropropionate is 36.6% compared to activity of the wild-type enzyme. The kcat value of wild-type enzyme is 4fold higher compared to mutant enzyme
W48A
activity with D-2-chloropropionate is 0.2% compared to activity of the wild-type enzyme
Y134F
activity with D-2-chloropropionate is 0.1% compared to activity of the wild-type enzyme
G50A
-
activity with D-2-chloropropionate is 5.1% compared to activity of the wild-type enzyme
-
N131D
-
activity with D-2-chloropropionate is 4.4% compared to activity of the wild-type enzyme
-
S204A
-
activity with D-2-chloropropionate is 4.9% compared to activity of the wild-type enzyme
-
W48A
-
activity with D-2-chloropropionate is 0.2% compared to activity of the wild-type enzyme
-
R134A
site-directed mutagenesis, the DehD mutant variant demonstrates increased propensity for binding haloalkanoic acid and is non-stereospecific towards halogenated substrates
Y135A
site-directed mutagenesis, the DehD mutant variant demonstrates increased propensity for binding haloalkanoic acid and is non-stereospecific towards halogenated substrates
L288I
activity with D-2-chloropropionate is 37.2% compared to activity of the wild-type enzyme
L288I
the mutation enlarges the size of the channel and allows the enzyme to accommodate L-enantiomers (L-2-bromopropionate). The wing flip of I288 induces hydrophobic interactions with the L-enantiomer and directly affects the catalytic efficiency
N203A
activity with D-2-chloropropionate is 1.2% compared to activity of the wild-type enzyme. The kcat value of wild-type enzyme is 355fold higher compared to mutant enzyme
N203A
mutant enzyme shows no enantioselective changes in contrast to the wild-type enzyme
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
40
-
strain AJ1/23, D-2-haloacid dehalogenase subtype, activity loss above 40°C, rapid protein denaturation and precipitation at 56°C
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene dehD, sequence comparisons, recombinant expression of wild-type and mutant enzymes in Escherichia coli
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
D-specific dehalogenase DehD from Rhizobium sp. strain RC1 can be exploited as a potential target enzyme for industrial, pharmaceutical and other biotechnological applications
additional information
-
D-specific dehalogenase DehD from Rhizobium sp. strain RC1 can be exploited as a potential target enzyme for industrial, pharmaceutical and other biotechnological applications
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Leigh, J.A.; Skinner, A.J.; Cooper, R.A.
Partial purification, stereospecificity and stoichiometry of three dehalogenases from a Rhizobium species
FEMS Microbiol. Lett.
49
353-356
1988
Rhizobium sp.
-
brenda
Soda, K.; Kurihara, T.; Liu, J.Q.; Nardi-Dei, V.; Park, C.; Miyagi, M.; Tsunasawa, S.; Esaki, N.
Bacterial 2-haloacid dehalogenases: Structures and catalytic properties
Pure Appl. Chem.
68
2097-2103
1996
Pseudomonas putida, Rhizobium sp., Pseudomonas putida AJ1/23
-
brenda
Cairns, S.S.; Cornish, A.; Cooper, R.A.
Cloning, sequencing and expression in Escherichia coli of two Rhizobium sp. genes encoding haloalkonoate dehalogenases of opposite stereospecificity
Eur. J. Biochem.
235
744-749
1996
Rhizobium sp.
brenda
Smith, J.M.; Harrison, K.; Colby, J.
Purification and characterization of D-2-haloacid dehalogenase from Pseudomonas putida strain AJ1/23
J. Gen. Microbiol.
136
881-886
1990
Pseudomonas putida, Pseudomonas putida AJ1/23
brenda
Higgins, T.P.; Hope, S.J.; Effendi, A.J.; Dawson, S.; Dancer, B.N.
Biochemical and molecular characterisation of the 2,3-dichloro-1-propanol dehalogenase and stereospecific haloalkanoic dehalogenases from a versatile Agrobacterium sp
Biodegradation
16
485-492
2005
Agrobacterium sp. (Q8KLS9)
brenda
Huang, J.; Xin, Y.; Cao, X.; Zhang, W.
Phylogenetic diversity and characterization of 2-haloacid degrading bacteria from the marine sponge Hymeniacidon perlevis
World J. Microbiol. Biotechnol.
27
1787-1794
2011
Hymeniacidon perlevis
brenda
Sudi, I.Y.; Shamsir, M.S.; Jamaluddin, H.; Wahab, R.A.; Huyop, F.
Interactions of non-natural halogenated substrates with D-specific dehalogenase (DehD) mutants using in silico studies
Biotechnol. Biotechnol. Equip.
28
949-957
2014
Rhizobium sp. (Q8KLS9), Rhizobium sp.
brenda
Sudi, I.Y.; Wong, E.L.; Joyce-Tan, K.H.; Shamsir, M.S.; Jamaluddin, H.; Huyop, F.
Structure prediction, molecular dynamics simulation and docking studies of D-specific dehalogenase from Rhizobium sp. RC1
Int. J. Mol. Sci.
13
15724-15754
2012
Rhizobium sp. (Q8KLS9), Rhizobium sp.
brenda
Feng, Y.; Wang, Y.; Chu, H.; Fan, Y.; Cao, X.; Liu, Y.; Li, G.; Xue, S.
Stereoselective catalysis controlled by a native leucine or variant isoleucine wing-gatekeeper in 2-haloacid dehalogenase
FEBS Lett.
593
308-318
2019
Pseudomonas putida (Q52086)
brenda
Wang, Y.; Feng, Y.; Cao, X.; Liu, Y.; Xue, S.
Insights into the molecular mechanism of dehalogenation catalyzed by D-2-haloacid dehalogenase from crystal structures
Sci. Rep.
8
1454
2018
Pseudomonas putida (Q52086), Pseudomonas putida AJ1/23 (Q52086), Pseudomonas putida AJ1/23
brenda
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